Beginning Jan 1, 1999: ++++------+------+------+------+------+------+------+------+------+------+ From: "Robert M. Horton" Subject: Video taping computer presentation Date: Mon, 04 Jan 1999 10:17:05 -0800 To: rasmol list Cc: SethHarris Seth Harris wrote: >...I am now trying to convert my movie scripts onto a VCR > for presentation at a departmental seminar. If you can hook your computer video out to a TV (i.e., show what is on the computer on a TV screen "live"), you should be able to hook it to a VCR just as easily. You should be able to use the computer like any other video source. Be aware that TV resolution is not nearly as good as computer monitor resolution, so it may be difficult for your audience to see small details (like labels or other text). Be sure to adjust text sizes and so forth to be large enough. I find that settings that are easy to see on a 640x480 screen usually translate marginally well to a TV, but most screens that are used at higher resolutions try to fit too much on the screen to work on a TV. A computer projector would have much better resolution (most of the middle-of-the-road projectors use true 800x600 resolution.) -- Robert M. Horton, Ph.D. 0 []~ ~ ~ ~ http://www.attotron.com ~ ~ ~ ~[] 0 |-/_| rmhorton@attotron.com |_\-| -\_|| He travels swiftest who telecommutes. ||_/- ++++------+------+------+------+------+------+------+------+------+------+ From: "Robert M. Horton" Subject: Chime presentation Date: Mon, 04 Jan 1999 10:37:07 -0800 To: rasmol list Cc: Seth Harris Seth; I am working on a Javascript-based Chime Scripting Wizard to help folks make presentations with Chime. The bad news is the project isn't very far along. The good (?) news is, I'm looking for presentations to make myself to try my metascripts. Make ya a deal: I'll (try to) help with your presentation if you agree to give me feedback on my Scripting Wizard if and when I get parts of it done. If you're really desperate, I can even loan you a laptop and projector (if you can come get them in Sacramento...) -- Robert M. Horton, Ph.D. 0 []~ ~ ~ ~ http://www.attotron.com ~ ~ ~ ~[] 0 |-/_| rmhorton@attotron.com |_\-| -\_|| He travels swiftest who telecommutes. ||_/- References: <004501be1a8c$9c23fb60$f370fed0@yeeho> <365FC723.F8BA7509@inn-prot.weizmann.ac.il> ++++------+------+------+------+------+------+------+------+------+------+ From: " Dr. Frank Eblinger" Subject: vdW radii Date: Tue, 05 Jan 1999 15:31:20 +0100 To: rasmol@dhcp-srv2.oit.umass.edu This is a multi-part message in MIME format. --------------B7225FA63FE74686BB1BC40D --------------A8D9598D2303587319BBA012 > Hi, Dear Rasmolians: We are preparing some websites with supramolecular structures represented by chime (still under construction): http://www.uni-sb.de/matfak/fb11/schneider/supram/supramolecular_structures.html I looked up some old emails from the RasmolList about atomic radii, but I still got a problem with the vdW radii in chime/rasmol: What is the default value for the spacefilling command (500 seems to be too high, 400 too small) if I use the pull down option in Rasmol (spacefilling --> vdW)? Is there any (easy) way to define vdW radii? As far as I know there is no information in a pdb file about atomic charges. Is this the reason why our 18C6/potassium complex looks that strange in the spacefilling model? (vdW radii for K and K+ are the same?!!) (see attached file) --------------A8D9598D2303587319BBA012
 Hi, Dear Rasmolians:


We are preparing some websites with supramolecular structures represented by chime (still under construction):

http://www.uni-sb.de/matfak/fb11/schneider/supram/supramolecular_structures.html

I looked up some old emails from the RasmolList about atomic radii, but I still got a problem with the vdW radii in chime/rasmol:
What is the default value for the spacefilling command (500 seems to be too high, 400 too small) if I use the pull down option in Rasmol (spacefilling --> vdW)?

Is there any (easy) way to define vdW radii?

As far as I know  there is no information in a pdb file about atomic charges.
Is this the reason why our 18C6/potassium complex looks that strange in the  spacefilling model? (vdW radii for K and K+ are the same?!!) (see attached file)
  --------------A8D9598D2303587319BBA012-- --------------B7225FA63FE74686BB1BC40D Content-Disposition: inline; filename="18C.PDB" HETATM 1 O 1 2.948 0.000 0.244 1.00 0.00 HETATM 2 C 2 3.488 1.188 -0.304 1.00 0.00 HETATM 3 C 3 2.776 2.424 0.284 1.00 0.00 HETATM 4 O 4 1.472 2.552 -0.260 1.00 0.00 HETATM 5 C 5 0.712 3.616 0.284 1.00 0.00 HETATM 6 C 6 -0.712 3.616 -0.300 1.00 0.00 HETATM 7 O 7 -1.472 2.552 0.248 1.00 0.00 HETATM 8 C 8 3.488 -1.192 -0.300 1.00 0.00 HETATM 9 C 9 2.776 -2.428 0.292 1.00 0.00 HETATM 10 O 10 1.472 -2.556 -0.248 1.00 0.00 HETATM 11 C 11 0.712 -3.620 0.300 1.00 0.00 HETATM 12 C 12 -0.712 -3.620 -0.288 1.00 0.00 HETATM 13 O 13 -1.472 -2.552 0.256 1.00 0.00 HETATM 14 C 14 -2.776 2.424 -0.296 1.00 0.00 HETATM 15 C 15 -3.488 1.188 0.296 1.00 0.00 HETATM 16 O 16 -2.948 0.000 -0.248 1.00 0.00 HETATM 17 C 17 -2.776 -2.428 -0.284 1.00 0.00 HETATM 18 C 18 -3.488 -1.192 0.300 1.00 0.00 HETATM 19 K 19 0.000 0.000 0.000 1.00 0.00 TER 20 19 END --------------B7225FA63FE74686BB1BC40D Content-Description: Card for Frank Eblinger Content-Disposition: attachment; filename="vcard.vcf" begin: vcard fn: Frank Eblinger n: Eblinger;Frank adr: In den Welkertswiesen 65;;;Saarbrücken;Saarland;66125;Germany email;internet: f.eblinger@rz.uni-sb.de title: Dr. tel;work: 0681-302-3949 tel;fax: 0681-302-4105 tel;home: 06897-764132 x-mozilla-cpt: ;0 x-mozilla-html: FALSE version: 2.1 end: vcard --------------B7225FA63FE74686BB1BC40D-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Hens Borkent Subject: Chime XYZ animations, mol editor Date: Fri, 08 Jan 1999 11:34:21 +0100 To: rasmol@dhcp-srv2.oit.umass.edu, mitch@mdli.com Chimers of the world, There have been several questions lately about Chime animations, based on multiple XYZ files. We have been using these animations for quite a while now, in our educational (organic chemistry) web pages Molecules in four dimensions (http://www.caos.kun.nl/wetche/organic/), Mol4D. Besides ready-made animations, Mol4D features a perl script based Chime molecule editor, to edit mopac input files and produce Chime'd xyz animations on the fly. (Netscape/Windows/MacPPC preferred) We have decided to make all the scripts available to the chime-using community. At the bottom of the page mentioned above there is a link to the 'technical background', that explains which script is used for what. The scripts are to some extent site-specific, of course, but could be adapted for local use. We would like to encourage the use of these scripts, in both ways: improvements on their tasks, and developing more applications in the field of organic chemistry. We intend to maintain a repository of the results, so please inform us if you have a contribution that is useful for others. -- ***** J.H. (Hens) Borkent, CAOS/CAMM Center, *CAOS * P.O. Box 9010, 6500 GL Nijmegen, The Netherlands * / * Tel 0031 24 36 52137 Fax 0031 24 36 52977 * CAMM* e-mail: borkent@caos.kun.nl ***** http://www.caos.kun.nl/staff/borkent.html pdb-l@pdb.pdb.bnl.gov bourne@sdsc.edu, helgew@sdsc.edu, jls@bnl.gov ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer/Comparator version 0.95 w/ NMR support Date: Sun, 10 Jan 1999 21:52:40 -0500 To: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu, Cc: rhodes@usm.maine.edu, brian.white@umb.edu, cmartin@chem.umass.edu, I put a new version of my Protein Explorer/Comparator at http://www.umass.edu/microbio/chime/explorer This version has all functionality that I have planned for version 1.0, designed to provide a RasMol-like interface in Chime. It is designated version 0.95 only because I have not yet written the tutorial for beginners, but those experienced with RasMol will have no problem using it. It is not yet linked to my public site pending completion of the tutorial; hence, this email announcement is its only publicity at this time. I would value feedback from anyone interested, especially Macintosh users. The entire package can be downloaded for local use. This version requires Chime 2.0, hence will work only on Windows95/NT4 or Macintosh PPC, and it requires Netscape Navigator 4.04 or later (4.5 recommended); Internet Explorer won't work properly. For SGI users, I have left the previous version 0.92 (which supports Chime 1.0 and, tho untested by me, may work with SGI Chime 0.9e) -- you'll see the link from the above URL. The Protein Explorer includes a command line input slot and a box for messages from Chime or from the Explorer itself. It allows you to load any PDB file from your disk, or via Internet from the closest mirror of the PDB. Convenience buttons are provided for spin, zoom, background color, water, hetero atoms. I have put a lot of effort into convenience features for exploring multiple-model NMR PDB files. When NMR files are loaded, the number of models is automatically detected, and an NMR control panel is offered. Initially, all models are shown overlayed. There are buttons to show one model at a time (in order, or any model you specify). There is a slot in which you can specify a list of particular model numbers, in any order. There is an [Auto] button which automatically steps through all models, one at a time, or the list of models you have specified in the order specified. You can specify one model as a reference model, and it is represented (by default) in black -- this model is always shown as you cycle through the other models. While Auto-stepping through a list of models, you can interrupt at any model and the Explorer will report which model you have selected. You can specify a custom color-scheme or rendering script which will supercede the defaults for all of the above features. All of these features also work in the Comparator, where you have two Chimes, so you can load two different PDB files (or the same file twice) and make side by side comparisons. The Comparator now includes a [Synch] button which makes one molecule follow all mouse-directed movements of the other molecule. This feature was added to Chime 2.0 by Tim Maffett, at my suggestion, just before it was released. I have included a document "Purpose of the Protein Explorer" which briefly discusses the history of Chime use, starting with linear tutorials on author-selected molecules (a la kinemages), and progressing to focussed tools which operate on a user-selected molecule (e.g. STING, Noncovalent Bond Finder, viewer for PDB Lite), and now to the Explorer, a totally general interface which invites the user to load any molecule and do anything of which Chime is capable. The long-range goal of the Protein Explorer (for future versions) is to make exploration and understanding of 3D structure more accessible to the general scientific public (educators, nonspecialists, and occasional users). I hope crystallographers and structure researchers will also find useful some of the convenience features which go beyond RasMol. It is planned to incorporate the Explorer directly into the PDB search interface. Cookies are used, and to reassure those who are worried about cookies, we have provided what I hope you'll agree is a thorough and authoritative discussion. The conclusion is not to worry; but you're told how to worry effectively if you insist. The Explorer/Comparator is free to all users (thanks to the NSF's Division of Undergraduate Education and UMass for support). Although it can be used directly from the web, it can also be downloaded for the convenience of local use. TECHNICAL INFORMATION This version first includes javascript for unscrambling the messages received from Chime via MessageCallback. This turned out to be complex but seems to be working reliably. The code for unscrambling alone exceeds 400 lines. The version/design document which is provided with the Explorer explains in more detail how this interface works. The scrambling which occurs is not due to a bug in Chime, according to Tim Maffett, but occurs somewhere in the 'black box' of the LiveConnect interface with Netscape. Hence it is not under the control of MDLI. Unscrambling is necessary to allow javascript to query Chime unambiguously for critical information such as how many NMR models were loaded, which model is displayed after interrupting auto-stepping, how many atoms are selected by a given command, etc. It is also necessary so that javascript can tell when Chime has completed executing a script, which in turn can be used not only to signal the user with a Ready/Busy indicator, but also to prevent sending a new script to Chime immediately following an interrupt, which results in interscrambling of both scripts (a condition even my 400+ line unscramble() can't deal with). Other developers of Chime resources may wish to use the unscrambling mechanism in their own work and are welcome to do so. Just download the Explorer and you get this code plus detailed documentation with it. Start in the Design Features document which directs you to the relevant functions and files. Happy 1999 to all rasmolians/chimeleons, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu UMass Chime Site - - - - - - - - - - - - - - - - - - - - - - - - - - - */ X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Mark Brooks Subject: Compiling Rasmol under Linux Date: Mon, 11 Jan 1999 20:20:54 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Hi! Sorry for asking another linux question, but I'm having a bit of a problem compiling Rasmol in Red Hat linux 5.2. I'm using the RasMol26 file from "ftp://nexus.roko.goe.net/pub/rasmol/" as told in the discussion group's history, and have defined "#define USE_FD_SET_TYPE" and 16bit for my display as instructed (I hope), but I still get the following output when I make it: [root@reeves RasMol2.6x1]# make gcc -O2 -fno-strength-reduce -I/usr/X11R6/include -I/include -Dlinux -D__i386__ -D_POSIX_C_SOURCE=199309L -D_POSIX_SOURCE -D_XOPEN_SOURCE=500L -D_BSD_SOURCE -D_SVID_SOURCE -DFUNCPROTO=15 -DNARROWPROTO -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DSIXTEENBIT -c rasmol.c -o rasmol.o rasmol.c: In function `ResetTerminal': rasmol.c:220: `TCSETAW' undeclared (first use this function) rasmol.c:220: (Each undeclared identifier is reported only once rasmol.c:220: for each function it appears in.) rasmol.c: In function `InitTerminal': rasmol.c:517: `TCGETA' undeclared (first use this function) rasmol.c:518: `IntrTerm' has an incomplete type rasmol.c:520: invalid use of undefined type `struct termio' rasmol.c:521: invalid use of undefined type `struct termio' rasmol.c:522: invalid use of undefined type `struct termio' rasmol.c:523: invalid use of undefined type `struct termio' rasmol.c:525: invalid use of undefined type `struct termio' rasmol.c:526: invalid use of undefined type `struct termio' rasmol.c:529: invalid use of undefined type `struct termio' rasmol.c:532: `TCSETAW' undeclared (first use this function) rasmol.c: At top level: rasmol.c:117: storage size of `OrigTerm' isn't known rasmol.c:118: storage size of `IntrTerm' isn't known make: *** [rasmol.o] Error 1 What could I be doing wrong please? Any advice to get this wonderful software working would be greatly appreciated! Thanks in advance, Mark. Mark Brooks, Institute of Neuropathology, CWRU, Cleveland, OH., 44106. Tel: (216) 368 3329. ++++------+------+------+------+------+------+------+------+------+------+ From: Albion Baucom Subject: Re: Compiling Rasmol under Linux Date: Mon, 11 Jan 1999 17:42:07 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu You may have a problem with includes and their paths. Under Linux 5.2 termio.h is in /usr/include, but it should be in the directory /usr/include/sys. To try this fix make a COPY of termio.h in /usr/include/sys and try a clean make (make clean, make). If this works let me know since people in our lab have had problems with this as well and havent got passed it yet. GCC is complaining that the functions ResetTerminal and InitTerminal cannot find the delerations for TCSETAW and TCGETA and the C struct termio which are all declared in termio.h since it can't find the file termio.h in /usr/include/sys. The Makefile is where the information about where includes are kept so if you are brave you can use a text editor to pick through this to find where the Makefile is looking for the termio.h and change it to the correct location (or make a copy as suggested above which is an easier patch at this point). Good luck! Albion Albion E. Baucom '71 R75/5 '74 R75/5 http://tito.ucsc.edu/baucom On Mon, 11 Jan 1999, Mark Brooks wrote: > Hi! > Sorry for asking another linux question, but I'm having a bit of a > problem compiling Rasmol in Red Hat linux 5.2. > > I'm using the RasMol26 file from > "ftp://nexus.roko.goe.net/pub/rasmol/" > as told in the discussion group's history, and have defined "#define > USE_FD_SET_TYPE" and 16bit for my display as instructed (I hope), but I > still get the following output when I make it: > > [root@reeves RasMol2.6x1]# make > gcc -O2 -fno-strength-reduce -I/usr/X11R6/include -I/include > -Dlinux -D__i386__ -D_POSIX_C_SOURCE=199309L -D_POSIX_SOURCE > -D_XOPEN_SOURCE=500L -D_BSD_SOURCE -D_SVID_SOURCE -DFUNCPROTO=15 > -DNARROWPROTO -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DSIXTEENBIT -c > rasmol.c -o rasmol.o > rasmol.c: In function `ResetTerminal': > rasmol.c:220: `TCSETAW' undeclared (first use this function) > rasmol.c:220: (Each undeclared identifier is reported only once > rasmol.c:220: for each function it appears in.) > rasmol.c: In function `InitTerminal': > rasmol.c:517: `TCGETA' undeclared (first use this function) > rasmol.c:518: `IntrTerm' has an incomplete type > rasmol.c:520: invalid use of undefined type `struct termio' > rasmol.c:521: invalid use of undefined type `struct termio' > rasmol.c:522: invalid use of undefined type `struct termio' > rasmol.c:523: invalid use of undefined type `struct termio' > rasmol.c:525: invalid use of undefined type `struct termio' > rasmol.c:526: invalid use of undefined type `struct termio' > rasmol.c:529: invalid use of undefined type `struct termio' > rasmol.c:532: `TCSETAW' undeclared (first use this function) > rasmol.c: At top level: > rasmol.c:117: storage size of `OrigTerm' isn't known > rasmol.c:118: storage size of `IntrTerm' isn't known > make: *** [rasmol.o] Error 1 > > What could I be doing wrong please? Any advice to get this wonderful > software working would be greatly appreciated! Thanks in advance, > > Mark. > > Mark Brooks, > Institute of Neuropathology, > CWRU, Cleveland, OH., 44106. > Tel: (216) 368 3329. > ++++------+------+------+------+------+------+------+------+------+------+ From: James Leong Mook seng Subject: Compile Rasmol Date: Wed, 13 Jan 1999 22:36:41 -0800 (PST) To: Rasmol Help I am using visual c++5.0 to compile rasmolv2.5 on a windows95 os.I am getting the following error: Raswin.obj:error LNK2001: unresolved external symbol _fstrnicmp .Could anyone help me in this problem or can anyone help in the compilation of rasmol. Thanks a lot in advance. Bye& _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com References: <19990114063641.21175.rocketmail@send105.yahoomail.com> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: Compile Rasmol Date: Thu, 14 Jan 1999 13:56:40 +0000 To: rasmol@dhcp-srv2.oit.umass.edu James Leong Mook seng wrote: > > I am using visual c++5.0 to compile rasmolv2.5 on a windows95 os.I am > getting the following error: Raswin.obj:error LNK2001: unresolved > external symbol _fstrnicmp .Could anyone help me in this problem or > can anyone help in the compilation of rasmol. Thanks a lot in advance. > Bye& Hi, I've used MS-C++ v.5.0 to compile Rasmol2.6b - but that's a long time ago ;-). The only 'help' I can give at the moment is to define '_WIN32' manually in rasmol.h. You do this by putting the line #define _WIN32 somewhere at the beginning of rasmol.h. The compiler (pre-compiler) then uses strnicmp instead of _fstrnicmp! I guess the whole '_f' stuff is something comming from win3.1 ... . Don't know if that works, let me know about the result (I'm sory I cannot test it as I've no win95 machine here), good luck, Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)171 2693405 | Fax : +44-(0)171 269 3258 email : a.mueller@icrf.icnet.uk | http://www.icnet.uk/bmm/ X-pmrqc: 1 ++++------+------+------+------+------+------+------+------+------+------+ From: "Michael Meredith" Subject: How do you show sections of molecules? Date: Thu, 14 Jan 1999 15:09:10 -0000 To: rasmol@dhcp-srv2.oit.umass.edu Can you help? I'm trying to compile a tutorial in RasMol and want to display only sections of some chains. I know how to restrict views of molecules to chains, but I only want to show part of a chain at a time. Thanks for you help, Michael ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Ideas solicited for Protein Explorer 0.96 Date: Thu, 14 Jan 1999 12:50:06 -0500 To: rasmol@dhcp-srv2.oit.umass.edu I've had some feedback from Macintosh users about the Protein Explorer 0.95, and a couple of new ideas myself. Here are my plans for version 0.96. Comments and suggestions to add to this list are welcome (tho I can't promise to do them all). New features planned: * User-configurable aliases. These are just typing conveniences. For example 's l' will expand to 'select ligand', 's 122-160 and n w' will expand to 'select 122-160 and not water' (can't alias 'a' to 'and' since 'a' already means adenosine), 'cs' will expand to 'center selected', 'spm' will expand to 'set picking monitor', etc. If you want to suggest other default aliases, the complete list I have in mind is below. Would anyone want 1-letter AA codes aliased? I don't plan to do it unless interest is expressed as it involves a bit of extra coding. It would be a user-enabled preference, not a default. Since a, t, g, c conflict with nucleotides, if you enabled this and then wanted to refer to nucleotides, you'd have to prefix them with a period, which will prevent alias expansion (for example 's .a,.t' would expand to 'select a,t' instead of 'select ala,thr'.) * User-configurable project folder(s). By default, RasMol's load command looks for PDB files in the folder from which it was started (or the working folder specified in a Windows shortcut icon). Similarly, the 'script' command looks for .spt files in that folder. PE does the same but its working folder is 'explorer' which already contains over 50 files not relevant to a particular project. I'll add the capability to set a project folder (for PDB files and scripts), and optionally different folders for scripts (primary and secondary). The secondary script folder would be for scripts shared between projects. What this means is that the commands 'load xxx.pdb' or 'script xxx.spt' will automatically get the specified project path prefixed to xxx. Unfortunately I have no way to change the present default that saving a PDB file from Chime puts the file in Netscape's program folder. * Thanks to the suggestion of Kurt Giles, I'll add an 'edit preferences' capability. His suggestion was to be able to start with spin off. Other ideas: automatically add .pdb to the filename in a load command, and .spt to the filename in a script command. And it might be useful to be able to turn off alias expansion. Any other ideas for preferences? (The preferences will be saved as a cookie so will survive between sessions.) Macintosh fixes: * After pressing Enter to send a manually typed command, the focus will be forced back to the command slot so you don't have to click there before typing the next command. (This is already the case under Windows). * 'Force ready' (you have to scroll below the message area to see it) will be improved to work reliably with a single click. This allows you to recover from the permanent busy condition which presently results from resizing the PE or Chime windows. Several people have reported that the [Synch] button doesn't work on Macintoshes. That's a bug which slipped by into Chime 2.0a and is not under my control (it has been reported to MDLI). I'll add a message which informs Mac users not to expect it to work. Here is the complete list of aliases which will ship with the PE (you can change these or add new ones but these will be the default): cs center selected js javascript l ligand ll lload ls lscript m (cadmium,calcium,iron,magnesium,manganese,zinc) n not s select sc script w water spi set picking identify spd set picking distance spm set picking monitor spa set picking angle spt set picking torsion spl set picking label spc set picking center nn funny funny not(protein,dna,rna,hetero) /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ rasmol@dhcp-srv2.oit.umass.edu References: <369DF798.E5783CBA@icrf.icnet.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: How do you show sections of molecules? Date: Thu, 14 Jan 1999 13:15:28 -0500 To: michael.meredith@continuing-education.oxford.ac.uk, For section of residues 23-44 in chain :a, 'restrict 23-44:a'. Or 'restrict none', then 'select 23-44:a', then render and color as desired. All this and more is explained in Select Commands in Chime and RasMol http://www.umass.edu/microbio/rasmol/seleccmd.htm At 1/14/99, Michael Meredith wrote: >Can you help? > >I'm trying to compile a tutorial in RasMol and want to display only >sections of some chains. I know how to restrict views of molecules >to chains, but I only want to show part of a chain at a time. > >Thanks for you help, > >Michael > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: James Leong Mook seng Subject: Color Date: Fri, 15 Jan 1999 21:32:14 -0800 (PST) To: Rasmol Help How can i customise the color of atoms(H,C, etc) in rasmolv2.5.Thank you very much in advance.& _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Recent stats for RasMol/Chime site Date: Sun, 17 Jan 1999 13:43:25 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Below are numbers of 'people' visiting my molecular visualization freeware site, where it is interesting to see the holiday/new-year dip. There is also an analysis of the past week's activity at the Chime branch. As I have seen in the past, the majority (70-90%) of people who visit my Chime resources never go very deep into them, which I interpret to mean that they don't have Chime installed. It is unfortunate that so many miss out due to the 'energy barrier' of the downloading and installation. A result which surprised me is that there appears to be more interest in the Noncovalent Bond Finder than in any other single topic/resource I have authored and provided on my Chime site. Here are the recent numbers of distinct IP addresses coming to my UMass Chime site, the RasMol Home Page, and the total. The total is less than the sum since many visitors go to both. The number of files fetched is on the order of 20 times these numbers. > Unique IP Addresses > -------------------- >Week ending Chime RasMol Total >Feb /97 831 2,746 2,929 (Dates are Month/Day/Year following US convention) >11/15/97 1,205 2,943 3,243 >02/07/98 1,448 3,502 3,897 >11/07/98 2,545 5,632 6,263 >11/28/98 2,133 4,578 5,163 (thanksgiving) >12/05/98 2,285 5,092 5,719 >12/12/98 2,068 4,521 5,128 (Christmas shopping?) >12/19/98 1,812 4,425 4,942 ditto >12/26/98 948 2,113 2,376 Xmas! > >01/02/99 898 1,917 2,195 New Years! >01/09/99 1,816 3,835 4,351 >01/16/99 2,163 4,499 5,192 The following details are for the week of January 10-16 1999 for the Chime site only. The number of distinct IP addresses ("people") visiting the site was 2,163 (as shown above). Numbers below (unless otherwise indicated) are numbers of times the indicated file was fetched. One visitor can fetch the same file more than once. In the Overview, MainPage is the number of fetches of index.htm (or equivalent), while Deeper is the number of fetches of a page not likely to be fetched unless Chime is installed. OVERVIEW (week of 1/10-16/99) Branch MainPage Deeper NCB Finder 472 65 (247 people; 21 people did 664 finding cycles!) DNA 342 95 Chime: How 271 30 Explorer 240 48 Hemoglobin 106 25 Template 100 20 (template for creating Chime presentations) ProtSecS 76 37 (non-supported, obsolete version) Antibody 73 8 MHC 50 4 Morpher 48 17 Downloads 263 n.a. (fetches of above chime packages for local use) World Index 371 n.a. (just a document) The astonishing thing here is the level of interest in the Noncovalent Bond Finder! Also amazing is the interest in the Explorer considering that is is not linked to my site (still a beta-test version), and has been announced only to about 1,000 people (PDB list and RasMol list). This may be a novelty effect for the Explorer, but the Finder has been on the web since April '98 and nothing has been done to it since (except for a minor fix to accomodate Chime 2 for Macs after its release in early Nov '98). The Finder is not available for download pending ongoing discussions about how best to support its future development. The Explorer is free to all users and was downloaded 42 times during the week. If anyone is interested, send me a request by email and I can provide a more detailed set of numbers for each of the above 'branches' (or even the raw web logs). /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu UMass Chime Site - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: <0F5P00453VUPZZ@rfd1.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Chen Hsiung Chan Subject: Re: Recent stats for RasMol/Chime site Date: Mon, 18 Jan 1999 02:55:48 +0800 To: rasmol@dhcp-srv2.oit.umass.edu On Sun, Jan 17, 1999 at 01:43:25PM -0500, Eric Martz wrote: [snipped] > There is also an analysis of the past week's activity at the Chime branch. > As I have seen in the past, the majority (70-90%) of people who visit my > Chime resources never go very deep into them, which I interpret to mean > that they don't have Chime installed. It is unfortunate that so many miss > out due to the 'energy barrier' of the downloading and installation. [snipped] There is indeed a energy barrier, but not from 'downloading and installation'. I am a FreeBSD/Linux/Digital Unix(alpha) user. Unfortunatelly chime does support these platforms. -- Chen-Hsiung Chan [¸âÂíºµ](BIG5) Department of Life Science http://waru.life.nthu.edu.tw/~frankch/ National Tsing Hua University email: frankch@waru.life.nthu.edu.tw Taiwan References: <0F5P00453VUPZZ@rfd1.oit.umass.edu> <19990118025548.B5424@waru.life.nthu.edu.tw> ++++------+------+------+------+------+------+------+------+------+------+ From: Chen Hsiung Chan Subject: Re: Recent stats for RasMol/Chime site Date: Mon, 18 Jan 1999 03:30:44 +0800 To: rasmol@dhcp-srv2.oit.umass.edu On Mon, Jan 18, 1999 at 02:55:48AM +0800, Chen Hsiung Chan wrote: > On Sun, Jan 17, 1999 at 01:43:25PM -0500, Eric Martz wrote: > [snipped] > > There is also an analysis of the past week's activity at the Chime branch. > > As I have seen in the past, the majority (70-90%) of people who visit my > > Chime resources never go very deep into them, which I interpret to mean > > that they don't have Chime installed. It is unfortunate that so many miss > > out due to the 'energy barrier' of the downloading and installation. > [snipped] > > There is indeed a energy barrier, but not from 'downloading and > installation'. I am a FreeBSD/Linux/Digital Unix(alpha) user. > Unfortunatelly chime does support these platforms. Oops. I lost the 'not'. Clearly I should not reply/post anything at 3:00am. -- Chen-Hsiung Chan [¸âÂíºµ](BIG5) Department of Life Science http://waru.life.nthu.edu.tw/~frankch/ National Tsing Hua University email: frankch@waru.life.nthu.edu.tw Taiwan References: <19990116053214.9490.rocketmail@send1e.yahoomail.com> x-mac-creator="4D4F5353" ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Color Date: Mon, 18 Jan 1999 08:12:10 -0500 To: rasmol@dhcp-srv2.oit.umass.edu James Leong Mook seng wrote: > How can i customise the color of atoms(H,C, etc) in rasmolv2.5.Thank > you very much in advance.& > > _________________________________________________________ > DO YOU YAHOO!? > Get your free @yahoo.com address at http://mail.yahoo.com James, One way to do this is to write a script using any generic text editor (WordPad, BBEdit), save it, then call it in Rasmol whenever you want to apply the color scheme. Your script (mycolors.spt) might look something like this, for example: # script mycolors.spt select carbon color [255,0,0] #red carbons select oxygen color [255,255,255] #white oxygens select nitrogen color [0,0,255] #blue nitrogens select hydrogen color [160,32,240] #purple hydrogens etc... and you can call it by typing 'script mycolors.spt' in the Rasmol command line. N.B. Be careful to put the script file in the same folder/directory as the Rasmol program or the script won't run. Happy coloring! Tim Driscoll ******************** Timothy Driscoll UMass Amherst Molecular and Cellular Biology Chemistry-Biology Interface Program * Department of Chemistry Amherst College Amherst, MA 01002 413 542 2738 * http://merckx.chem.amherst.edu/tdriscoll/ ******************** ++++------+------+------+------+------+------+------+------+------+------+ From: James Leong Mook seng Subject: Load a file automatically. Date: Mon, 18 Jan 1999 07:18:13 -0800 (PST) To: Rasmol Help Hello, I would like to automatically load a file (pdb extension) when rasmol starts. Can anyone help me. thank you very much in advance for your help.& == James Leong Mook seng Clairfonds No 2, Vacoas Mauritius. _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Load a file automatically. Date: Mon, 18 Jan 1999 10:59:04 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Depends on what operating system you are using. In Windows, you can make a file rasmol.ini which contains script commands, or calls another script file. See the Reference Manual for unix. I don't know how to do this on Mac. You should probably be using Chime instead. It is designed for presentations, whereas RasMol's great strength is interactive self-directed exploration. When you start trying to get RasMol to do things automatically, you'll find it very limiting -- unlike Chime. At 1/18/99, you wrote: >Hello, > I would like to automatically load a file (pdb extension) when >rasmol starts. Can anyone help me. thank you very much in advance for >your help.& > >James Leong Mook seng >Clairfonds No 2, Vacoas >Mauritius. RasMol Reference Manual: http://www.umass.edu/microbio/rasmol/distrib/rasman.htm /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: James Leong Mook seng Subject: Rasmol Bonds Date: Mon, 18 Jan 1999 11:11:24 -0800 (PST) To: Rasmol Help Hello, What should I include in the pdb file format to show double and triple bonds in rasmol. Could anyone help me. Thank very much you in advance. If anyone is trying to launch rasmol and loading a pdb file to display from visual c++, i can help.& == James Leong Mook seng Clairfonds No 2, Vacoas Mauritius. _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ++++------+------+------+------+------+------+------+------+------+------+ From: James Leong Mook seng Subject: Rasmol Bonds Date: Mon, 18 Jan 1999 11:11:52 -0800 (PST) To: Rasmol Help Hello, What should I include in the pdb file format to show double and triple bonds in rasmol. Could anyone help me. Thank very much you in advance. If anyone is trying to launch rasmol and loading a pdb file to display from visual c++, i can help.& == James Leong Mook seng Clairfonds No 2, Vacoas Mauritius. _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ++++------+------+------+------+------+------+------+------+------+------+ From: James Leong Mook seng Subject: Rasmol Bonds Date: Mon, 18 Jan 1999 11:04:28 -0800 (PST) To: Rasmol Help Hello, What should I include in the pdb file format to show double and triple bonds in rasmol. Could anyone help me. Thank very much you in advance. If anyone is trying to launch rasmol and loading a pdb file to display from visual c++, i can help.& == James Leong Mook seng Clairfonds No 2, Vacoas Mauritius. _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com Anmar Ali ++++------+------+------+------+------+------+------+------+------+------+ From: " Dr. Frank Eblinger" Subject: [Fwd: FW: Virus Warning !!] Date: Tue, 19 Jan 1999 16:20:10 +0100 To: "Dr. Jürgen Gauer" , This is a multi-part message in MIME format. --------------2F4FB00959E4758343C7942D --------------2F4FB00959E4758343C7942D Content-Disposition: inline "'Chantal Felten'" , "'Ciaravino Ilda'" , "'Clos Harald'" , "'Deutscher Bernd'" , "'Faller Thomas'" , "'Federico Marcellino'" , "'Fisch Jo'" , "'Frank Grossmann'" , "'Fred Winsmann'" , "'Hafner Thorsten'" , "'Harth Detlev'" , "'Jochen Meister'" , "'Klein Christina'" , "'Lobo'" , "'Lombarski Thorsten'" , "'Loutzoglou Franziska'" , "'Marcellino Federico'" , "Arangio, Mario" , "'Martin Welp'" , "'Massachussets University'" , "'Matheis Joachim'" , "'Meissner Christian'" , "'Miguel'" , "'Odilo'" , "'Poggiolini Alessandra'" , "'Poppi'" , "'Ravagni Alberto'" , "'Ronellenfitsch Enrike'" , "'Schneider Patrick'" , "'Secular L. Donna'" , "'Silvana'" , "'Straub Holger'" , "'Treitz Manfred'" , "'Treitz Manfred home'" , "'Volker Bomm'" , "'Windy'" ++++------+------+------+------+------+------+------+------+------+------+ From: "Arangio, Mario" Subject: FW: Virus Warning !! Date: Tue, 19 Jan 1999 09:44:47 -0500 To: "'Cervone Brunella e Claudio'" , > I was sent this email by a friend of mine. It might not be true, but > be aware just in case. > > Thanks, > Mario > > > > > ---------- > From: Kaplan, Alan > Sent: Tuesday, January 19, 1999 8:22 AM > To: All ArQule Employees > Subject: FW: Virus Warning !! > > > > > > Subject: Virus Warning !! > > > > Just to let you know > > Someone is sending out a very desirable screen-saver, the Budweiser > Frogs > > - > > "BUDDYLST.ZIP". If you download it, you will lose everything!!! > > Your hard drive will crash and someone from the Internet will get > your > > screen name and password! DO NOT DOWNLOAD THIS UNDER ANY > CIRCUMSTANCES!!! > > IT JUST WENT INTO circulation yesterday, as far as we know. Please > > distribute/inform this message. This is a new, very malicious virus > and > > not > > many people know about it. This information was announced yesterday > > morning > > from Microsoft. Please share it with everyone that might access the > > Internet. Once again, pass this along to EVERYONE in your address > book so > > that this may be stopped. Also do not open or even look at any mail > that > > says "RETURNED OR UNABLE TO DELIVER". This virus will attach itself > to > > your > > computer components and render them useless. Immediately delete mail > items > > that say this. AOL has said that this is a very dangerous virus and > that > > there is NO remedy for it at this time. Please practice cautionary > > measures > > and forward this to all your on-line friends ASAP > > > > > > > > --------------2F4FB00959E4758343C7942D Content-Description: Card for Frank Eblinger Content-Disposition: attachment; filename="vcard.vcf" begin: vcard fn: Frank Eblinger n: Eblinger;Frank adr: In den Welkertswiesen 65;;;Saarbrücken;Saarland;66125;Germany email;internet: f.eblinger@rz.uni-sb.de title: Dr. tel;work: 0681-302-3949 tel;fax: 0681-302-4105 tel;home: 06897-764132 x-mozilla-cpt: ;0 x-mozilla-html: FALSE version: 2.1 end: vcard --------------2F4FB00959E4758343C7942D-- ++++------+------+------+------+------+------+------+------+------+------+ From: Alan Wolfson Subject: Re: [Fwd: FW: Virus Warning !!] Date: Tue, 19 Jan 1999 10:50:00 -0500 To: rasmol@dhcp-srv2.oit.umass.edu, gauer@inm-gmbh.de At 04:20 PM 1/19/99 +0100, Dr. Frank Eblinger wrote: While there may be screen savers containing viruses, that particular one appears to be a hoax. You can easily determine whether it is a hoax or not by doing a little investigation. I assume that most of us here on this list are scientists and are not afraid of doing a little research :-) A quick check of Microsoft's web site (http://www.microsoft.com) did not turn up any virus warning despite the citation in the emailed warning. Here's some information from the Internet Tourbus, a free newsletter that has a lot of useful information in it: ----------- begin included information ----------- To help you combat the sea of urban legends that fills your inbox every day, your fearless bus driver has created the Urban Legend Combat Kit. The Combat Kit is a *FREE* collection of canned email responses that helps you debunk some of the Internet's most prevalent myths and urban legends. Just cut and paste whatever you need. You can find the Combat Kit on my Web site at http://netsquirrel.com/combatkit/ . ----------- end included information ----------- Please make an attempt to verify these type of things before posting them to a list such as this one. Alan Alan Wolfson Senior Consultant MDL Information Systems ++++------+------+------+------+------+------+------+------+------+------+ From: Scot Wherland Subject: Inorganic teaching resources Date: Tue, 19 Jan 1999 08:02:22 -0800 To: rasmol@dhcp-srv2.oit.umass.edu This is an announcement of the enhancement, or at least growth, of my WWW resource page. It is quite a primitive use of Chime, but the collection of structures may be of interest. It has two parts. 1. A periodic table with the elements represented as spheres of their appropriate size. This is viewed with Chime, and has not changed. Note in response to recent posts: I should add a set of vdw radii, but they are hard to find, especially measured ones. 2. A database of experimental structures of about 250 molecules. This has been greatly enlarged through the addition of a number of transition metal complexes showing different coordination numbers and isomers. I now recommend Chime 2 for viewing the structures since it now has the ability to measure bond lengths and angles and is commonly used, but WebLab Viewer is still supported and has advantages. As always, comments and requests are solicited. There is some activity above "background" according to the counter so it appears some use is being made outside the Palouse. I have started extracting subsets of the structures to use in General Chemistry. This is easily done since the structures are individual files. The site is: http://www.wsu.edu/~wherland/ Enjoy, Scot Scot Wherland Voice: 509-335-3360 Prof. of Chemistry FAX: 509-335-8867 Dept. of Chemistry Email: scot_wherland@wsu.edu Washington State University Pullman, WA 99164-4630 USA ++++------+------+------+------+------+------+------+------+------+------+ From: "Marc Bianciotto" Subject: Re: [Fwd: FW: Virus Warning !!] Date: Tue, 19 Jan 1999 17:16:16 +0100 To: rasmol@dhcp-srv2.oit.umass.edu Hi, Be careful about this type of alerts. According to the well-known anti-virus producer Symantec, (I cite) "BUDDYLST.ZIP is not a virus. It is a hoax. The "virus" does not exist. There is currently no virus that has the characteristics ascribed to BUDDYLST.ZIP." I refer to this URL : http://www.symantec.com/avcenter/venc/data/buddylst.zip.html and to this one about hoaxes : http://www.symantec.com/avcenter/hoax.html Go there and see. You have to trust in some people on the Internet, about Rasmol, I trust in this mailing-list, about viruses, I trust in them... Well, this type of message is coming frequently in mailboxes ( Good Times, Penpal Greetings) and it would be quite nice if it wasn't nearly all the time hoaxes like this. Do you know the virus called Paranoia ? Good Rasmol & Chime! Marc Bianciotto *************************************** * Marc Bianciotto * * L.S.P.C.O./I.R.S.A.M.C * * * 118, route de Narbonne * * 1000 Toulouse * * biancio@irsamc1.ups-tlse.fr * *************************************** References: <19990118191124.13425.rocketmail@send102.yahoomail.com> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: "Jeffrey J. Ayres" Subject: Re: Rasmol Bonds Date: Tue, 19 Jan 1999 10:18:11 -0700 To: rasmol@dhcp-srv2.oit.umass.edu, James Leong Mook seng James, A letter was posted several days ago briefly describing the process necessary to display double bonds in rasmol. First you probably need rasmol 2.6, 2.5 does not show double bonds. Second, if you have a large file it could take awhile since you must manually enter an extra "conect" line for each double bond. The method I am using is convert the pdb file to a MDLmol file, before adding hydrogens. Then checking the structure to verify the double bonds are in the correct place. Sometimes in the conversion the double bonds are not correctly placed, this too is a time consuming process. Then add the hydrogens. Rasmol will show MDLmol files as well as PDB. If I can assist you further send an email. Jeff Ayres James Leong Mook seng wrote: > Hello, > What should I include in the pdb file format to show double and > triple bonds in rasmol. Could anyone help me. Thank very much you in > advance. If anyone is trying to launch rasmol and loading a pdb file > to display from visual c++, i can help.& > > == > > James Leong Mook seng > Clairfonds No 2, Vacoas > Mauritius. > > _________________________________________________________ > DO YOU YAHOO!? > Get your free @yahoo.com address at http://mail.yahoo.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Adrian Kornhauser (lab3)" Subject: Re: [Fwd: FW: Virus Warning !!] Date: Tue, 19 Jan 1999 12:12:42 -0600 (CST) To: rasmol@dhcp-srv2.oit.umass.edu Antoher interesting place to "nail" hoaxes is: http://ciac.llnl.gov/ In this particular case the information on the "Bud Frogs Screen Saver" hoax is at: http://ciac.llnl.gov/ciac/CIACHoaxes.html#budfrogs Adrian Kornhauser ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Visitor-maintained index of Chime resources? Date: Tue, 19 Jan 1999 18:45:36 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Dear Chimeleons: Many of you are aware of a page on my site presumptiously titled "World Index: BioMolecular Tutorials in Chime by Subject plus RasMol 'movie' scripts and Chime authoring resources" where 40-some Chime tutorials and resources are indexed and linked (http://www.umass.edu/microbio/rasmol/tutbymol.htm). This project is quite hopeless since time is never available properly to index and link the many new and excellent Chime sites being developed. My apologies to many of you who have pointed out sites to me and got no response. In June, I provided a guestbook so visitors could add their own links and descriptions, but the server we contracted to provide CGI service (not available from the computer center on our campus) has been defunct recently and although a kind colleague has offered us an account at the San Diego Supercomputer Center, we haven't yet installed the guestbook there. In any case, the guestbook contributions are not ideal since they are not indexed and appear on a separate page from the 'World Index'. I think there is a real need for such an index because it is not possible, to my knowledge, to search for pages which invoke Chemscape Chime via Yahoo, Alta Vista, Hotbot, Infoseek, etc. This is because these services (when last I checked) don't index words in tags, so you can't search for .spt or .pdb or application/x-spt or chemical/x-pdb. And of course html files which invoke Chime don't necessarily contain the word Chime, and even the embed tag may be hidden in a separate javascript file which constructs the tag on the fly. If I have missed some trick here, someone please enlighten me! I think the solution is to develop CGI scripts which allow visitors to the World Index to contribute their own index entries and site descriptions with a web form, which will then (after approval by a moderator) be incorporated into a sorted data file, which in turn can be used to regenerate the entire HTML document after every update. This goes beyond the usual guestbook in that the resulting html will contain multiple sections (subject index, author index, and site list with site descriptions) and will always be appropriately alphabetized. Once operational, aside from moderation (approval/rejection/request for revision), the only human effort involved would be on the part of the visitor/contributor. This type of "Visitor-maintained index" is surely needed for areas other than Chime and perhaps someone has already developed code for a different application, in which case I'd love to know about it. We are beginning to plan, and will then code, the PERL required for such a "Visitor-maintained [but moderated to prevent graffiti] index of Chime resources". However we are PERL and CGI novices and it will be a struggle. We would gladly accept assistance from those more experienced should such volunteers wish to come forth! -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu UMass Chime Site - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Fwd: RE: Visitor-maintained index of Chime resources? Date: Wed, 20 Jan 1999 14:26:22 -0500 To: rasmol@dhcp-srv2.oit.umass.edu David's idea below sounds excellent and I think we should all strive towards it. It would help if MDL would encourage people who write Chime-based resources to use a standard meta-tag, and I'll plan to incorporate it into my template and recommend this elsewhere on my site. Nevertheless I still strongly favor the visitor-maintained index both because there will always be some sites which forget to use these meta-tags, and because a visitor-maintained index with site descriptions written by site authors would be a very useful complement to whole-web searching. -Eric Martz >From: "David Hole" >To: >Subject: RE: Visitor-maintained index of Chime resources? >Or encourage the uniform use of a metatag that would get indexed and would >be easy to search for. Adding a meta tag to most of our pages would be >relatively painless. The key is to get everyone to use the same tag so >searches could be simple. >One possible example would be... > > >David Hole http://wheat.usu.edu/ >Assoc. Professor Utah State University >435-797-2235 dhole@mendel.usu.edu References: <0F5V00GB2HUEUC@rfd1.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: " Dr. Frank Eblinger" Subject: Re: Visitor-maintained index of Chime resources? Date: Thu, 21 Jan 1999 16:34:40 +0100 To: rasmol@dhcp-srv2.oit.umass.edu This is a multi-part message in MIME format. --------------2892CBFB13FE985FEB23B4E3 Hi to all, 1) For me it's no problem to insert the meta tag in my web sites, but I do not understand how to search for the keywords (.spt, chime...) I tried with altavista: thousands of hits.. 2) Another problem: About 10 days ago I was asking some questions about VdW radii. Did you forget ...? What number does Chime or RasMol use for vdw spacefilling ? 500 is too much, 400 too less.. Does the programm take into account different radii for atoms and ions? Thanks for your help in advance Frank (please visit our web site about supramolecular structures at: http://www.uni-sb.de/matfak/fb11/schneider/supram/supramolecular_structures.html --------------2892CBFB13FE985FEB23B4E3 Content-Description: Card for Frank Eblinger Content-Disposition: attachment; filename="vcard.vcf" begin: vcard fn: Frank Eblinger n: Eblinger;Frank adr: In den Welkertswiesen 65;;;Saarbrücken;Saarland;66125;Germany email;internet: f.eblinger@rz.uni-sb.de title: Dr. tel;work: 0681-302-3949 tel;fax: 0681-302-4105 tel;home: 06897-764132 x-mozilla-cpt: ;0 x-mozilla-html: FALSE version: 2.1 end: vcard --------------2892CBFB13FE985FEB23B4E3-- ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: Visitor-maintained index of Chime resources? Date: Thu, 21 Jan 1999 11:25:10 -0700 (MST) To: "Dr. Frank Eblinger" Cc: rasmol@dhcp-srv2.oit.umass.edu Hi Frank, > Another problem: About 10 days ago I was asking some questions about > VdW radii. Did you forget ...? What number does Chime or RasMol use > for vdw spacefilling? 500 is too much, 400 too less.. Does the programm > take into account different radii for atoms and ions? The table of Van der Waal's radii used by RasMol can be found in the source code in the file "abstree.h". This file contains a the array "Element" which contains the atomic symbol, the covalent radius, the VdW radius, the CPK colour and the name of each element in the periodic table. For example, carbon has a VdW radius of 387 (1.548 Angstroms), nitrogen of 350 (1.4 Angstroms) and oxygen of 337 (1.348 Angstroms). These are the values used for molecules containing hydrogen atoms. However, most protein structures in PDB do not contain explicit hydrogens as these are not resolved by X-ray crystallography. As a result for molecules without hydrogen atoms, RasMol use "united atom" Van der Waal's radii for carbon, nitrogen, oxygen and sulphur. This is the effective size of an atom plus its hydrogens (commonly used in forcefields and a better approximation of the molecule's surface). These values (also defined in abstree.h) are 468 for carbon (1.872 Angstroms), 375 for nitrogen (1.5 Anstroms) and 350 for oxygen (1.4 Angstroms). Note that the increase for carbon is larger than for oxygen, this is caused by both the average number of aditional hydrogens and how closely they're bound to their parent atom. Unfortunately, RasMol does not maintain a table of ionic radii for each possible charge state of an element, and so the values used by RasMol for displaying salts or similar structures are incorrect. Complete and reliable tables of ionic radii are both rare and harder to encode in computer software. For example, the CRC handbook lists five ionic radii for selenium: -2 (1.91A), -1 (2.32A), +1 (0.66A), +4 (0.50A) and +6 (0.42A). This series fits well with the VdW radius (as used by RasMol) of 0.9A in the uncharged state. One issue is which values should a molecular graphics program use if it doesn't have the required charge state in its tables (Se+2). Each element has an upper bound on its charge, but can theoretically have an arbitrary negative charge. Roger -- Roger Sayle, E-mail: roger@metaphorics.com Bioinformatics Group, Metaphorics, WWW: http://www.metaphorics.com/ 419 East Palace Avenue, Tel: (+1) 505-984-0613 Santa Fe, New Mexico, 87501. Fax: (+1) 505-989-1200 Content-Disposition: inline X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id BAA17515 ++++------+------+------+------+------+------+------+------+------+------+ From: Jean Debord Subject: Lipophilicity calculation with Chime Date: Fri, 22 Jan 1999 01:37:28 -0500 To: Rasmol List Dear Colleagues, Some time ago I have asked some questions about lipophilicity calculation with Chime. I thank Tim Maffett and Annie Van de Wiele for their replies. With their explanations I was able to modify Eric Martz's command-line demo into a web page which computes the lipophilicity of a molecule and displays its lipophilicity potential. You can download this document from: http://ourworld.compuserve.com/homepages/JDebord/lipophil.zip I hope you will find it useful. Best regards, Jean Debord Laboratoire de Pharmacologie, Faculte de Medecine 2 Rue du Docteur Marcland, 87025 Limoges, France http://ourworld.compuserve.com/homepages/JDebord ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas Gunda" Subject: Re: Rasmol Bonds Date: Fri, 22 Jan 1999 14:00:24 +1 To: rasmol@dhcp-srv2.oit.umass.edu > > James Leong Mook seng wrote: > > > Hello, > > What should I include in the pdb file format to show double and > > triple bonds in rasmol. Could anyone help me. Thank very much you in > > advance. If anyone is trying to launch rasmol and loading a pdb file > > to display from visual c++, i can help.& > > > > == > > > > James Leong Mook seng > > Clairfonds No 2, Vacoas > > Mauritius. > > One possibility is to read the pdb file into e.,g. Mol2mol, add hydrogens, add double bonds, and convert it into an MDL molfile. This MDL molfile will contain the necessary bond order information. Tamas E. Gunda ************************************************************************ Dr Tamas E. Gunda phone: (+36-52) 316666-2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 http://www.klte.hu/~gundat H-4010 Debrecen Hungary ************************************************************************ References: <199901220137_MC2-678E-B0E4@compuserve.com> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: "Brian White" Subject: Re: Lipophilicity calculation with Chime Date: Fri, 22 Jan 1999 09:25:10 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Jean - This does not work for macs. It adds too many /// for the file://// command & thus generates an error. I think Eric Martz fixed a similar problem with his protein explorer. Perhaps you can find out about his solution. Thanks for posting this! Brian Jean Debord wrote: > Dear Colleagues, > > Some time ago I have asked some questions about lipophilicity calculation > with Chime. I thank Tim Maffett and Annie Van de Wiele for their replies. > With their explanations I was able to modify Eric Martz's command-line demo > into a web page which computes the lipophilicity of a molecule and displays > its lipophilicity potential. > > You can download this document from: > > http://ourworld.compuserve.com/homepages/JDebord/lipophil.zip > > I hope you will find it useful. > > Best regards, > > Jean Debord > Laboratoire de Pharmacologie, Faculte de Medecine > 2 Rue du Docteur Marcland, 87025 Limoges, France > http://ourworld.compuserve.com/homepages/JDebord -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://omega.cc.umb.edu/~bwhite/ References: <199901220137_MC2-678E-B0E4@compuserve.com> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Macintosh file://// problem (Lipophilicity site) Date: Fri, 22 Jan 1999 17:34:06 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Re: Jean Debord's lipophilicity Chime site, At 1/22/99, Brian White wrote: >Jean - > This does not work for macs. It adds too many /// for the file://// >command & thus generates an error. I think Eric Martz fixed a similar problem >with his protein explorer. Perhaps you can find out about his solution. >Thanks for posting this! My solution can be seen in full by downloading the protein explorer http://www.umass.edu/microbio/chime/explorer/ The file loading code is in shared\loadit2.js If you seach that file for 'Macintosh' you'll find this nugget: if (pdb_name.substring(0, 7) != "http://" && pdb_name.substring(0, 10) != "../shared/") { if (pdb_name.charAt(0) == "/") // for Macintosh! pdb_name = "file://" + pdb_name; else pdb_name = "file:///" + pdb_name; } You need 3 slashes but for some reason the Netscape browse form slot delivers a prefixed slash on the Mac but not on Windows. In general, I'd suggest that people who want to build Chime sites "from scratch" start with the present protein explorer (and cut out what you don't want) rather than the old "command line demo" which lacks all the refinements I've been adding during the last year as I built the PE. Of course if you wait another week (?) it will have command aliasing, working folder configuration, preferences which survive between sessions, and a few more bug fixes when I release version 0.96. :-) -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Dr Walter Breau Subject: Protein Explorer JavaScript error Date: Tue, 26 Jan 1999 12:10:55 -0800 To: rasmol@dhcp-srv2.oit.umass.edu Hello, I have been trying to get Protein Explorer to work on my system (Pentium II, 266Mhz, Win95 using Netscape 4.04). I have tried the explorer on Eric's web site and as a download on my harddrive. When I click on the "Load molecule" button I always get the message: JavaScript Error: file///Raswin/Chime2/shared/cookie.js. line 77: test for equality (==) mistype as assignment (=)? Assuming equality test. while (s1 = raw.indexOf ( " ; " , s0) ) .............................................................^ Any suggestions to fix the problem would be appreciated Walter Breau Department of Biology Elms College Chicopee, MA USA 01013 breauw@elms.edu ++++------+------+------+------+------+------+------+------+------+------+ From: lynna@cgl.ucsf.EDU Subject: setting a scale Date: Tue, 26 Jan 1999 15:44:45 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu Hello. I am using RasMol to generate a series of GIFs of many different molecules. I would like to have all of the molecules displayed at the same scale, but I cannot figure out how to do this. Searching through the FAQs and the user's guide has yielded no satisfactory answer. I have enclosed parts of two posts that are most relevant. If anyone has a possible solution, even an inelegant one, please post it. Thanks. -Aenoch Lynn On Wed, 24 Apr 1996 17:40:28 +0100 (BST), Sayle Dr R A wrote: > Dear Michael, > > 1. Is there a way of setting an absolute scale for a figure? I am > > trying to print different molecules on the same scale for comparison > > purposes. I have tried the ZOOM command but that doesn't seem to work. > > Thanks very much for your email. For a long time, I didn't think that > this was possible but have recently found a bizarre solution. > > The solution is based upon the fact that the maximum "zoom" allowed by > RasMol is dependent upon the size of a molecule. It transpires that for > any molecule the maximum zoom provides an image where 1 Angstrom is equal > to about 128 pixels. > > Hence you load in two molecules, for example "crambin" and "aspirin" into > two different RasMol's. You then determine from the RasMol command line > the maximum allowed zoom parameter. For example, if "zoom 500" reports > "Parameter value too large!", then 500 is too high, otherwise if the (zoom > command is successful) the value is probably too low. > > On my local machine the maximum zoom for "crambin" is 362, and the > maximum scale for "aspirin" is 118. This means that the two images > have the same scale when the ratio of the two zooms is 362:118. > For example, to display "aspirin" on the same scale as the default > "crambin", you should type "zoom 32" into the aspirin window > (and "zoom 100" into the crambin window). On Thu, 17 Oct 1996 22:46:33 -0700, Tim Maffett wrote: > At 12:25 PM 10/17/96 +0100, Andrea Bernini wrote: > >First, thanks to Roger Sayle and Tim Maffett for explanations on write > >command and Chime, now i'm making movies! Now i have two more question > >( i've searched all the manuals and mailing list archives before ask you, > >but find nothing): how can i hide selected atom expression and set the > >work area to a determinate size? > > You can use the 'restrict' command to limit what is displayed. > > I am not sure what you mean you say 'determinate size', but with the > next version of Chime, due out any day now (v 0.99), you can > set the angstroms per inch for a Chime plugin, allowing you to > have several Chime plugins on a page, all displaying molecules in > the same absolute scale. This is currently done with an > tag argument, but I may be adding a rasmol script command for this as > well. X-MSMail-Priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: "Van de Wiele Annie" Subject: are Chime and Rasmol usable with Windows 98 ? Date: Wed, 27 Jan 1999 12:48:10 +0100 To: "rasmol lists" Dear Rasmol Users, Before taking Windows 98, I prefer to know if there is not too much problems with Chime and Rasmol ? My PC is a pentium 233 MMX. Is Window 98 compatible with Chime 2.0 Beta3 ? I have begun a work with Rasmol and as I am a beginner, I do not want to be stopped after because of Windows 98. Thanks to all. Annie I' am working on a mushroom toxin for a french thésis in Lille. Annie Van de Wiele, Pharmacie de la Lys 12 Rue Leon Six, Bousbecque 59166 France tel 0320235267 fax from abroad(00 33)320236234 E.mail :avandewiele@nordnet.fr X-Confirm-reading-to: pacsch@ritvax.isc.rit.edu X-PMrqc: 1 ++++------+------+------+------+------+------+------+------+------+------+ From: "Paul A. Craig" Subject: Re: are Chime and Rasmol usable with Windows 98 ? Date: Wed, 27 Jan 1999 09:34:31 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Annie: I just switched to WIndows 98 on a Digital computer with a Pentium 233 MMX and have not had any trouble so far. I am running Chime 2.0 full release version. I am using Internet Explorer 4.0 40-bit encryption and Netscape Communicator 4.5 128-bit encryption. Good luck. Paul Craig Date sent: Wed, 27 Jan 1999 12:48:10 +0100 Send reply to: rasmol@lists.umass.edu From: Van de Wiele Annie Subject: are Chime and Rasmol usable with Windows 98 ? To: rasmol lists > Dear Rasmol Users, > > Before taking Windows 98, I prefer to know if there is not too much > problems with Chime and Rasmol ? My PC is a pentium 233 MMX. > Is Window 98 compatible with Chime 2.0 Beta3 ? > I have begun a work with Rasmol and as I am a beginner, I do not want to be > stopped after because of Windows 98. > Thanks to all. > > Annie > > I' am working on a mushroom toxin for a french thésis in Lille. > Annie Van de Wiele, Pharmacie de la Lys > 12 Rue Leon Six, Bousbecque 59166 France > tel 0320235267 fax from abroad(00 33)320236234 > E.mail :avandewiele@nordnet.fr > > Paul A. Craig Phone: 716-475-6145 Rochester Institute of Technology FAX: 716-475-5766 Dept. of Chemistry Lab: 716-475-2495 1 Lomb Memorial Dr. e-mail: pacsch@rit.edu Rochester, NY 14623 WWW: http://www.rit.edu/~pac8612 ++++------+------+------+------+------+------+------+------+------+------+ From: James Leong Mook seng Subject: Rasmol bonds Date: Wed, 27 Jan 1999 08:35:37 -0800 (PST) To: Rasmol Help Hello, How can I display double bonds and triple bonds using rasmolv2.5. Thanks a lot in advance for your help. Bye, James == James Leong Mook seng Clairfonds No 2, Vacoas Mauritius. _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Protein Explorer JavaScript error Date: Wed, 27 Jan 1999 12:32:54 -0500 To: breauw@elms.edu, rasmol@dhcp-srv2.oit.umass.edu Thanks for reporting this bug, Walter. I have fixed it and when version 0.96 goes on the website the fix will be in it (sometime in the next couple of weeks I hope ...) The bug is harmless, however. If you upgrade to Netscape 4.5, you won't even notice it, because this version doesn't pop javascript errors up in your face like 4.04 and require acknowledgement. I'm not sure that I like this new feature of Netscape 4.5-- its the reason I overlooked the bug! At 1/26/99, you wrote: >Hello, > >I have been trying to get Protein Explorer to work on my system (Pentium >II, 266Mhz, Win95 using Netscape 4.04). I have tried the explorer on >Eric's web site and as a download on my harddrive. When I click on the >"Load molecule" button I always get the message: > >JavaScript Error: file///Raswin/Chime2/shared/cookie.js. line 77: >test for equality (==) mistype as assignment (=)? Assuming equality >test. > > while (s1 = raw.indexOf ( " ; " , s0) ) >.............................................................^ > >Any suggestions to fix the problem would be appreciated > >Walter Breau >Department of Biology >Elms College >Chicopee, MA USA 01013 >breauw@elms.edu > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: <199901262344.PAA20672@socrates.cgl.ucsf.EDU> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: "Jeffrey J. Ayres" Subject: Re: setting a scale Date: Wed, 27 Jan 1999 14:04:21 -0700 To: rasmol@dhcp-srv2.oit.umass.edu Aenoch, Good question. I have noticed if you edit a molecule into several segments, save each of the segments as a .pdb file, then open the save file the scaling changes. If you receive responses please post them. Thanks, Jeff Ayres References: <19990127163537.10061.rocketmail@send102.yahoomail.com> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: "Jeffrey J. Ayres" Subject: Re: Rasmol bonds Date: Wed, 27 Jan 1999 14:07:48 -0700 To: rasmol@dhcp-srv2.oit.umass.edu James, A letter was posted several days ago briefly describing the process necessary to display double bonds in rasmol. First you probably need rasmol 2.6, 2.5 does not show double bonds. Second, if you have a large file it could take awhile since you must manually enter an extra "conect" line for each double bond. The method I am using is convert the pdb file to a MDLmol file, before adding hydrogens. Then checking the structure to verify the double bonds are in the correct place. Sometimes in the conversion the double bonds are not correctly placed, this too is a time consuming process. Then add the hydrogens. Rasmol will show MDLmol files as well as PDB. If I can assist you further send an email. Jeff Ayres James Leong Mook seng wrote: > Hello, > How can I display double bonds and triple bonds using rasmolv2.5. > Thanks a lot in advance for your help. > > Bye, > James > > == > > James Leong Mook seng > Clairfonds No 2, Vacoas > Mauritius. > > _________________________________________________________ > DO YOU YAHOO!? > Get your free @yahoo.com address at http://mail.yahoo.com X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: "Brian White" Subject: I get text instead of chime.... Date: Thu, 28 Jan 1999 14:41:17 -0500 To: rasmol Hi - I've modified some of Eric Martz's pages for my course & I have the following problem. Some pages, when they are loaded into "fresh" netscape (netscape that hasn't seen chime since it was launched) show text instead of the chime frame or the javascript frame. If you go back and forward with netscape's buttons, the problem is fixed & all other loads work fine - until netscape is re-launched. Although it is easily fixed, it scares my computer-phobic students.... This does not happen on all computers - just my all-in-one G3s with netscape 4.5 & chime 2. Does anyone know what's up? How can I fix this? site with this problem: http://intro.bio.umb.edu/111-112/OLLM/111F98/RasPract/RasPract.html thanks! Brian -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://omega.cc.umb.edu/~bwhite/ Eric Martz References: <36B0BD5D.4B8DD123@umb.edu> x-mac-creator="4D4F5353" ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: I get text instead of chime.... Date: Thu, 28 Jan 1999 15:01:59 +0000 To: brian.white@umb.edu, Rasmol List , Brian White wrote: > Hi - > I've modified some of Eric Martz's pages for my course & I have the > following problem. Some pages, when they are loaded into "fresh" > netscape (netscape that hasn't seen chime since it was launched) show > text instead of the chime frame or the javascript frame. If you go back > and forward with netscape's buttons, the problem is fixed & all other > loads work fine - until netscape is re-launched. Although it is easily > fixed, it scares my computer-phobic students.... > This does not happen on all computers - just my all-in-one G3s with > netscape 4.5 & chime 2. > Does anyone know what's up? How can I fix this? > > site with this problem: > http://intro.bio.umb.edu/111-112/OLLM/111F98/RasPract/RasPract.html > Brian, I just logged onto your site above and was able to view the Chime window fine (I'm on a Mac PowerPC, Chime 2.0a and NS 4.5). However, there were a host of javascript error messages, all reading the same thing: JavaScript Error: http://intro.bio.umb.edu/111-112/OLLM/111F98/RasPract/chim2way.js, line 4: top.control_fr.document.c2w_form has no properties. My guess is that you broke a JS link when you made the modifications, although Eric of course would know better which one. The reason that you see text instead of the Chime window at first may be a result of your NS version: NS 4.5 seems to handle JS errors more subtly than earlier versions. I'm sending this to Eric, too, in case the error message I saw can help him debug it. Good luck! Tim Driscoll -- ******************** Timothy Driscoll UMass Amherst Molecular and Cellular Biology Chemistry-Biology Interface Program * Department of Chemistry Amherst College Amherst, MA 01002 413 542 2738 * http://merckx.chem.amherst.edu/tdriscoll/ ******************** ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: I get text instead of chime.... Date: Tue, 02 Feb 1999 07:52:14 -0500 To: brian.white@umb.edu, rasmol Cc: tdriscoll@amherst.edu I went to the URL you gave (Netscape 4.5, Windows 95). I got the same JS errors Tim reported. "c2w_form" is Chime-2-Way-Form which is the command line slot and message box. JavaScript Error: http://intro.bio.umb.edu/111-112/OLLM/111F98/RasPract/chim2way.js, line 4: top.control_fr.document.c2w_form has no properties. I suspect the errors are because you have eliminated these from your first window, but not your second. I get the errors before pushing the button, as well as more errors after. However, I get no additional errors when going to part II. I looked in the chim2way.js file I have, and line 4 is a comment, so perhaps you (or we?) modified your copy of this file? -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id IAA05063 ++++------+------+------+------+------+------+------+------+------+------+ From: =?iso-8859-1?Q?=22Dr=2E_Sabine_K=F6pper=22?= Subject: double bonds in xyz files Date: Tue, 2 Feb 1999 14:46:34 +0100 To: "'rasmol@dhcp-srv2.oit.umass.edu'" Hi you all, is it possible to display double or triple bonds in .xyz and multiple .xyz files? The CONECT statement does not work in .xyz, is that correct? Thanks in advance Sabine Köpper ********************************************************* PD Dr. Sabine Köpper Carl v. Ossietzky Universität Oldenburg FB Chemistry P O Box 2503 D-26111 Oldenburg Phone +49 (0) 441-798-3706 FAX +49 (0)441-798 3329 koepper@chemie.uni-oldenburg.de *******************************!!************************ ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: Re: I get text instead of chime.... Date: Tue, 2 Feb 1999 09:53:38 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu Has anyone else on this list had netscape 4.06 or later spontaneously lose it's preferences dll's? (you get an error message to reinstall netscape when you try to access your preferences settings). I'm trying to figure out if it's caused by a plugin, and if so, which one. Thank you kindly...... ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Loss of DLL's Date: Wed, 03 Feb 1999 09:39:26 -0500 To: rasmol@dhcp-srv2.oit.umass.edu This happened to me when one of several copies of Netscape (different versions) was "uninstalled" rather than just deleting the files in its specific folder. We simply had to reinstall the current version. At 2/2/99, you wrote: >Has anyone else on this list had netscape 4.06 or later spontaneously lose >it's preferences dll's? (you get an error message to reinstall netscape >when you try to access your preferences settings). I'm trying to figure >out if it's caused by a plugin, and if so, which one. >Thank you kindly...... > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: lynna@cgl.ucsf.EDU Subject: sprouting hydrogens Date: Wed, 3 Feb 1999 18:14:52 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu Cc: lynna@cgl.ucsf.EDU Hello. I am trying to find a program that will be able to place hydrogens onto any molecular structure (in pdb format). The program must run on a linux box (I need the source code) and be able to place hydrogens for not only proteins and nucleic acids, but for other small molecules as well. I ran across references to BABEL, but there were also reports that it did not place hydrogens for modified RNA bases correctly. I also couldn't connect to the URL that I found for BABEL's web site. What do people do to add hydrogens to, say, crystalized structures? What would people suggest? Pointers to web sites or other lists would also be welcome. -Aenoch ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Re: sprouting hydrogens Date: Wed, 3 Feb 1999 22:35:35 -0500 To: rasmol@dhcp-srv2.oit.umass.edu SwissPdbViewer (version 3.1) sprouts hydrogens. Use Add Hydrogens on the Build menu. SPV is available for Macs and PC's, with SGI version on the way. I have never had any trouble reading SPV's PDB files on other platforms. To get the program, go to http://www.pdb.bnl.gov/expasy/spdbv/mainpage.html Cheers! ***************************** Gale Rhodes mailto:rhodes@usm.maine.edu http://macweb.acs.usm.maine.edu/chemistry/GR/GRHomePage.html Professor of Chemistry Chemistry Department University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 Phone: (207)780-4734 Fax: (207)780-5607 References: <199902040214.SAA23127@socrates.cgl.ucsf.EDU> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: sprouting hydrogens Date: Thu, 04 Feb 1999 14:32:44 +0000 To: rasmol@dhcp-srv2.oit.umass.edu lynna@cgl.ucsf.EDU wrote: > > Hello. > > I am trying to find a program that will be able to place hydrogens > onto any molecular structure (in pdb format). The program must > run on a linux box (I need the source code) and be able to place > hydrogens for not only proteins and nucleic acids, but for other > small molecules as well. I ran across references to BABEL, but > there were also reports that it did not place hydrogens for > modified RNA bases correctly. I also couldn't connect to the URL > that I found for BABEL's web site. > > What do people do to add hydrogens to, say, crystalized structures? > What would people suggest? Pointers to web sites or other lists > would also be welcome. > > -Aenoch Hi, try MolMol at http://www.mol.biol.ethz.ch/wuthrich/software/molmol/ it can add hydrogens to protein structures (I'm not sure about other molecules then proteins). good luck, Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)171 2693405 | Fax : +44-(0)171 269 3258 email : a.mueller@icrf.icnet.uk | http://www.icnet.uk/bmm/ pdb-l@pdb.pdb.bnl.gov ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer now has Preferences, Aliases, Projects Date: Thu, 04 Feb 1999 09:54:01 -0500 To: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu, Version 0.96 of my Protein Explorer is now available at http://www.umass.edu/microbio/chime/explorer The Protein Explorer is a RasMol-like interface implemented in Chime. However, the Protein Explorer can offer much greater assistance and automation than is available in RasMol, and Chime version 2's built-in Select Menu is not available in RasMol. The goal of the Protein Explorer is to make visual exploration of protein structure much more accessible to novices, occasional users, or nonspecialists, as well as making it much more convenient than with RasMol, EVEN FOR EXPERTS. Those wishing to explore NMR structures will find the Explorer's model-selection panel especially useful. An alternative form of the Explorer is provided called the Protein Comparator, which allows two molecules to be loaded side by side and manipulated independently, with or without "follow-me" synchronization for mouse-directed movements and zooms. Version 0.96 adds nonvolatile preference settings (such as whether molecules should be spinning immediately after loading), alias expansion with a user-configurable alias list (for example "s l" expands to "select ligand"), and the ability to specify a project folder on your disk for development of command script files. Instructions are provided for how to shorten scripts saved from Chime which, like those saved from RasMol, are usually unnecessarily long and slow to execute. Version 0.96 has not been linked to the UMass Chime Resources site pending provision of a tutorial for those who have no experience with RasMol. For those who have used RasMol, version 0.96 will be straightforward. Its unique features are extensively documented. The Protein Explorer is freely downloadable for local use with or without an Internet connection. Long range plans for the Protein Explorer include building an automated Guide for novices, and integrating it into the Protein Data Bank interface. As usual, I will be especially interested to know if problems occur on Macintoshes, since I have tested this version only on Windows. (On Macintosh Navigator 4.5, the message list keeps focus at the bottom, unlike all other platforms/versions. A preference setting has been provided to add messages to the bottom of the list, rather than the top, so the newest messages will remain in view.) [Further information not repeated here was detailed in the announcement of version 0.95 on January 10, 1999 to this list, viewable at ftp://marlin.bio.umass.edu/pub/shareware/rasmol/email-history ] -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu UMass Chime Site - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: <199902040214.SAA23127@socrates.cgl.ucsf.EDU> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: "Jeffrey J. Ayres" Subject: Re: sprouting hydrogens Date: Thu, 04 Feb 1999 08:04:35 -0700 To: rasmol@dhcp-srv2.oit.umass.edu Lynn, Many versions of the BABEL program are located at http://ccl.osc.edu/ccl/software.html I was able to download the program several months ago. I am not sure if there is a Linux version. It does sprout hydrogens, however the placement of hydrogens is sometimes incorrect. The errors are hydrogens used in hydrogen bonding between base pairs, and occasionally aromatic hydrogens located on the bases. If you have a large molecule it could require a lot of extra work. Jeff Ayres lynna@cgl.ucsf.EDU wrote: > Hello. > > I am trying to find a program that will be able to place hydrogens > onto any molecular structure (in pdb format). The program must > run on a linux box (I need the source code) and be able to place > hydrogens for not only proteins and nucleic acids, but for other > small molecules as well. I ran across references to BABEL, but > there were also reports that it did not place hydrogens for > modified RNA bases correctly. I also couldn't connect to the URL > that I found for BABEL's web site. > > What do people do to add hydrogens to, say, crystalized structures? > What would people suggest? Pointers to web sites or other lists > would also be welcome. > > -Aenoch ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Re: Protein Explorer now has Preferences, Aliases, Projects Date: Thu, 4 Feb 1999 10:05:46 -0500 To: rasmol@dhcp-srv2.oit.umass.edu >Version 0.96 has not been linked to the UMass Chime Resources site pending >provision of a tutorial for those who have no experience with RasMol. For >those who have used RasMol, version 0.96 will be straightforward. Its >unique features are extensively documented. In the meantime, my RasMol Tutorial might be useful to beginnners who want to use Protein Explorer. See http://macweb.acs.usm.maine.edu/chemistry/GR/GraphicsGallery/RasTut.html I am hoping to find time to adapt this tutorial for Protein Explorer, once I see from "customer" response that the whole package is reliable on Macs. Maybe by summer. Cheers! ***************************** Gale Rhodes mailto:rhodes@usm.maine.edu http://macweb.acs.usm.maine.edu/chemistry/GR/GRHomePage.html Professor of Chemistry Chemistry Department University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 Phone: (207)780-4734 Fax: (207)780-5607 References: <199902040214.SAA23127@socrates.cgl.ucsf.EDU> <36B9B703.1D0D6B01@ycpo.yavapai.cc.az.us> x-mac-creator="4D4F5353" ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: sprouting hydrogens Date: Thu, 04 Feb 1999 10:37:02 +0000 To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu "Jeffrey J. Ayres" wrote: > Lynn, > Many versions of the BABEL program are located at > http://ccl.osc.edu/ccl/software.html > I was able to download the program several months ago. I am not sure if > there is a Linux version. It does sprout hydrogens, however the > placement of hydrogens is sometimes incorrect. The errors are hydrogens > used in hydrogen bonding between base pairs, and occasionally aromatic > hydrogens located on the bases. If you have a large molecule it could > require a lot of extra work. > > Jeff Ayres Unfortunately, this link is not functional at the moment (I just tried it and found a message in the README that says it's "under development"). Any other suggestions where to check out BABEL? Tim Driscoll ******************** Timothy Driscoll UMass Amherst Molecular and Cellular Biology Chemistry-Biology Interface Program * Department of Chemistry Amherst College Amherst, MA 01002 413 542 2738 * http://merckx.chem.amherst.edu/tdriscoll/ ******************** ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: sprouting hydrogens Date: Thu, 04 Feb 1999 11:05:10 -0500 To: rasmol@dhcp-srv2.oit.umass.edu

Date: Thu, 4 Feb 1999 10:39:31 +0200 (IST)

MOLMOL, this program runs on a linux, PC, UNIX workstation,
but complicated enough.
http://www.mol.biol.ethz.ch/wuthrich/software/molmol/

Elena.

From: sinvae@mail.biu.ac.il
References: <199902040214.SAA23127@socrates.cgl.ucsf.EDU> ++++------+------+------+------+------+------+------+------+------+------+ From: James Milner-White Subject: Chime on iMacs Date: Thu, 4 Feb 1999 16:59:24 +0000 To: rasmol@dhcp-srv2.oit.umass.edu Has anyone experience of using Chime2.0a on iMacs? We had lots of problems on older Macs but maybe iMacs are better? James Milner-White Dr E. James Milner-White Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, G128QQ, UK. E-mail: E.J.Milner-White@bio.gla.ac.uk FAX: +44(0)141-330-4620 Tel.: +44(0)141-330-5283 Research Interests: http://www.enzyme.gla.ac.uk/Biostructures/discoveries.html http://www.biochem.gla.ac.uk/BMB/Res/BSA/EJM.html Teaching Interests: http://www.enzyme.gla.ac.uk/Biostructures/teaching.html ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: Big scripts crash RasMac Date: Thu, 04 Feb 1999 19:08:34 +0200 To: RasMol list , info@rcsb.org A simple search interface has been released by the new PDB (www.rcsb.org). For each structure there is a 'Geometry' check, from which a "Fold Deviation Score' can be seen graphically with RasMol. This is a very easy way to see which parts of a structure deviate in bond lengths and angles from standard. I've tested RasMol on UNIX, Windows and Macintosh, and all are fine for small structures (less that 100 residues), but for large structure these scripts crash the Mac (even if you assign it a large amount of memory) - tested on Mac powerbook G3/OS 8.1/Netscape 4.5 Do other people suffer the same problem? Can anyone think of another way around this? Kurt -- --------------------------------------------------------------- Dr. Kurt Giles kurt@inn-prot.weizmann.ac.il Israeli National Node Biological Computing Unit Tel: +-972-8-9342614 Weizmann Institute of Science Fax: +-972-8-9466269 Rehovot 76100, Israel http://inn-prot.weizmann.ac.il/ --------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: jayres@ycpo.yavapai.cc.az.us Subject: Re: sprouting hydrogens Date: Thu, 4 Feb 1999 10:26:09 PDT To: tdriscoll@amherst.edu Cc: rasmol@dhcp-srv2.oit.umass.edu Hello again, An alternative address for the Babelwin program is from Dr. Jeffrey Gosper's Home Page at Brunel University. http://www.brunel.ac.uk/depts/chem/ch241s/re_view/tagon.htm It is an active link. Jeff Ayres ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Big scripts crash RasMac Date: Thu, 04 Feb 1999 19:25:25 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Redirected for Helge Weissig to circumvent technical difficulties: >Date: Thu, 4 Feb 1999 10:57:27 -0800 >From: Helge Weissig >To: Kurt Giles >cc: RasMol list , info@rcsb.org >Subject: Re: Big scripts crash RasMac > >Dear Kurt, > > I am a Mac person myself and I, unfortunately, can only report the >same problems. In fact, I have never been able to make any Mac run RasMac >with a script, not even small ones. > >We decided to release the Structure Explorer pages including the script >producing features nevertheless because a majority of users connects from >different platforms. I am very open to any suggestions as to how we can >warn Macintosh people *subtely* about the restrictions. > >Chime as an alternative would actually be most desireable! Unfortunately, >vs. 2.0 of the plugin does not fare well (at least in our hands) on the >Macs either. > >best, >h. > >+--------------------------------------------+ >| Helge Weissig | >| Project Manager, Structural Bioinformatics | >| San Diego Supercomputer Center +-----------------------------------+ >| voice: +1 619 534 8399 | mail: PO Box 85608 | >| fax: +1 619 822 0873 | San Diego, CA 92186-5608 | >+---------------------------------| direct: 10100 John J. Hopkins Dr. | > | La Jolla, CA 92093-0537 | > +-----------------------------------+ > > > > >On Thu, 4 Feb 1999, Kurt Giles wrote: > >> A simple search interface has been released by the new PDB (www.rcsb.org). >> >> For each structure there is a 'Geometry' check, from which a "Fold Deviation >> Score' can be seen graphically with RasMol. >> This is a very easy way to see which parts of a structure deviate in bond >> lengths and angles from standard. >> I've tested RasMol on UNIX, Windows and Macintosh, and all are fine for >> small structures (less that 100 residues), but for large structure these >> scripts crash the Mac (even if you assign it a large amount of memory) - >> tested on Mac powerbook G3/OS 8.1/Netscape 4.5 >> Do other people suffer the same problem? Can anyone think of another way >> around this? >> >> Kurt >> >> -- >> --------------------------------------------------------------- >> Dr. Kurt Giles kurt@inn-prot.weizmann.ac.il >> Israeli National Node >> Biological Computing Unit Tel: +-972-8-9342614 >> Weizmann Institute of Science Fax: +-972-8-9466269 >> Rehovot 76100, Israel http://inn-prot.weizmann.ac.il/ >> --------------------------------------------------------------- >> > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Steven Verhey Subject: Re: Big scripts crash RasMac Date: Thu, 4 Feb 1999 17:23:39 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu I'm a little confused by all these mac problems. I've used scripts extensively both with my PPC6500 (Netscape 4.5, Chime 2.0, Rasmol 2.6) and with various Powerbooks. At home, I have an iMac that runs Chime just fine (I haven't tried scripts there). And when I go to www.rcsb.org, get 2hhb, and choose geometry/fold deviation score I get something that I don't understand, but that doesn't crash my computer. Steve Verhey The Evergreen State College On Thu, 4 Feb 1999, Eric Martz wrote: > Redirected for Helge Weissig to circumvent technical difficulties: > > >Date: Thu, 4 Feb 1999 10:57:27 -0800 > >From: Helge Weissig > >To: Kurt Giles > >cc: RasMol list , info@rcsb.org > >Subject: Re: Big scripts crash RasMac > > > >Dear Kurt, > > > > I am a Mac person myself and I, unfortunately, can only report the > >same problems. In fact, I have never been able to make any Mac run RasMac > >with a script, not even small ones. > > > >We decided to release the Structure Explorer pages including the script > >producing features nevertheless because a majority of users connects from > >different platforms. I am very open to any suggestions as to how we can > >warn Macintosh people *subtely* about the restrictions. > > > >Chime as an alternative would actually be most desireable! Unfortunately, > >vs. 2.0 of the plugin does not fare well (at least in our hands) on the > >Macs either. > > > >best, > >h. > > > >+--------------------------------------------+ > >| Helge Weissig | > >| Project Manager, Structural Bioinformatics | > >| San Diego Supercomputer Center +-----------------------------------+ > >| voice: +1 619 534 8399 | mail: PO Box 85608 | > >| fax: +1 619 822 0873 | San Diego, CA 92186-5608 | > >+---------------------------------| direct: 10100 John J. Hopkins Dr. | > > | La Jolla, CA 92093-0537 | > > +-----------------------------------+ > > > > > > > > > >On Thu, 4 Feb 1999, Kurt Giles wrote: > > > >> A simple search interface has been released by the new PDB (www.rcsb.org). > > >> > >> For each structure there is a 'Geometry' check, from which a "Fold > Deviation > >> Score' can be seen graphically with RasMol. > >> This is a very easy way to see which parts of a structure deviate in bond > >> lengths and angles from standard. > >> I've tested RasMol on UNIX, Windows and Macintosh, and all are fine for > >> small structures (less that 100 residues), but for large structure these > >> scripts crash the Mac (even if you assign it a large amount of memory) - > >> tested on Mac powerbook G3/OS 8.1/Netscape 4.5 > >> Do other people suffer the same problem? Can anyone think of another way > >> around this? > >> > >> Kurt > >> > >> -- > >> --------------------------------------------------------------- > >> Dr. Kurt Giles kurt@inn-prot.weizmann.ac.il > >> Israeli National Node > >> Biological Computing Unit Tel: +-972-8-9342614 > >> Weizmann Institute of Science Fax: +-972-8-9466269 > >> Rehovot 76100, Israel http://inn-prot.weizmann.ac.il/ > >> --------------------------------------------------------------- > >> > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Eric Martz, Professor (Immunology), Dept Microbiology > Morrill IVN 203, U Mass, Amherst MA US 01003-5720 > 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu > > Molecular visualization in bioscience education at the > RasMol Home Page > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > RasMol list References: ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: Running scripts on RasMac Date: Fri, 05 Feb 1999 13:24:10 +0200 To: Helge Weissig , Cc: info@rcsb.org > I am a Mac person myself and I, unfortunately, can only report the > same problems. In fact, I have never been able to make any Mac run RasMac > with a script, not even small ones. > > We decided to release the Structure Explorer pages including the script > producing features nevertheless because a majority of users connects from > different platforms. I am very open to any suggestions as to how we can > warn Macintosh people *subtely* about the restrictions. The trick to running scripts on RasMac is to edit the MIME type so that the File Type is RSML and not TEXT. See http://www.pdb.bnl.gov/pdb-docs/Mac_conf.html (or the equivalent page from your local PDB mirror) Kurt -- --------------------------------------------------------------- Dr. Kurt Giles kurt@inn-prot.weizmann.ac.il Israeli National Node Biological Computing Unit Tel: +-972-8-9342614 Weizmann Institute of Science Fax: +-972-8-9466269 Rehovot 76100, Israel http://inn-prot.weizmann.ac.il/ --------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: Subject: Re: Running scripts on RasMac Date: Fri, 5 Feb 1999 11:38:35 +0000 (GMT) To: rasmol@dhcp-srv2.oit.umass.edu Kurt, > The trick to running scripts on RasMac is to edit the MIME type so that the > File Type is RSML and not TEXT. > > See http://www.pdb.bnl.gov/pdb-docs/Mac_conf.html > (or the equivalent page from your local PDB mirror) I too have problems running RasMol scripts from a web-page on my Mac. This is definitely the way to get RasMac to recognize the file as a script, but it also causes my Mac to crash. Any more ideas anyone? (PowerBook 5300cs, 7.5.3, NS3.04, RasMac 2.6) Andrew -- Dr. Andrew Raine, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom. Tel: +44 1223 333744, FAX: +44 1223 766002, email: A.R.C.Raine@bioc.cam.ac.uk WWW:http://www-ccmr-nmr.bioc.cam.ac.uk/~arcr1/ References: ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: Re: Big scripts crash RasMac Date: Fri, 05 Feb 1999 14:28:13 +0200 To: Steven Verhey Cc: rasmol@dhcp-srv2.oit.umass.edu Steven Verhey wrote: > > I'm a little confused by all these mac problems. I've used scripts > extensively both with my PPC6500 (Netscape 4.5, Chime 2.0, Rasmol 2.6) > and with various Powerbooks. At home, I have an iMac that runs Chime > just fine (I haven't tried scripts there). And when I go to > www.rcsb.org, get 2hhb, and choose geometry/fold deviation score I get > something that I don't understand, but that doesn't crash my computer. The 'Fold Deviation Score' link for 2hhb crashes my machine (Powerbook G3/OS 8.1/Netscape 4.5) as soon as it starts up RasMac. I tried reinstalling RasMac, first from the PDB, then from Eric Martz's site, and the same happened both times (at University of Edinburgh, I couldn't get into v2.6beta folder for some reason). Can you remember where you downloaded your version from? Is it 2.6b2a you're using (i.e. does stereo work OK)? Smaller files, such as 1HUP are fine on 'Fold Deviation Score' with RasMac - the crashing only occurs with bigger structures. Kurt -- --------------------------------------------------------------- Dr. Kurt Giles kurt@inn-prot.weizmann.ac.il Israeli National Node Biological Computing Unit Tel: +-972-8-9342614 Weizmann Institute of Science Fax: +-972-8-9466269 Rehovot 76100, Israel http://inn-prot.weizmann.ac.il/ --------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: RacMac crashing problem solved (maybe) Date: Fri, 05 Feb 1999 14:44:24 +0200 To: RasMol list I think I understand the RasMac crashing problem - it may be to do with the type of line feed/carriage return used. The fds-cgi file sent from the "Fold Deviation Score" link is a script followed by the (CA only) PDB file. Looking at this file in a text editor (BBEdit Lite), the script is OK, but the PDB file is one long line. For smaller PDB files RasMac can still manage, but for bigger files this line is too long and RasMac crashes (at least for some of us). Kurt -- --------------------------------------------------------------- Dr. Kurt Giles kurt@inn-prot.weizmann.ac.il Israeli National Node Biological Computing Unit Tel: +-972-8-9342614 Weizmann Institute of Science Fax: +-972-8-9466269 Rehovot 76100, Israel http://inn-prot.weizmann.ac.il/ --------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: Steven Verhey Subject: Re: Big scripts crash RasMac Date: Fri, 5 Feb 1999 09:40:59 -0800 (PST) To: Kurt Giles Cc: rasmol@dhcp-srv2.oit.umass.edu I got my Rasmac from Eric Martz's site, and stereo works fine. FDS sends a file called fds.cgi. It's when I open that with Rasmac that I get something I don't understand, but no crash. Reading the script, I don't think I'm seeing what I'm supposed to be seeing. What I see is the four heme groups in wireframe/cpk, and nothing else. There's more to be seen by running the menus, but only the heme groups show on opening. Steve On Fri, 5 Feb 1999, Kurt Giles wrote: > Steven Verhey wrote: > > > > I'm a little confused by all these mac problems. I've used scripts > > extensively both with my PPC6500 (Netscape 4.5, Chime 2.0, Rasmol 2.6) > > and with various Powerbooks. At home, I have an iMac that runs Chime > > just fine (I haven't tried scripts there). And when I go to > > www.rcsb.org, get 2hhb, and choose geometry/fold deviation score I get > > something that I don't understand, but that doesn't crash my computer. > > The 'Fold Deviation Score' link for 2hhb crashes my machine (Powerbook G3/OS > 8.1/Netscape 4.5) as soon as it starts up RasMac. I tried reinstalling > RasMac, first from the PDB, then from Eric Martz's site, and the same > happened both times (at University of Edinburgh, I couldn't get into > v2.6beta folder for some reason). > Can you remember where you downloaded your version from? Is it 2.6b2a you're > using (i.e. does stereo work OK)? > > Smaller files, such as 1HUP are fine on 'Fold Deviation Score' with RasMac - > the crashing only occurs with bigger structures. > > > Kurt > -- > --------------------------------------------------------------- > Dr. Kurt Giles kurt@inn-prot.weizmann.ac.il > Israeli National Node > Biological Computing Unit Tel: +-972-8-9342614 > Weizmann Institute of Science Fax: +-972-8-9466269 > Rehovot 76100, Israel http://inn-prot.weizmann.ac.il/ > --------------------------------------------------------------- > References: ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: Re: Big scripts crash RasMac Date: Fri, 05 Feb 1999 20:03:44 +0200 To: Steven Verhey Cc: rasmol@dhcp-srv2.oit.umass.edu Steven Verhey wrote: > > I got my Rasmac from Eric Martz's site, and stereo works fine. FDS > sends a file called fds.cgi. It's when I open that with Rasmac that I get > something I don't understand, but no crash. Reading the script, I don't > think I'm seeing what I'm supposed to be seeing. What I see is the four > heme groups in wireframe/cpk, and nothing else. There's more to be seen > by running the menus, but only the heme groups show on opening. No, you're not getting what you're supposed to be seeing: you should get a 'backbone' representation of the structure coloured by it's deviation from 'normal' bond lengths and angles (blue is OK, varying up to red which is very unusual lengths/angles). It sounds as if you don't have the 'File Type' on your MIME type set to RSML. Doing this, you will read the scripts properly (but be warned, it will probably crash with large PDB files, try something small first). It appears the problem is with the size of the PDB file and not the script: see my mail "RacMac crashing problem solved (maybe)" from 12.44 GMT. Kurt -- --------------------------------------------------------------- Dr. Kurt Giles kurt@inn-prot.weizmann.ac.il Israeli National Node Biological Computing Unit Tel: +-972-8-9342614 Weizmann Institute of Science Fax: +-972-8-9466269 Rehovot 76100, Israel http://inn-prot.weizmann.ac.il/ --------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: Steven Verhey Subject: Re: Big scripts crash RasMac Date: Fri, 5 Feb 1999 11:19:11 -0800 (PST) To: Kurt Giles Cc: rasmol@dhcp-srv2.oit.umass.edu Cool! I've succeeded in getting my mac to crash! After making the MIME change you suggest, FDS results in a bomb ("Error in 'Finder' of Type 10" or something like that). I haven't tried smaller files, but I accept your diagnosis of the problem. Unfortunately, I seem to have lost your "Rasmac crashing problem solved (maybe)" e-mail. Could you resend it to me offlist? Steve On Fri, 5 Feb 1999, Kurt Giles wrote: > Steven Verhey wrote: > > > > I got my Rasmac from Eric Martz's site, and stereo works fine. FDS > > sends a file called fds.cgi. It's when I open that with Rasmac that I get > > something I don't understand, but no crash. Reading the script, I don't > > think I'm seeing what I'm supposed to be seeing. What I see is the four > > heme groups in wireframe/cpk, and nothing else. There's more to be seen > > by running the menus, but only the heme groups show on opening. > > No, you're not getting what you're supposed to be seeing: you should get a > 'backbone' representation of the structure coloured by it's deviation from > 'normal' bond lengths and angles (blue is OK, varying up to red which is > very unusual lengths/angles). > > It sounds as if you don't have the 'File Type' on your MIME type set to > RSML. Doing this, you will read the scripts properly (but be warned, it will > probably crash with large PDB files, try something small first). > It appears the problem is with the size of the PDB file and not the script: > see my mail "RacMac crashing problem solved (maybe)" from 12.44 GMT. > > > Kurt > > -- > --------------------------------------------------------------- > Dr. Kurt Giles kurt@inn-prot.weizmann.ac.il > Israeli National Node > Biological Computing Unit Tel: +-972-8-9342614 > Weizmann Institute of Science Fax: +-972-8-9466269 > Rehovot 76100, Israel http://inn-prot.weizmann.ac.il/ > --------------------------------------------------------------- > ++++------+------+------+------+------+------+------+------+------+------+ From: James Leong Mook seng Subject: Rasmol Bonds Date: Fri, 5 Feb 1999 13:30:14 -0800 (PST) To: Rasmol Help Hello, Could anyone please tell me how to represent double and triple bonds using rasmolv2.5.thank you very much in advance. I have try the CONECT but it does not work. May be i had not used it correctly,could anyone help.& == James Leong Mook seng Clairfonds No 2, Vacoas Mauritius. _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: RasMac crashing problem/RasMac 2.6.4 Date: Mon, 08 Feb 1999 11:58:23 +0200 To: RasMol list The RasMac crashing problem (it indeed turned out to be a script size problem and not a line feed/carriage return problem), as dicussed over the last week, is a bug in version 2.6b2. This is the version available at Eric Martz's site and through the (Brookhaven) PDB mirror sites. Version 2.6.4 of RasMac (containing minor bug fixes, and overcoming the crashing problem), is available at ftp://ftp.dcs.ed.ac.uk/pub/rasmol/rasmac.sit.hqx or http://inn-prot.weizmann.ac.il/download/rasmac.sit.hqx Kurt -- --------------------------------------------------------------- Dr. Kurt Giles kurt@inn-prot.weizmann.ac.il Israeli National Node Biological Computing Unit Tel: +-972-8-9342614 Weizmann Institute of Science Fax: +-972-8-9466269 Rehovot 76100, Israel http://inn-prot.weizmann.ac.il/ --------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: Don't download RasMac 2.6.4 (yet) Date: Mon, 08 Feb 1999 13:39:30 +0200 To: RasMol list Although 2.6.4 lets you look at the very nice 'Fold Deviation Score' from the new PDB, it has a more serious problem of not letting you look at the standard structures from the new PDB, old PDB, SCOP etc. Kurt -- --------------------------------------------------------------- Dr. Kurt Giles kurt@inn-prot.weizmann.ac.il Israeli National Node Biological Computing Unit Tel: +-972-8-9342614 Weizmann Institute of Science Fax: +-972-8-9466269 Rehovot 76100, Israel http://inn-prot.weizmann.ac.il/ --------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: Subject: Re: RasMac crashing problem/RasMac 2.6.4 Date: Mon, 8 Feb 1999 11:46:59 +0000 (GMT) To: rasmol@dhcp-srv2.oit.umass.edu Dear List, Kurt Giles wrote: > > The RasMac crashing problem (it indeed turned out to be a script size > problem and not a line feed/carriage return problem), as dicussed over the > last week, is a bug in version 2.6b2. This is the version available at Eric > Martz's site and through the (Brookhaven) PDB mirror sites. > > Version 2.6.4 of RasMac (containing minor bug fixes, and overcoming the > crashing problem), is available at > > ftp://ftp.dcs.ed.ac.uk/pub/rasmol/rasmac.sit.hqx > > or > > http://inn-prot.weizmann.ac.il/download/rasmac.sit.hqx and indeed my Mac now doesn't crash when I attempt to run a script. However, when I use RasMac as a helper to Netscape, I now get (from RasMac) the error message: "", line 1: Script command line too long! Which looks as if it *could* be a CR/LF translation problem. The web-server I am trying to download from (which is also mine, and uses httpd) is a UNIX machine, and UNIX uses just LFs to mark end-of-line. Can anyone tell me: (a) What the Mac uses for EOL? (is it just CR?) (b) How to tell either Netscape on the Mac, or httpd on the server to do the appropriate translation? Andrew -- Dr. Andrew Raine, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom. Tel: +44 1223 333744, FAX: +44 1223 766002, email: A.R.C.Raine@bioc.cam.ac.uk WWW:http://www-ccmr-nmr.bioc.cam.ac.uk/~arcr1/ References: ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: Re: RasMac crashing problem/RasMac 2.6.4 Date: Mon, 08 Feb 1999 15:15:28 +0200 To: RasMol list > > and indeed my Mac now doesn't crash when I attempt to run a script. However, > when I use RasMac as a helper to Netscape, I now get (from RasMac) the error > message: > > "", line 1: Script command line too long! > > Which looks as if it *could* be a CR/LF translation problem. The > web-server I am trying to download from (which is also mine, and uses > httpd) is a UNIX machine, and UNIX uses just LFs to mark end-of-line. > Yes, I discovered the same problem (hence the later warning not to get 2.6.4), but I don't think this is a CR/LF problem, and so can't be solved with a simple translation. As far as I can work out, the difference between the following scripts: http://www.rcsb.org/pdb/cgi/render.cgi/1IGD.pdb?pdbId=1IGD&format=rasmol_default http://www.rcsb.org/pdb/cgi/fds.cgi?id=1IGD is that the first starts: load pdb inline exit whereas the second, starts with the same line, but has a number of commands before the exit. The first one cause the problem you describe, but the second work OK. Kurt boundary="----_=_NextPart_001_01BE537C.B8E88990" ++++------+------+------+------+------+------+------+------+------+------+ From: Morgan Ryan Subject: Rasmac 24 bit--anyone got one? Date: Mon, 8 Feb 1999 11:11:44 -0500 To: "'rasmol@lists.umass.edu'" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01BE537C.B8E88990 Does anyone has a Rasmac 2.6 complied for 24-bit version that they could email me? I had one long ago but it has disappeared. And I have no access to a compiler, and I'm too simple to figure out how to do the compile myself using the freeware compiler from Apple. A url or an email would be greatly appreciated. Morgan Ryan mryan@worthpub.com ------_=_NextPart_001_01BE537C.B8E88990 Rasmac 24 bit--anyone got one?

Does anyone has a Rasmac 2.6 = complied for 24-bit version that they could email me? I had one long = ago but it has disappeared. And I have no access to a compiler, and I'm = too simple to figure out how to do the compile myself using the = freeware compiler from Apple. A url or an email would be greatly = appreciated.

Morgan Ryan = mryan@worthpub.com

------_=_NextPart_001_01BE537C.B8E88990-- ++++------+------+------+------+------+------+------+------+------+------+ From: Subject: Re: RasMac crashing problem/RasMac 2.6.4 Date: Mon, 8 Feb 1999 17:12:45 +0000 (GMT) To: rasmol@dhcp-srv2.oit.umass.edu Kurt Giles wrote: > As far as I can work out, the difference between the following scripts: > > http://www.rcsb.org/pdb/cgi/render.cgi/1IGD.pdb?pdbId=1IGD&format=rasmol_default > > http://www.rcsb.org/pdb/cgi/fds.cgi?id=1IGD > > is that the first starts: > > load pdb inline > exit > > whereas the second, starts with the same line, but has a number of commands > before the exit. > The first one cause the problem you describe, but the second work OK. I have just used Netscape to download those files to my UNIX machine (i.e. not passing them to rasmol for interpretation) and looked at them with od. The big difference, other than the one you point out, is that ends of lines in http://www.rcsb.org/pdb/cgi/fds.cgi?id=1IGD are marked by just a newline (octal 012) character (which is the UNIX-style), but http://www.rcsb.org/pdb/cgi/render.cgi/1IGD.pdb?pdbId=1IGD&format=rasmol_default uses a carriage-return;newline (carriage-return is octal 015) pair (which is the DOS-style). >From the behaviour, this is the opposite to what I'd expect if the problem was indeed end-of-line translations, so I'm not sure where this all gets us! Andrew -- Dr. Andrew Raine, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom. Tel: +44 1223 333744, FAX: +44 1223 766002, email: A.R.C.Raine@bioc.cam.ac.uk WWW:http://www-ccmr-nmr.bioc.cam.ac.uk/~arcr1/ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: gzipping on a Mac? Date: Tue, 09 Feb 1999 13:39:16 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Does anyone know how to gzip a PDB file on a Macintosh so Chime can read it? (For those who don't have access to a Windows machine) -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: <199902091836.NAA07720@marlin.bio.umass.edu> x-mac-creator="4D4F5353" ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: gzipping on a Mac? Date: Tue, 09 Feb 1999 14:20:57 +0000 To: rasmol@dhcp-srv2.oit.umass.edu Eric Martz wrote: > Does anyone know how to gzip a PDB file on a Macintosh so Chime can read > it? (For those who don't have access to a Windows machine) > > -Eric > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Eric Martz, Professor (Immunology), Dept Microbiology > Morrill IVN 203, U Mass, Amherst MA US 01003-5720 > 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu > > Molecular visualization in bioscience education at the > RasMol Home Page > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ I have a straightforward program called ZipIt (shareware; $15) which seems to work great: I can zip and unzip files with no problem. But is there a secret to viewing zipped files with Chime? A zipped pdb appears to load into the Protein Explorer just fine, for example, but no structure shows up, and neither the Chime menu nor the command line interface have any effect. The unzipped format of the same pdb file works fine, though. Any suggestions? (BTW, ZipIt can be found at http://www.awa.com/softlock/zipit/zipit.html) Tim ******************** Timothy Driscoll UMass Amherst Molecular and Cellular Biology Chemistry-Biology Interface Program * Department of Chemistry Amherst College Amherst, MA 01002 413 542 2738 * http://merckx.chem.amherst.edu/tdriscoll/ ******************** ++++------+------+------+------+------+------+------+------+------+------+ From: Steven Vik Subject: Re: gzipping on a Mac? Date: Tue, 9 Feb 1999 13:31:57 -0600 To: rasmol@dhcp-srv2.oit.umass.edu >Does anyone know how to gzip a PDB file on a Macintosh so Chime can read >it? (For those who don't have access to a Windows machine) > The MacGzip homepage is at: http://persephone.cps.unizar.es/general/gente/spd/gzip/gzip.html -Steve Vik ***************************************************************** Steven B. Vik Department of Biological Sciences Southern Methodist University Dallas, TX 75275-0376 Phone (214) 768-4228 Fax (214) 768-3955 E-mail svik@mail.smu.edu WWW www.smu.edu/~svik ++++------+------+------+------+------+------+------+------+------+------+ From: Subject: Re: RasMac crashing problem/RasMac 2.6.4 Date: Wed, 10 Feb 1999 12:31:14 +0000 (GMT) To: rasmol@dhcp-srv2.oit.umass.edu Dear All, Kurt wrote: > Yes, I discovered the same problem (hence the later warning not to get > 2.6.4), but I don't think this is a CR/LF problem, and so can't be solved > with a simple translation. I have had a look through the RasMol (& therefore RasMac) source, and I have found some lines which (I think) explain the problem. In command.c: line 704 is: while( (ch!='\n') && (ch!=EOF) ) should be: (?) while( (ch!='\n') && (ch!='\r') && (ch!=EOF) ) line 2300 is: while( (ch!='\n') && (ch!=EOF) ) should be: (?) while( (ch!='\n') && (ch!='\r') && (ch!=EOF) ) Whereas, in infile.c, line 147 we find: } while( (ch!='\n') && (ch!='\r') && (ch!=EOF) ); which looks as if it deals with all CR/LF possibilities correctly. I'd love to recompile RasMac to try this out, but I don't have a compiler for the Mac. Is anyone out there prepared to have a go for me? Andrew -- Dr. Andrew Raine, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom. Tel: +44 1223 333744, FAX: +44 1223 766002, email: A.R.C.Raine@bioc.cam.ac.uk WWW:http://www-ccmr-nmr.bioc.cam.ac.uk/~arcr1/ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: NIH policy:deposition of atomic coordinates (fwd) Date: Thu, 11 Feb 1999 09:34:36 -0500 To: rasmol@dhcp-srv2.oit.umass.edu I forward this from the PDB List since it may be of interest to rasmol/chime/SPDV users. In brief, this message says that new NIH policy requires atomic coordinates resulting from NIH-grant supported research to be released upon the date of publication, without any 'hold' period. The PDB list has averaged less than one message per day, so I encourage those interested to subscribe (see URL at bottom). -Eric Martz _______________________________________________________________________ NIH POLICY RELATING TO DEPOSITION OF ATOMIC COORDINATES INTO STRUCTURAL DATABASES Release Date: January 29, 1999 P.T. National Institutes of Health This notice is a revision of the one that appeared in the NIH Guide for Grants and Contracts on September 11, 1992, Vol. 21, No. 33. This revised notice changes one aspect of that policy that the NIH has implemented. The previous notice focused on policy relating to the distribution of unique research resources by biomedical research investigators, and included the issue of the deposition into molecular structure databases of atomic coordinates from X-ray crystallographic and nuclear magnetic resonance experiments. The previous NIH policy announcement pointed to concerns that in some cases these data were not promptly deposited into the databases (see article in Science, Vol. 245, p. 1179, 1989). This issue was addressed by the International Union of Crystallography (IUCr) (See Acta Cryst. Vol. 45, p. 658, 1989), which adopted a resolution calling on crystallographers to deposit the atomic coordinates and related data into the appropriate structural database at the time of submission for publication of a research article drawing conclusions from these data. The IUCr policy permits authors/depositors to instruct the database to delay release of the data for one year from the date of publication, referred to as a "one-year hold." The previous NIH Guide announcement referenced above adopted the IUCr policy in the administration and funding of NIH grants. The purpose of the current NIH Guide policy announcement is to modify the policy stated above to remove the "one-year hold" option for the deposition of atomic coordinates by NIH grant recipients. Under the new NIH policy, the atomic coordinates should be deposited for immediate release upon publication of the research article. This change is instituted in response to the dramatic decrease in the time required to determine the structure of most proteins as well as the need to make these results available for other investigators engaged in wide-ranging research involving protein structure -- such as protein folding, protein family organization, structure prediction, mechanism of action, and drug design studies. Several scientific journals have recently adopted an immediate release policy, as have several special NIH research grant programs. In addition, the IUCr is currently considering new guidelines that would reduce the "hold" period to 6 months in general and eliminate it completely for publicly funded research. The proposed IUCr policy change for publicly funded research is consistent with the NIH policy change adopted in this announcement. Another aspect of the IUCr policy involves the deposition of experimental structure factors. The NIH continues to support the IUCr policy on this issue. In summary, the new NIH policy requires that atomic coordinates from X-ray crystallographic and nuclear magnetic resonance experiments that were supported by NIH grants to be deposited into the appropriate structural database at the time of submission of a research article drawing conclusions from these data. This information should be released immediately at the time of publication. ___________________________________________________________________________ --------------------------------------------- Dr. Alexander Wlodawer Director, Macromolecular Structure Laboratory NCI-FCRDC, Frederick, MD 21702, USA until March 31, 1999: Visiting Fellow at Sidney Sussex College, University of Cambridge, Cambridge CB2 3HU, UK phone 44-1223-766-011, fax 44-1223-766-002 --------------------------------------------- *** Details on how to be removed from this list as well as an *** *** archive of recent postings are available at *** *** http://www.rcsb.org/pdb/lists/pdb-l *** prediction? (fwd) ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: How can I find a test set for protein structure Date: Thu, 11 Feb 1999 09:38:26 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Here's another gem from the PDB list by Kevin Karplus, summarizing up to date evidence that secondary structure prediction from sequence is highly unreliable. -Eric Martz --------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: Kevin Karplus Date: Wed, 10 Feb 1999 10:02:59 -0800 Unfortunately, getting a good test set for secondary-structure prediction is not easy. In posters at the CASP-3 conference this year, people showed that minor differences in how you define your 3-state (helix, strand, other) alphabet can make enormous differences in the accuracy of the prediction method---much larger than the differences between different machine-learning techniques. Small changes in the training and test set also have similar large changes in the performance, as the variance in performance depending on which protein is used is much larger than the variance based on what machine-learning method was used. If you want to inflate your numbers, define helices based on DSSP as H (excluding runs of exactly 4 Hs, which DSSP has too many of) G but only in a run adjacent to Hs and define strands as E. This gives you one of the most easily predicted definitions of helix and strand. The standard (used in the CASP contests) is to include all G and H as helix, E as strand, and everything else as other. There is considerable debate about the appropriateness of this standard, since DSSP is known to classify too many structures as 4-long helices. There is no agreed-upon test set for secondary structure predictors. One of the most commonly used ones is the one that Burkhardt Rost used several years ago in training and testing PhD. Unfortunately, several of the PDB files in that list have become obsolete, and the test set does not cover a large part of the fold space. In the CASP3 contest for secondary-structure prediction, the best methods used fairly strightfoward machine learning techniques (neural nets), and seem to be getting their superior performance mainly from using better multiple alignments than older techniques. The multiple alignments used were from PSIBLAST and SAM-T98. See http://www.cse.ucsc.edu/research/compbio/HMM-apps/HMM-applications.html for access to and information about the SAM-T98 mutiple alignment method, which I believe to be the best remote homolog finder and multiple aligner that uses only sequence information. *** Details on how to be removed from this list as well as an *** *** archive of recent postings are available at *** *** http://www.rcsb.org/pdb/lists/pdb-l *** /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: x-mac-creator="4D4F5353" ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: gzipping on a Mac? Date: Thu, 11 Feb 1999 09:05:52 +0000 To: rasmol@dhcp-srv2.oit.umass.edu Thanks to Steven and Fergus, I have been able to download MacGzip. Thank you! Tim ******************** Timothy Driscoll UMass Amherst Molecular and Cellular Biology Chemistry-Biology Interface Program * Department of Chemistry Amherst College Amherst, MA 01002 413 542 2738 * http://merckx.chem.amherst.edu/tdriscoll/ ******************** Steven Vik wrote: > >Does anyone know how to gzip a PDB file on a Macintosh so Chime can read > >it? (For those who don't have access to a Windows machine) > > > > The MacGzip homepage is at: > > http://persephone.cps.unizar.es/general/gente/spd/gzip/gzip.html > > -Steve Vik > > ***************************************************************** > Steven B. Vik > Department of Biological Sciences > Southern Methodist University > Dallas, TX 75275-0376 > Phone (214) 768-4228 > Fax (214) 768-3955 > E-mail svik@mail.smu.edu > WWW www.smu.edu/~svik X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id KAA27634 ++++------+------+------+------+------+------+------+------+------+------+ From: Jean Richelle Subject: CHIME input file for small molecule Date: Thu, 11 Feb 1999 16:05:19 +0100 (MET) To: rasmol@dhcp-srv2.oit.umass.edu Dear all, Is there any simple way/tool to create CHIME or RASMOL input files describing (with standard geometry) small organic (or not) molecules ? Thank you for help Jean _____________________________________________________________________________ Jean Richelle Unité de Conformation des Macromolécules Biologiques Tel: +32 (0)2 650 3587 Université libre de Bruxelles FAX: +32 (0)2 648 8954 av. FD Roosevelt 50 - CP160/16, B-1050 Bruxelles, Belgium _____________________________________________________________________________ References: <0F6L00K4V1WH5Q@pobox1.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Sinasi Ellialtioglu Subject: Rasmol on Unix Date: Thu, 11 Feb 1999 17:44:52 +0200 To: rasmol@dhcp-srv2.oit.umass.edu I heve been using the Rasmol on Windows 95. Now we have also installed RasMol2 on our Unix machine. If I run it on the Unix Machine(Dec alpha for instance) it works fine and opens up the second window, etc. But if I open an X-window on my pentium using Exceed6.0 and login to Unix machine and run RasMol2, then I get the following message (just as it is mentioned in the ../doc/manual.doc file) : RasMol Molecular Renderer Roger Sayle, August 1995 Version 2.6 [8bit version] No suitable display detected! And no second window appears to render the molecule. I tried setenv DISPLAY etc which opens a second window for gnuplot or any other xterm on my pentium (pc win95), but not rasmol. Is there a way to make RasMol2 to recognize my X-window created by Exceed? Or what else should I do to solve this not-so -important-but-convenience-problem? Thanks Sinasi References: <0F6L00K4V1WH5Q@pobox1.oit.umass.edu> <36C2FAF4.327E4699@rorqual.cc.metu.edu.tr> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: Rasmol on Unix Date: Thu, 11 Feb 1999 16:21:30 +0000 To: rasmol@dhcp-srv2.oit.umass.edu Sinasi Ellialtioglu wrote: > > I heve been using the Rasmol on Windows 95. > Now we have also installed RasMol2 on our Unix machine. > If I run it on the Unix Machine(Dec alpha for instance) it works > fine and opens up the second window, etc. But if I open an X-window > on my pentium using Exceed6.0 and login to Unix machine and run > RasMol2, then I get the following message (just as it is mentioned in the > ../doc/manual.doc file) : > > RasMol Molecular Renderer > Roger Sayle, August 1995 > Version 2.6 > [8bit version] > > No suitable display detected! > > And no second window appears to render the molecule. I tried setenv DISPLAY etc > which opens a second window for gnuplot or any other xterm on my pentium > (pc win95), but not rasmol. Is there a way to make RasMol2 to recognize my > X-window created by Exceed? Or what else should I do to solve this not-so > -important-but-convenience-problem? > > Thanks > > Sinasi Hi All, I'm not sure but maybe you could change the Colordepth on your pc to 256 colors or better recompile rasmol on your DEC with the colordepth of your pc (16 bit for 64 thousand colors, or 32 bit for 16 Mio colors). You do this by editing 'rasmol.h' at the to of the file ...: #define THIRTYTWOBIT /* #define SIXTEENBIT */ /* #define EIGHTBIT */ (to get a 32 bit diplay Rasmol ). RasMol has to be compiled with the colordepth the X-Server is running, but alas, I don't know who Exceed handles the depth of the framebuffer, maybe it doens't behave like a real X-Server ... :-( Good, luck, Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)171 2693405 | Fax : +44-(0)171 269 3258 email : a.mueller@icrf.icnet.uk | http://www.icnet.uk/bmm/ References: <0F6M0072DX905T@rfd1.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: SKG Subject: Re: CHIME input file for small molecule Date: Thu, 11 Feb 1999 09:41:58 -0800 To: rasmol@dhcp-srv2.oit.umass.edu If you can figure out SMILES, you can do it on the web and download the results at http://www2.ccc.uni-erlangen.de/ or you can get a number of molecular modeling programs that allow you to construct your own models (pdb files, etc). Do a web search on molecular modeling for more info......... - - - - - - - - - - - - _ _ _ _ _ _ _ _ _ Steven K. Gill "Against the ruin of the world there is only one defense - the creative act." Kenneth Rexroth X-Envelope-to: rasmol@lists.umass.edu X-VMS-To: IN%"rasmol@lists.umass.edu" X-VMS-Cc: WCOLEMAN ++++------+------+------+------+------+------+------+------+------+------+ From: FLICK COLEMAN Subject: Re: CHIME input file for small molecule Date: Thu, 11 Feb 1999 20:18:05 -0500 (EST) To: rasmol@dhcp-srv2.oit.umass.edu I use several different programs to draw small molecule structures, minimize them and view them with Chime or RasMol. WebLabViewer Pro - from MSI - www.msi.com - easy to draw, reasonable minimiza- tion, save as a variety of file types - there is also a free version WebLab- Viewer that aloows manipulation and visualization, but no drawing or energy minimization - the viewer has a number of attractive features that are more difficult to access in RasMol or Chime (and several CD-ROM that have just been released to accompany Introductory Chemistry texts include the Proversion, so I suspect the price may be going down for it) HyperChem - a computational program from HyperCube - I use it only because I have it for molecular orbital and other calculations - drawing a little crude, but minimization routines are superb - does enable you to draw metal complexes with a little bit of work - the .pdb files it produces frequently act a little odd, but the .mol versions are fine. ISIS-Draw - I should have mentioned this above in conjunction with WebLabViewer Pro. ISIS is a powerful (and free) program for drawing 2-d structures (works best for organics and non-metal inorganics) - those structures can be copied and pasted directly into WebLabViewer Pro - ISIS-Draw is from the Chime folks and can be found at www.mdli.com (I forgot to mention above that the HyperCube home page is www.hyper.com). I hope this is useful to you, Flick Coleman William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 email: wcoleman@wellesley.edu phone: 781-283-3129 fax: 781-283-3642 web: http://www.wellesley.edu/Chemistry/colemanw.html ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: CHIME input file for small molecule Date: Fri, 12 Feb 1999 09:32:00 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Cc: sales@wavefun.com Thanks to Flick Coleman for that excellent short overview of some capabilities of 3 commercial software packages. I have played a bit with PC Spartan (http://www.wavefun.com/ -- and there are also Mac and unix versions) and you can build arbitrary organic molecules and minimize them (up to 100 atoms or so). It can also build short alpha helices or beta strands. One problem with PC Spartan 1.3 is that the PDB files it saves for peptides lack amino acid residue names or atom designations beyond simply the element, e.g. CA for alpha carbons. These limitations make Spartan-saved PDB files useless in RasMol and Chime, which don't even recognize them as peptides (no backbone etc., only ball and stick). Perhaps someone with more experience with Spartan can comment further? And I'd like to know how well the other 3 packages save peptide PDB files, Flick. BTW, Jean Richelle, unless your molecules are unusual, you can probably find PDB files for them already on the web. Start with the links at 'molecules galore' on my site, or the links on the MDLI site (www.mdli.com) under Chime. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: "Andy Tucker" Subject: hyperchem and PDB files Date: Fri, 12 Feb 1999 10:20:46 EST To: rasmol@dhcp-srv2.oit.umass.edu I use hyperchem for modeling labeled proteins, and have been very impressed with the way it exports PDB files. I start with a structure from the PDB, then modify residues and add labels to the model, and then perform my calculations. When I save a pdb file for visualization in rasmol, everything gets carried over perfectly, including the original file headers from Brookhaven. I find this impressive since the molecule has been stored in the hyperchem .hin format in between. Hyperchem generates good connect records for the labels that I attach, which is where I have run into problems with other software. In particular, some older versions of the Biosym software would output pdb files that needed considerable editing before I could visualize proteins with nonstandard residues or capping groups. (Keep in mind that I havent used Biosym software for at least 5 years, and it is bound to be better by now) In general, I find Hyperchem to be one of the easiest packages to learn how to use (CaChe is the easiest, in my opinion), and my students have no problems quickly learning how to build structures with it. However, the graphics leave something to be desired when working with biomolecules, and the mouse functions are not as well thought out as those in other programs. (CaChe, InsightII, Spartan, and Rasmol) andy Dr. W. Andrew Tucker Queens College Chem. Dept. tuckera@rex.queens.edu 1900 Selwyn Ave. (704)337-2317 Charlotte, NC 28277 Re: Eric Martzs question as to how well 3 software packages save peptide PDB files. ++++------+------+------+------+------+------+------+------+------+------+ From: "Douglas J. Beecher" Subject: FoldIt (light) and pdb files Date: Fri, 12 Feb 1999 10:15:21 -0600 To: rasmol@dhcp-srv2.oit.umass.edu References: <199902121429.JAA15072@marlin.bio.umass.edu> Re: Eric Martzs question as to how well 3 software packages save peptide PDB files. I havent used any of the programs mentioned by Eric Martz and Flick Coleman, but I routinely use a program called FoldIt (light) for the Macintosh. This program has a variety of modeling and analysis functions, but is especially useful for quickly constructing peptides and viewing them as idealized sheets or helices. Individual bond angles can be manipulated as desired (which is a little tedious). Peptides are constructed simply by typing a sequence with single letter amino acid designations. The resulting structure can be saved as a pdb file that is complete enough for programs with better imaging capabilities (such as Rasmol or SwissPdbViewer) to open and manipulate. I use the combination of FoldIt (light) and Rasmol to help identify potential transmembrane and coiled coil amphipathic helices. The resulting models are much more informative than the helical wheel diagrams often used for that purpose. FoldIt (light) was written by Jean-Claude Jesior (jean-claude.jesior@imag.fr) and can be obtained free at: ftp://ftp.imag.fr/pub/TIMC/FoldIt.html Hope this is useful Doug Beecher ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: Re: CHIME input file for small molecule Date: Fri, 12 Feb 1999 13:06:53 -0500 To: rasmol@dhcp-srv2.oit.umass.edu > One problem with PC Spartan 1.3 is that the PDB files it saves for >peptides lack amino acid residue names or atom designations beyond simply >the element, e.g. CA for alpha carbons. These limitations make >Spartan-saved PDB files useless in RasMol and Chime, which don't even >recognize them as peptides (no backbone etc., only ball and stick). It might be possible to make these files useful by opening them in Swiss PDB Viewer (SPV) and doing a "Save as..." command. When saving a pdb file, SPV will add atom numbers to pdb files that don't have them (I don't know about the residue names, clearly that would be very useful). Frieda _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ Frieda Reichsman, Ph.D. _/_/_/_/_/ Biochemistry and Molecular Biology _/_/_/_/_/ University of Massachusetts _/_/_/_/_/ Amherst, MA 01003 _/_/_/_/_/ Phone: (413) 545-4029 _/_/_/_/_/ Fax: (413) 545-3291 _/_/_/_/_/ http://www.bio.umass.edu/biochem/reichsman _/_/_/_/_/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ "Time flies like an arrow, but fruit flies like a banana." -Groucho Marx ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle (by way of Eric Martz ) Subject: Re: How can I find a test set for protein structure prediction? Date: Fri, 12 Feb 1999 20:13:19 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Hi Eric, > Here's another gem from the PDB list by Kevin Karplus, summarizing up to > date evidence that secondary structure prediction from sequence is highly > unreliable. -Eric Martz I must comment upon your interpretation of Kevin Kaplus' comments. I was also an attendee at CASP3. 31 teams took part in the secondary structure prediction category, with most good predictions averaging between 68% and 73% correct on Q3 (the three state helix, sheet or coil prediction for each residue). The top two teams making a significant break through around 78% on average, better than Rost's PHD at around 72%-74% that won CASP2 two years ago. This is much better than the structure prediction accuracy of ab initio folding methods, and shows recent improvement in prediction techniques. Kevin Karplus's comment is that the data set used to train the structure prediction methods is one of the largest factors the differentiate the best methods from the worst. And it is this rather than the choice of neural network architectures, inductive logic programming or hidden markov models that predict accuracy. For example, the two top ranked teams were the only two to use PSI-blast generated training sets, even though Karplus used HMMs and Jones used NNs. Some may still consider 78% "unreliable", but these programs are dramatically better than human prediction methods, and much cheaper than the experiment they predict. Indeed one lesson learned from the CASP experiments is that, unlike multiple sequence alignments, tinkering with the structure prediction output by hand never improves the resulting prediction accuracy. Roger -- References: <199902091836.NAA07720@marlin.bio.umass.edu> X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id WAA06620 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: gzipping on a Mac? Gzipping for Chime: how and why. Date: Fri, 12 Feb 1999 22:22:34 -0500 To: rasmol@dhcp-srv2.oit.umass.edu At 2/9/99, Tim Driscoll wrote: > >    I have a straightforward program called ZipIt (shareware; $15) which > seems to work great:  I can zip and unzip files with no problem.  But is > there a secret to viewing zipped files with Chime?  A zipped pdb appears to > load into the Protein Explorer just fine, for example, but no structure > shows up, and neither the Chime menu nor the command line interface have > any effect.  The unzipped format of the same pdb file works fine, though. > Any suggestions? Chime can only decompress PDB files which have been compressed using the specific method of gzip; Chime cannot decompress PDB files compressed by other methods (pkzip, winzip, unix compress, etc., evidently including zipit). I have written a new FAQ entry on gzipping PDB files for Chime at http://www.umass.edu/micro bio/rasmol/faq_em.htm It says (click on the above URL to get the links which were lost in copying below): All PDB files placed on servers for use by Chime should be gzipped. (Note, however, that if the same copy of the file is to be used for RasMol, it should not be gzipped since only unix-RasMol can understand gzipped PDB files -- RasWin and RasMac cannot!) Chime will automatically decompress and display PDB files compressed with the gzip method. Such compression reduces the sizes of PDB files by about 3.5-fold, and reduces the time required to transfer the files through the Internet by a similar amount. When Chime's "File, Save Molecule As" menu option is used, the file will be saved decompressed (as plain text), even if Chime received the file gzipped. Gzip is a freeware program available for a wide variety of computer platforms. Gzip originates from the Free Software Foundation, but they do not provide the application program directly. To download gzip, see the paragraph below for Windows or Macintosh. Gzipping on Windows: Download gzip.exe (which is also available on most shareware/freeware web sites). To gzip, for example, 1d66.pdb, open a DOS window, and type the command "gzip 1d66.pdb". This will produce the file 1d66.pdz which you should probably rename to 1d66.pdb (see below). To decompress a gzipped PDB file: If you run gzip with no parameters, just "gzip", it will reply "For help, type: gzip -h". From the help, you will learn that to decompress a file, the command is "gzip -d ". However, the filename must end in "z", so before decompressing, you'll need to rename, for example, 1d66.pdb back to 1d66.pdz. Then after you "gzip -d 1d66.pdz" it will produce 1d66.pd, which you'll have to rename back to 1d66.pdb. Gzipping on Macintosh: The source of the application is MacGzip Home Page (Spain). Serving gzipped PDB files: In most cases, after gzipping a PDB file for use on a web server, you will need to rename the gzipped file back to a name ending in .pdb. This is because typically the server will be configured to serve files ending in .pdb as MIME type chemical/x-pdb, which directs the browser to hand these files to the Chime plug-in for display. Unless you can get the server administrator to reconfigure the server to serve other types of files (for example ending .pdb.gz or .pdz) as chemical/x-pdb, other file types won't be displayed in Chime. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Rasmol, Alternate Conformers, NMR and CIF Date: Sat, 13 Feb 1999 18:33:49 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Would you like a new free version of RasMol that can distinguish alternate conformers, display multiple NMR models, and knows how to read both small molecule core CIF and mmCIF datasets? Take a look at: RasMol, version 2.6_CIF(Rev 1), based on Roger Sayle's version 2.6, at: http://www.bernstein-plus-sons.com/software/rasmol/ Precompiled versions for SGI (IRIX 5.3 and IRIX 6.4), Windows and Macintosh are available via links on http://www.bernstein-plus-sons.com/software/rasmol/INSTALL.html Complete source and documentation with an updated manual and reference card are available via these web pages. Distribution of additional precompiled binaries would depend on arrangements for access to appropriate systems. If you use the switch "-cif", this version will read a core CIF or mmCIF dataset. Coloring of alternate conformers and multiple NMR models is supported. Fractional coordinates are supported. THIS IS A PRELIMINARY RELEASE INVOLVING EXTENSIVE MODIFICATIONS ***** USE WITH CAUTION ****** Comments and suggestions for improvement appreciated. -- Herbert J. Bernstein yaya@bernstein-plus-sons.com ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-516-286-1339 FAX: 1-516-286-1999 ===================================================== References: <0F6L00K4V1WH5Q@pobox1.oit.umass.edu> <36C2FAF4.327E4699@rorqual.cc.metu.edu.tr> ++++------+------+------+------+------+------+------+------+------+------+ From: Marc Saric Subject: Re: Rasmol on Unix Date: Thu, 11 Feb 1999 20:30:21 +0100 To: rasmol@dhcp-srv2.oit.umass.edu Sinasi Ellialtioglu wrote: > RasMol Molecular Renderer > Roger Sayle, August 1995 > Version 2.6 > [8bit version] > > No suitable display detected! Most likely this indicates that Rasmol can´t open a rendering window due to problems with the color-depths. Maybe you should check wath color-depth (2,4,8,16,24,32 bit per Pixel) is set by Exceed). Maybe it runs in high- or true-color which generaly causes problems with Rasmol under unix. On the other hand: Why do you want to open a X-Windows on a Windows-PC when you can run rasmol localy at a higher speed??? I am also using a heterogeneous environment with UNIX (SGI, DEC, SUN, Linux) and Windows-PCs but I prefer a local program whenever possible -X-Window is quite slow over a network. -- Bye, Marc Saric Visit my homepage http://homepage.ruhr-uni-bochum.de/Marc.Saric/ Visit the FS98 3D-accelerators FAQ at http://www.simflight.com/marc -----BEGIN PGP SIGNATURE----- Version: PGP for Personal Privacy 5.0 Charset: noconv iQA/AwUBNVixqiPrGHYouWn/EQLa7ACgr2TjKYnCykN5wcBA12HKdJQHCo0AoJYQ OcHnuzgguAy+EvWhe/fwG+3m =JQ9Y -----END PGP SIGNATURE----- References: <0F6M0072DX905T@rfd1.oit.umass.edu> X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id FAA12705 ++++------+------+------+------+------+------+------+------+------+------+ From: David Crout Subject: Re: CHIME input file for small molecule Date: Mon, 15 Feb 1999 10:06:24 GMT To: rasmol@dhcp-srv2.oit.umass.edu Jean We use the molecular modelling package RASMOL. This minimises the structures of small molecules and allows one to save them in various formats. One can also input X-ray crystallographic data files. There is one glitch- there is a "save in PDB format" option. However, using the Macintosh version, Rasmol (Rasmac) won't open the file. However, if the PCMODEL file is saved as an Alchemy file (xxxx.alc), Rasmac opens it quite happily. (This may have been cured in versions more up to date than mine). PCMODEL is sold by Serena Software of Bloomington, Indiana. The academic price is very reasonable. You can contact Serena via the manager, Kevin Gilbert, at gilbert@indiana.edu. PCMODEL runs on various platforms including PC and Mac. Hope this is helpful, David Crout >Dear all, > >Is there any simple way/tool to create CHIME or RASMOL input files >describing (with standard geometry) small organic (or not) molecules ? > >Thank you for help > >Jean > >_____________________________________________________________________________ >Jean Richelle >Unité de Conformation des Macromolécules Biologiques Tel: +32 (0)2 650 3587 >Université libre de Bruxelles FAX: +32 (0)2 648 8954 >av. FD Roosevelt 50 - CP160/16, B-1050 Bruxelles, Belgium >_____________________________________________________________________________ Professor D.H.G. Crout Department of Chemistry University of Warwick Coventry CV4 5AL UK Tel: +44 0(1203) 523961 FAX: +44 0(1203) 524429 References: <0F6L00K4V1WH5Q@pobox1.oit.umass.edu> <36C2FAF4.327E4699@rorqual.cc.metu.edu.tr> <36C3038A.D7E231D6@icrf.icnet.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Sinasi Ellialtioglu Subject: Re: Rasmol on Unix Date: Mon, 15 Feb 1999 14:40:28 +0200 To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu Thanks to Arne and Marc, the solution was as simple as they thought. Life is more comfortable now. Sinasi ++++------+------+------+------+------+------+------+------+------+------+ From: "Jeffrey A. Cohlberg" Subject: Chime problem Date: Mon, 15 Feb 1999 16:38:02 -0700 To: rasmol@dhcp-srv2.oit.umass.edu I was a happy user of Chime 1 until today, when I downloaded Chime 2. I did the installation using the Chime Installer. I installed it in my Plug-Ins folder in both Netscape Navigator 3.0 and Netscape Communicator 4.0. I checked to see that Chime was located in both Plug-Ins Folders. I checked the Helpers menu under Options and About Plug-Ins in both versions and saw Chime listed as the helper for several Mime types. So far so good. But when, using either version of Netscape, I tried to view Eric Martz's hemoglobin tutorial, Chime failed to load. I got a message that the plug-in had failed to load and that I should check the memory or check to see that the plug-in was correctly installed. I increased the memory allocation of Netscape Navigator 3 from 15000 K to 40000 K, but that did not help. (I have 90 Mbytes of RAM on a Power Mac 7100/80 and am running virtual memory for a total size of 132 Mbytes.) So, by downloading Chime 2, I seem to have completely eliminated my ability to view pdb files on Netscape. HELP!! Jeff Cohlberg -- Jeffrey A. Cohlberg, Professor Department of Chemistry and Biochemistry California State University, Long Beach 1250 Bellflower Blvd. Long Beach, CA 90840 phone (562) 985-4944 fax (562) 985-8557 ++++------+------+------+------+------+------+------+------+------+------+ From: Subject: Re: Chime problem Date: Mon, 15 Feb 1999 17:00:14 -0800 To: "Rasmol Email List" According to MDLI's readme, Chime 2.0a on the Mac requires either Netscape 3.04, or 4.05 and higher. Depending on what you mean by Netscape 3.0 and 4.0, that could be your problem. Also, I don't recall if Eric's Hemoglobin tutorial utilizes LiveConnect, but I'm not sure if any of the Netscape 3.0x version support LiveConnect. Regardless, I'd suggest downloading the latest (4.5) Netscape Communicator, installing Chime 2.0a for that, and giving it a go. regards, Slaton Lipscomb C4: Computers in Chemistry at Cabrillo College http://c4.cabrillo.cc.ca.us On 2/15/99 3:38 PM Jeffrey A. Cohlberg wrote: >I was a happy user of Chime 1 until today, when I downloaded Chime 2. I >did the installation using the Chime Installer. I installed it in my >Plug-Ins folder in both Netscape Navigator 3.0 and Netscape Communicator >4.0. I checked to see that Chime was located in both Plug-Ins Folders. >I checked the Helpers menu under Options and About Plug-Ins in both >versions and saw Chime listed as the helper for several Mime types. So >far so good. ++++------+------+------+------+------+------+------+------+------+------+ From: Seth Harris Subject: Re: Chime problem Date: Mon, 15 Feb 1999 21:20:45 -0800 To: rasmol@dhcp-srv2.oit.umass.edu Once when I installed Chime it was listed as the helper for several Mime types, as you say, but the "pdb" type was specifically disabled and I had to enable it under the plug-ins menu part. Prior to that I had similar error messages so I thought (hoped) it was something that simple for you. Just a starting suggestion, Seth >I was a happy user of Chime 1 until today, when I downloaded Chime 2. I >did the installation using the Chime Installer. I installed it in my >Plug-Ins folder in both Netscape Navigator 3.0 and Netscape Communicator >4.0. I checked to see that Chime was located in both Plug-Ins Folders. >I checked the Helpers menu under Options and About Plug-Ins in both >versions and saw Chime listed as the helper for several Mime types. So >far so good. > >But when, using either version of Netscape, I tried to view Eric Martz's >hemoglobin tutorial, Chime failed to load. I got a message that the >plug-in had failed to load and that I should check the memory or check >to see that the plug-in was correctly installed. I increased the memory >allocation of Netscape Navigator 3 from 15000 K to 40000 K, but that did >not help. (I have 90 Mbytes of RAM on a Power Mac 7100/80 and am >running virtual memory for a total size of 132 Mbytes.) > >So, by downloading Chime 2, I seem to have completely eliminated my >ability to view pdb files on Netscape. HELP!! > >Jeff Cohlberg >-- >Jeffrey A. Cohlberg, Professor >Department of Chemistry and Biochemistry >California State University, Long Beach >1250 Bellflower Blvd. >Long Beach, CA 90840 >phone (562) 985-4944 fax (562) 985-8557 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Seth Harris Botchan Lab UC Berkeley (510)642-5932 References: <36C8AFDA.1939@csulb.edu> x-mac-creator="4D4F5353" ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Chime problem Date: Tue, 16 Feb 1999 07:39:31 +0000 To: rasmol@dhcp-srv2.oit.umass.edu Jeff, I experienced the same problem when I first downloaded Chime 2.0a on my Mac (Netscape 4.5). My main symptoms were: Every structure or button that tried to load results in an error message: "Could not load the plug-in 'Chemscape Chime 2.0a' for the MIME type 'chemical/x-pdb'. Make sure enough memory is available and that the plug-in is installed correctly." The page hangs trying to load the last object and I am forced to push STOP to stop the loading or it goes on interminably (the application does not freeze, however). Increasing Netscape's RAM allocation to 25M had no effect. In addition, many of the Chime MIME types are not accessible through the Netscape preferences (dimmed). After lots of debugging (with help from the Chime Team at MDL) I figured out that something on my hard drive was interefering with the proper installation of Chime 2.0. I suggest that you start by stripping all Chime from your disk, restarting with Extensions off (Shift-Restart) and reinstalling a SINGLE copy of Chime - more than one Netscape Plugins folder usually confuses my computer, though I don't know if Netscape 4.5 feels better about it (3.x did NOT like it at all). If that doesn't work, you may have to do what I did: I cleaned all software off of my HD, clean installed the OS from the System CD, then put Netscape and Chime on as the first and second software installations. Subsequently reinstalling all of my other software worked fine (though it took a while!) and I have been error-free ever since. If you want, I can forward to you the comments from MDL concerning my installation proplems and you can run through their suggestions as well. Good luck! Tim Driscoll "Jeffrey A. Cohlberg" wrote: > I was a happy user of Chime 1 until today, when I downloaded Chime 2. I > did the installation using the Chime Installer. I installed it in my > Plug-Ins folder in both Netscape Navigator 3.0 and Netscape Communicator > 4.0. I checked to see that Chime was located in both Plug-Ins Folders. > I checked the Helpers menu under Options and About Plug-Ins in both > versions and saw Chime listed as the helper for several Mime types. So > far so good. > > But when, using either version of Netscape, I tried to view Eric Martz's > hemoglobin tutorial, Chime failed to load. I got a message that the > plug-in had failed to load and that I should check the memory or check > to see that the plug-in was correctly installed. I increased the memory > allocation of Netscape Navigator 3 from 15000 K to 40000 K, but that did > not help. (I have 90 Mbytes of RAM on a Power Mac 7100/80 and am > running virtual memory for a total size of 132 Mbytes.) > > So, by downloading Chime 2, I seem to have completely eliminated my > ability to view pdb files on Netscape. HELP!! > > Jeff Cohlberg > -- > Jeffrey A. Cohlberg, Professor > Department of Chemistry and Biochemistry > California State University, Long Beach > 1250 Bellflower Blvd. > Long Beach, CA 90840 > phone (562) 985-4944 fax (562) 985-8557 -- ******************** Timothy Driscoll UMass Amherst Molecular and Cellular Biology Chemistry-Biology Interface Program * Department of Chemistry Amherst College Amherst, MA 01002 413 542 2738 * http://merckx.chem.amherst.edu/tdriscoll/ ******************** mmciflist@ndbdev.rutgers.edu ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Combining RasMol Variants Date: Tue, 16 Feb 1999 16:38:51 -0500 To: pdb-l@rcsb.org, rasmol@dhcp-srv2.oit.umass.edu, After discussion with Roger Sayle, we have decided to bring at least three of the current RasMol variants together into a common version. Anyone using any of the following variants of RasMol is invited to submit bug reports over the next couple of weeks to rasmol@bernstein-plus-sons.com: RasMol_2.6.4 (Roger Sayle's February 1999 version) from ftp://ftp.dcs.ed.ac.uk/pub/rasmol/RasMol2.tar.gz RasMol_2.6b2x1 (Arne Mueller's May 1998 variant) from ftp://nexus.roko.goe.net/pub/rasmol/RasMol26b2x1.tar.gz RasMol_2.6_CIF.1 (Herbert Bernstein's January 1999 variant) from http://www.bernstein-plus-sons.com/software/rasmol If you are using any other versions and having a problem, please get one of these three versions and check if your problem is reproducible with one of these three versions. Sometime in mid-March, we will release version 2.7.0 of RasMol containing as many of the features and bug fixes related to these three versions as we can get to work in a single version in such a short time-frame, and will then create versions 2.7.1, 2.7.2, etc. as problems are reported. Features from other variants of RasMol will be considered for inclusion in RasMol 2.7.n if the features are particularly popular and if available resources (or helpful colleagues) make inclusion of those features feasible. When we are done, probably in the early fall, the resulting best version should be a reasonably stable and reliable single version combining most of the features of the major current variants of RasMol. -- Herbert J. Bernstein ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-516-286-1339 FAX: 1-516-286-1999 ===================================================== References: <36C8AFDA.1939@csulb.edu> <36C920B2.8E327CAC@unix.amherst.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Jeffrey A. Cohlberg" Subject: Re: Chime problem Date: Tue, 16 Feb 1999 16:11:14 -0700 To: tdriscoll@amherst.edu Cc: rasmol@dhcp-srv2.oit.umass.edu Timothy Driscoll wrote: > > Jeff, > > I experienced the same problem when I first downloaded Chime 2.0a on my > Mac (Netscape 4.5). My main symptoms were: > > Every structure or button that tried to load results in > an error message: "Could not load the plug-in 'Chemscape Chime 2.0a' for > the MIME type 'chemical/x-pdb'. Make sure enough memory is available and > that the plug-in is installed correctly." The page hangs trying to load > the last object and I am forced to push STOP to stop the loading or it goes > > on interminably (the application does not freeze, however). Increasing > Netscape's > RAM allocation to 25M had no effect. In addition, many of the Chime MIME > types are not accessible through the Netscape preferences (dimmed). > > After lots of debugging (with help from the Chime Team at MDL) I > figured out that something on my hard drive was interefering with the > proper installation of Chime 2.0. I suggest that you start by stripping > all Chime from your disk, restarting with Extensions off (Shift-Restart) > and reinstalling a SINGLE copy of Chime - more than one Netscape Plugins > folder usually confuses my computer, though I don't know if Netscape 4.5 > feels better about it (3.x did NOT like it at all). I TRIED THIS BUT IT DIDN'T WORK. > > If that doesn't work, you may have to do what I did: I cleaned all software > off of my HD, clean installed the OS from the System CD, then put Netscape > and Chime on as the first and second software installations. Subsequently > reinstalling all of my other software worked fine (though it took a while!) > and I have been error-free ever since. > > If you want, I can forward to you the comments from MDL concerning my > installation proplems and you can run through their suggestions as well. > FORGET IT! IT REALLY ISN'T WORTH THE TROUBLE. I WILL TRY TO REINSTALL CHIME VERSION 1. FOR THOSE OF US WHO ARE NOT COMPUTER FANATICS AND JUST WANT TO USE THE SOFTWARE TO LOOK AT MOLECULES, LIFE IS TOO SHORT FOR THIS SORT OF THING. THANKS FOR THE ADVICE. I'LL CONTACT YOU IF I CHANGE MY MIND. JEFF > Good luck! > > Tim Driscoll > -- Jeffrey A. Cohlberg, Professor Department of Chemistry and Biochemistry California State University, Long Beach 1250 Bellflower Blvd. Long Beach, CA 90840 phone (562) 985-4944 fax (562) 985-8557 ++++------+------+------+------+------+------+------+------+------+------+ From: Alexander Garcia Subject: berkeley rasmol Date: Tue, 16 Feb 1999 23:30:12 -0500 To: "rasmol@lists.umass.edu" Where can I download the berkeley rasmol and it's documantation? cheers PS sorry if I am writting berkeley in the wrong way. cheers any way ++++------+------+------+------+------+------+------+------+------+------+ From: " Dr. Frank Eblinger" Subject: compiling RasMol for PC Date: Wed, 17 Feb 1999 10:02:43 +0100 To: "rasmol@lists.umass.edu" This is a multi-part message in MIME format. --------------A01669D223D4691813C8B4B5 Hi people, Today I saw an interesting version of rasmol which produces povray files. I downloaded Arne Müllers version of rasmol (RasMol26b2x1.tar). Unfortunately its only the source code! How do I compile the program? I'm working on 300 MHz pentium II /Windows 98 PC. What kind of compiler do I need; where can I get it? How do I use it to get the win98 executable? Thanks in advance Frank --------------A01669D223D4691813C8B4B5 Content-Description: Card for Frank Eblinger Content-Disposition: attachment; filename="vcard.vcf" begin: vcard fn: Frank Eblinger n: Eblinger;Frank adr: In den Welkertswiesen 65;;;Saarbrücken;Saarland;66125;Germany email;internet: f.eblinger@rz.uni-sb.de title: Dr. tel;work: 0681-302-3949 tel;fax: 0681-302-4105 tel;home: 06897-764132 x-mozilla-cpt: ;0 x-mozilla-html: FALSE version: 2.1 end: vcard --------------A01669D223D4691813C8B4B5-- References: <36CA85B3.674C4BC5@rz.uni-sb.de> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: compiling RasMol for PC Date: Wed, 17 Feb 1999 12:41:38 +0000 To: rasmol@dhcp-srv2.oit.umass.edu " Dr. Frank Eblinger" wrote: > > Hi people, > > Today I saw an interesting version of rasmol which produces povray > files. I downloaded > Arne Müllers version of rasmol (RasMol26b2x1.tar). Unfortunately its > only the source code! How do I compile the program? I'm working on 300 > MHz pentium II /Windows 98 PC. > What kind of compiler do I need; where can I get it? How do I use it to > get the win98 executable? > > Thanks in advance > > Frank Hi All, I managed to build the program with MS Visual C++ version 5.0 . Alas, there're some 'inconsistencies' between windows and unix/x11 which especially effects the POVRay output of RasMol26b2x1 - the coordinate systems are different and so your POVRay rendered image is different from what you have in your RasMol window! It doesn't seem to be that trivial I thought to fix this bug and at the moment I've no opportunity to access any windows computer, so this nasty bug will be remain for the (near ?) future :-( . At the moment only the unix/linux version works ... sorry, Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)171 2693405 | Fax : +44-(0)171 269 3258 email : a.mueller@icrf.icnet.uk | http://www.icnet.uk/bmm/ ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Misinformation! Date: Fri, 19 Feb 1999 13:13:51 -0500 To: rasmol@dhcp-srv2.oit.umass.edu I must apologize for misinforming RasMol List readers about a feature of SwissPdbViewer. I said that SPdbV supports sprouting of hydrogens, but at the moment, that feature is still under development. I hope that my message did not cause you any inconvenience. Cheers! ***************************** Gale Rhodes mailto:rhodes@usm.maine.edu http://macweb.acs.usm.maine.edu/chemistry/GR/GRHomePage.html Professor of Chemistry Chemistry Department University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 Phone: (207)780-4734 Fax: (207)780-5607 ++++------+------+------+------+------+------+------+------+------+------+ From: James Leong Mook seng Subject: What is the format of MDL mol. Date: Fri, 19 Feb 1999 13:17:14 -0800 (PST) To: Rasmol Help Hello everybody I am currently using PDB format to view molecules but I would like to use MDL mol file format to view double and triple bonds. For PDB:- ATOM 1-6 etc, Could anyone show me the format of the MDL mol file format. Thanks a lot in advance.& _________________________________________________________ DO YOU YAHOO!? Get your free @yahoo.com address at http://mail.yahoo.com ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: Re: What is the format of MDL mol. Date: Fri, 19 Feb 1999 15:32:21 -0800 To: rasmol@dhcp-srv2.oit.umass.edu --=====================_919495941==_ > > Could anyone show me the format of the MDL mol file format. >Thanks a lot in advance.& > Download a copy of babel & convert pdb's to mol files to your heart's content.....meanwhile, here's an example (attached) --=====================_919495941==_ Content-Disposition: attachment; filename="ptaq.mol" Unnamed WLViewer 3D 0 28 31 0 0 0 0 0 0 0 0 0 -3.3151 4.3908 -0.4107 C 0 0 0 0 0 0 0 0 0 0 -2.2859 3.5422 0.3743 C 0 0 0 0 0 0 0 0 0 0 -1.9889 2.0873 -0.1701 C 0 0 0 0 0 0 0 0 0 0 -3.2891 1.2941 -0.2829 C 0 0 0 0 0 0 0 0 0 0 -4.4831 1.9175 -0.4053 C 0 0 0 0 0 0 0 0 0 0 -4.6052 3.4951 -0.3165 C 0 0 0 0 0 0 0 0 0 0 -1.0188 1.7076 0.9692 C 0 0 0 0 0 0 0 0 0 0 -0.0389 2.9734 1.0289 C 0 0 0 0 0 0 0 0 0 0 -0.9654 4.0568 0.6198 C 0 0 0 0 0 0 0 0 0 0 -5.6893 1.0522 -0.5363 C 0 0 0 0 0 0 0 0 0 0 -5.9605 4.0921 -0.6587 C 0 0 0 0 0 0 0 0 0 0 -5.5445 3.8335 0.8397 C 0 0 0 0 0 0 0 0 0 0 -0.6321 5.2384 0.5195 O 0 0 0 0 0 0 0 0 0 0 -3.5135 5.6326 0.2393 O 0 0 0 0 0 0 0 0 0 0 -2.9451 4.7715 -1.8996 C 0 0 0 0 0 0 0 0 0 0 -1.4029 2.0904 -1.5358 O 0 0 0 0 0 0 0 0 0 0 1.2403 3.0508 0.1747 C 0 0 0 0 0 0 0 0 0 0 -1.2312 0.8339 -2.2413 C 0 0 0 0 0 0 0 0 0 0 -1.0523 1.2650 -3.7498 C 0 0 0 0 0 0 0 0 0 0 0.3701 1.7388 -3.7524 C 0 0 0 0 0 0 0 0 0 0 1.3914 0.5967 -3.4579 C 0 0 0 0 0 0 0 0 0 0 0.7753 -0.4390 -2.4195 C 0 0 0 0 0 0 0 0 0 0 -0.0252 0.2262 -1.5893 O 0 0 0 0 0 0 0 0 0 0 -1.2066 0.2282 -4.7098 O 0 0 0 0 0 0 0 0 0 0 0.7553 2.2464 -5.0060 O 0 0 0 0 0 0 0 0 0 0 1.6635 -0.0986 -4.6636 O 0 0 0 0 0 0 0 0 0 0 1.8052 -1.2052 -1.6786 C 0 0 0 0 0 0 0 0 0 0 2.5783 -1.9145 -2.6050 O 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 2 3 1 0 0 0 3 4 1 0 0 0 4 5 2 0 0 0 5 6 1 0 0 0 6 1 1 0 0 0 7 8 1 0 0 0 8 9 1 0 0 0 2 9 1 0 0 0 3 7 1 0 0 0 5 10 1 0 0 0 6 11 1 0 0 0 11 12 1 0 0 0 12 6 1 0 0 0 9 13 2 0 0 0 1 14 1 0 0 0 1 15 1 0 0 0 3 16 1 0 0 0 8 17 1 0 0 0 16 18 1 0 0 0 18 19 1 0 0 0 19 20 1 0 0 0 20 21 1 0 0 0 21 22 1 0 0 0 22 23 1 0 0 0 23 18 1 0 0 0 19 24 1 0 0 0 20 25 1 0 0 0 21 26 1 0 0 0 22 27 1 0 0 0 27 28 1 0 0 0 M END --=====================_919495941==_ --=====================_919495941==_-- ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: Re: What is the format of MDL mol. Date: Fri, 19 Feb 1999 15:33:26 -0800 To: rasmol@dhcp-srv2.oit.umass.edu Ooops - apologies - meant to send that to the inquirer, not the whole list! X-pmrqc: 1 ++++------+------+------+------+------+------+------+------+------+------+ From: "Michael Meredith" Subject: Script won't run on Netscape & Explorer Date: Wed, 24 Feb 1999 09:51:09 -0000 To: rasmol@dhcp-srv2.oit.umass.edu Hello, Can anyone help? I am trying to run scripts on both Internet Explorer AND Netscape on the same machine. For some reason Netscape will load the script but IE will not. Any ideas? Am I missing some simple piece HTML code? Please help it's driving me round the bend!! Michael Meredith **************************************** Dr Michael Meredith Course Designer (Immunology), University of Oxford, Department for Continuing Education, Rewley House, 1 Wellington Square, Oxford. OX1 2JA Tel: +44(01865)270 284 Fax: +44(01865)270 309 **************************************** mmciflist@ndbdev.rutgers.edu ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: OpenVMS version of RasMol_2.6_CIF Date: Wed, 24 Feb 1999 07:59:19 -0500 To: pdb-l@rcsb.org, rasmol@dhcp-srv2.oit.umass.edu, There is an updated release of the CIF-aware version of RasMol which now includes OpenVMS binaries. This is version 2.6_CIF(Rev 2), based on Roger Sayle's version 2.6, at: http://www.bernstein-plus-sons.com/software/rasmol/ Version 2.6_CIF(Rev 2) is a minor update to version 2.6_CIF(Rev 1) which now provides the following list of precompiled binaries via links on http://www.bernstein-plus-sons.com/software/rasmol/INSTALL.html System Binary SGI (IRIX 5.3): RasMol_2.6_CIF.SGI/IRIX_5.3/rasmol_8BIT.gz RasMol_2.6_CIF.SGI/IRIX_5.3/rasmol_16BIT.gz RasMol_2.6_CIF.SGI/IRIX_5.3/rasmol_32BIT.gz SGI (IRIX 6.4): RasMol_2.6_CIF.SGI/IRIX_6.4/rasmol_8BIT.gz RasMol_2.6_CIF.SGI/IRIX_6.4/rasmol_16BIT.gz RasMol_2.6_CIF.SGI/IRIX_6.4/rasmol_32BIT.gz Alpha (OpenVMS 7.1): RasMol_2.6_CIF.DEC/OpenVMS_7.1/rasmol_8bit.exe RasMol_2.6_CIF.DEC/OpenVMS_7.1/rasmol_16bit.exe RasMol_2.6_CIF.DEC/OpenVMS_7.1/rasmol_32bit.exe VAX (OpenVMS 6.2): RasMol_2.6_CIF.DEC/OpenVMS_6.2/rasmol_8bit.exe RasMol_2.6_CIF.DEC/OpenVMS_6.2/rasmol_16bit.exe RasMol_2.6_CIF.DEC/OpenVMS_6.2/rasmol_32bit.exe Mac: RasMol_2.6_CIF_mac_FAT RasMol_2.6_CIF_mac_PPC RasMol_2.6_CIF_mac_68K Windows: RasWin.exe Note that the SGI the binaries are "gzipped". Don't forget to "ungzip" them before trying to use them. A problem with the prior build of the Mac 68K version has been corrected, and you should re-download that version if your platform is a 68K Apple Macintosh. Distribution of additional precompiled binaries would depend on arrangements for access to appropriate systems. If you use the switch "-cif", this version will read a core CIF or mmCIF dataset. Coloring of alternate conformers and multiple NMR models is supported. Fractional coordinates are supported. THIS IS A PRELIMINARY RELEASE INVOLVING EXTENSIVE MODIFICATIONS ***** USE WITH CAUTION ****** This is _not_ the combination of RasMol variants (RasMol 2.7.0) which is coming in a few weeks. Many thanks to those who have reported bugs and made suggestions for that project. Our thanks to David Atkinson at BU, Bob Sweet at BNL, Helen Berman at John Westbrook at Rutgers for access to computers used for some of the compilations for this release. Comments and suggestions to rasmol@bernstein-plus-sons.com very much appreciated. -- Herbert J. Bernstein yaya@bernstein-plus-sons.com ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-516-286-1339 FAX: 1-516-286-1999 ===================================================== References: <19990219211714.23902.rocketmail@send103.yahoomail.com> X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id UAA19220 ++++------+------+------+------+------+------+------+------+------+------+ From: Rick Lee Subject: NT Server & MIME problem Date: Wed, 24 Feb 1999 17:21:45 -0800 To: rasmol@dhcp-srv2.oit.umass.edu Hi all, This should be simple... We just got a new internal WinNT 4.0 Server (SP3), and I was moving our internal web site over to it. So I have to serve Chime MIME types. I edited the registry as I had done previously on a system running Win95 and the Personal Web Server, but it's not working. I rechecked the MDL support page and made sure I followed all the instructions for IIS. The additions were put into the registry at: HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\ Inetinfo\Parameters\MimeMap What could we have done wrong? Yes, I rebooted. :-) Thanks, Rick ******************************************** *  Richard H. Lee, PhD *  Editor/Lead Scientist, Biochemistry *  rick@sciencemedia.com * *  ScienceMedia, Inc. *  6540 Lusk Blvd., Suite C148 *  San Diego, CA 92121-2767 * *  TEL: 619/625-9261, Ext. 7 *  FAX: 619/625-9262 * *  http://www.sciencemedia.com ********************************************* mmciflist@ndbdev.rutgers.edu ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Alpha Dunix version of RasMol_2.6_CIF Date: Wed, 24 Feb 1999 21:56:26 -0500 To: pdb-l@rcsb.org, rasmol@dhcp-srv2.oit.umass.edu, David Atkinson (ATKINSON@med-biophe.bu.edu) has contributed DEC Alpha Dunix compiled binaries for the CIF-aware version of Rasmol, version 2.6_CIF.2 (based on Roger Sayle's version 2.6). These binaries have been added to the web pages at: http://www.bernstein-plus-sons.com/software/rasmol/ Comments and suggestions to rasmol@bernstein-plus-sons.com very much appreciated. -- Herbert J. Bernstein yaya@bernstein-plus-sons.com ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-516-286-1339 FAX: 1-516-286-1999 ===================================================== ++++------+------+------+------+------+------+------+------+------+------+ From: debanzie Subject: Rasmol to Quicktime Date: Thu, 25 Feb 1999 14:52:59 -0600 To: rasmol@dhcp-srv2.oit.umass.edu I would like to be able to save Rasmol rotations as Quicktime movies. Does anyone know how to do this? I know I can create movies in MacMolecule, but I want to use the "cartoon" display, and MacMolecule doesn't do this. Thanks, John de Banzie debanzie@cherokee.nusok.edu ++++------+------+------+------+------+------+------+------+------+------+ From: lynna@cgl.ucsf.EDU Subject: Re: Rasmol to Quicktime Date: Thu, 25 Feb 1999 13:17:42 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu, rasmol@dhcp-srv2.oit.umass.edu On Thu, 25 Feb 1999 14:52:59 -0600, debanzie wrote: > > I would like to be able to save Rasmol rotations as Quicktime movies. > Does anyone know how to do this? I know I can create movies in > MacMolecule, but I want to use the "cartoon" display, and MacMolecule > doesn't do this. > I made a Quicktime movie once using iView. You can find it at: http://www.scriptsoftware.com/iview/index.html Load in all the gifs in the order you want them, then save as a Quicktime movie. -Aenoch ++++------+------+------+------+------+------+------+------+------+------+ From: lynna@cgl.ucsf.EDU Subject: transparent gifs? Date: Thu, 25 Feb 1999 13:21:44 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu I've been trying to save gifs from Rasmol with transparent backgrounds. All I've gotten have been black backgrounds with "set transparent on", then "write gif file.gif". What am I missing? -Aenoch ++++------+------+------+------+------+------+------+------+------+------+ From: "Dr. Don Harden" Subject: Re: transparent gifs? Date: Thu, 25 Feb 1999 17:03:26 -0500 (EST) To: rasmol@dhcp-srv2.oit.umass.edu > I've been trying to save gifs from Rasmol with transparent backgrounds. > All I've gotten have been black backgrounds with "set transparent on", > then "write gif file.gif". What am I missing? background color # set the background to the color you want. background white # white, for example Then Export >> GIF Use an image editor (I like PaintShop Pro from Jasc software http://www.jasc.com/) to re-save the file with a transparent backgroundB Good luck, Don ---------------------------------------------------- Dr. Don Harden don-harden@Gsu.EDU Department of Chemistry Georgia State University ph: (404) 651-3580 Atlanta, Ga. 30303 fax: (404) 651-1416 http://chemistry.Gsu.EDU/glactone ++++------+------+------+------+------+------+------+------+------+------+ From: lynna@cgl.ucsf.EDU Subject: Re: transparent gifs? Date: Thu, 25 Feb 1999 15:38:52 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu On Thu, 25 Feb 1999 17:03:26 -0500 (EST), Dr. Don Harden wrote: > > > I've been trying to save gifs from Rasmol with transparent backgrounds. > > All I've gotten have been black backgrounds with "set transparent on", > > then "write gif file.gif". What am I missing? > > > background color # set the background to the color you want. > background white # white, for example > > Then Export >> GIF > > Use an image editor (I like PaintShop Pro from Jasc software > http://www.jasc.com/) to re-save the file with a transparent backgroundB > This is not what I was looking for. I have several thousand gifs that I need to make with transparent backgrounds, and this will just not work. (Okay, it will work, but I'm unwilling to do this.) From reading the Rasmol manual at: http://www.umass.edu/microbio/rasmol/distrib/rasman.htm#settransparent I believe Rasmol is capable of writing gifs with a transparent background, but following the directions does not give me a transparent background. If it makes a difference, I'm running Rasmol 2.6 under Linux. -Aenoch charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3155.0 ++++------+------+------+------+------+------+------+------+------+------+ From: "Dr.Fisher" Subject: RE: Rasmol to Quicktime Date: Thu, 25 Feb 1999 16:51:37 -0500 To: I'd like to follow up on I'd like to follow debanzie's question but was unable to locate www.scriptsoftware.com/ Does anyone have an updated/other url? GFisher > -----Original Message----- > From: owner-rasmol@lists.umass.edu > [mailto:owner-rasmol@lists.umass.edu]On Behalf Of lynna@cgl.ucsf.EDU > Sent: Thursday, February 25, 1999 4:18 PM > To: rasmol@dhcp-srv2.oit.umass.edu; rasmol@dhcp-srv2.oit.umass.edu > Subject: Re: Rasmol to Quicktime > > > On Thu, 25 Feb 1999 14:52:59 -0600, debanzie wrote: > > > > I would like to be able to save Rasmol rotations as Quicktime movies. > > Does anyone know how to do this? I know I can create movies in > > MacMolecule, but I want to use the "cartoon" display, and MacMolecule > > doesn't do this. > > > > I made a Quicktime movie once using iView. You can find it at: > http://www.scriptsoftware.com/iview/index.html Load in all the gifs in the order you want them, then save as a Quicktime movie. -Aenoch ++++------+------+------+------+------+------+------+------+------+------+ From: lynna@cgl.ucsf.EDU Subject: RE: Rasmol to Quicktime Date: Thu, 25 Feb 1999 16:48:30 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu On Thu, 25 Feb 1999 16:51:37 -0500, Dr.Fisher wrote: > I'd like to follow debanzie's question but was unable to locate > www.scriptsoftware.com/ Does anyone have an updated/other url? > I neglected to say that this program runs on Macintosh only. You can get the file from: http://members.aol.com/iviewmedia/iview.hqx -Aenoch References: <199902260048.QAA21685@socrates.cgl.ucsf.EDU> ++++------+------+------+------+------+------+------+------+------+------+ From: " Dr. Frank Eblinger" Subject: Re: Rasmol to Quicktime Date: Fri, 26 Feb 1999 08:33:08 +0100 To: rasmol@dhcp-srv2.oit.umass.edu This is a multi-part message in MIME format. --------------157CEE9F50D2262E2CDE1616 Hi all, I don't know how to produce Quicktime movies, but there are possibilities to produce avi videos with a screen cam (e.g. http://www.hyperionics.com/). Just let your molecule rotate in chime or whatever you want and save all the screen action to a video-- very easy! Frank --------------157CEE9F50D2262E2CDE1616 Content-Description: Card for Frank Eblinger Content-Disposition: attachment; filename="vcard.vcf" begin: vcard fn: Frank Eblinger n: Eblinger;Frank adr: In den Welkertswiesen 65;;;Saarbrücken;Saarland;66125;Germany email;internet: f.eblinger@rz.uni-sb.de title: Dr. tel;work: 0681-302-3949 tel;fax: 0681-302-4105 tel;home: 06897-764132 x-mozilla-cpt: ;0 x-mozilla-html: FALSE version: 2.1 end: vcard --------------157CEE9F50D2262E2CDE1616-- References: <199902252117.NAA02583@socrates.cgl.ucsf.EDU> ++++------+------+------+------+------+------+------+------+------+------+ From: Preston Garrison Subject: RE: Rasmol to Quicktime Date: Fri, 26 Feb 1999 04:18:46 -0600 To: rasmol@dhcp-srv2.oit.umass.edu >I'd like to follow up on >I'd like to follow debanzie's question but was unable to locate >www.scriptsoftware.com/ Does anyone have an updated/other url? > >GFisher > That url is correct. Don't know why you couldn't find it. Preston N. Garrison, Ph.D. UTHSCSA-Biochem. Dept. Insert the usual disclaimers here. 7703 Floyd Curl Dr. San Antonio, TX 78284-7760 210-567-3702 garrisonp@arwen.uthscsa.edu References: <199902260048.QAA21685@socrates.cgl.ucsf.EDU> ++++------+------+------+------+------+------+------+------+------+------+ From: " Dr. Frank Eblinger" Subject: Re: Rasmol to Quicktime Date: Fri, 26 Feb 1999 13:01:26 +0100 To: rasmol@dhcp-srv2.oit.umass.edu This is a multi-part message in MIME format. --------------CE06343F4A0E9C5353FAEA35 Hi, another way to construct movies from gif files (and the other way round) under windows is making use of the gif_construction_set (http://www.mindworkshop.com ) Frank --------------CE06343F4A0E9C5353FAEA35 Content-Description: Card for Frank Eblinger Content-Disposition: attachment; filename="vcard.vcf" begin: vcard fn: Frank Eblinger n: Eblinger;Frank adr: In den Welkertswiesen 65;;;Saarbrücken;Saarland;66125;Germany email;internet: f.eblinger@rz.uni-sb.de title: Dr. tel;work: 0681-302-3949 tel;fax: 0681-302-4105 tel;home: 06897-764132 x-mozilla-cpt: ;0 x-mozilla-html: FALSE version: 2.1 end: vcard --------------CE06343F4A0E9C5353FAEA35-- References: <199902260048.QAA21685@socrates.cgl.ucsf.EDU> <36D68D16.DC25FCF0@rz.uni-sb.de> ++++------+------+------+------+------+------+------+------+------+------+ From: Alexander Garcia Subject: Re: Rasmol to Quicktime Date: Fri, 26 Feb 1999 10:02:23 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu to construct movies from almost any graphic format there are some very easy programs such as for example Director 6.0 (allows the definition of real movies), the gif construction set (very easy to use, allows only the use of gif files), the adobe package has one program that allows the definition of .avi files from gifs, bmps, and or jpgs. all you have to do is to export the molecule in a valid graphic format (one that may be reconized by the software you use) for exmaple if you are using the gif construction set you may have to export the files as gif fiels, with the director you may use bmp. It is very easy. Dr. Frank Eblinger wrote: > Hi, > another way to construct movies from gif files (and the other way > round) > under windows is making use of the gif_construction_set > (http://www.mindworkshop.com ) > > Frank > > > ------------------------------------------------------------------------------------------------------------- > > Frank Eblinger > Dr. > > Frank Eblinger > Dr. > In den Welkertswiesen 65 Work: 0681-302-3949 > Saarbrücken Fax: 0681-302-4105 > Saarland Home: 06897-764132 > 66125 Netscape Conference Address > Germany Netscape Conference DLS Server > Additional Information: > Last Name Eblinger > First Name Frank > Version 2.1 References: <3.0.6.32.19990219153326.0079a480@asis.com> ++++------+------+------+------+------+------+------+------+------+------+ From: "Gregory Louie" Subject: Re: NT Server & MIME problem Date: Sun, 28 Feb 1999 18:15:32 +0000 To: rasmol@dhcp-srv2.oit.umass.edu Dear subscribers, Hello, I am new to the rasmol list. I am trying to utilize chime for my high school web pages. Our school is networked and each computer has the chime plug-in up and running. However, I have a problem which is similar to Rick Lee's. My local pdb files work fine, but when I upload the same files to the server they are not recognized properly by Netscape. My network technician followed the procedure described on MDL's site to instruct the server (in this case, Windows NT) to describe the files properly by changing some lines in the registry. This was done, but the molecular coordinate files (.pdb in this case) still do not run properly. Netscape reports the following: Information on this page requires a plug-in for: application/octet-stream If I associate Netscape Navigator with the file and double click on the file, Chime is invoked, the source file is correct, but no display. The same file on my networked drive displays correctly, but not off of the server. Does anyone know of the fix? Thank you all. Greg Louie Greg Louie Xavier High School 30 W. 16th Street NY, NY 10011 References: <199902252338.PAA15757@socrates.cgl.ucsf.EDU> ++++------+------+------+------+------+------+------+------+------+------+ END OF 98.01-02 Beginning March 1, 1999: ++++------+------+------+------+------+------+------+------+------+------+ From: " Dr. Frank Eblinger" Subject: Re: transparent gifs? Date: Mon, 01 Mar 1999 10:44:20 +0100 To: rasmol@dhcp-srv2.oit.umass.edu --------------10D4397AECF87E2149BB72F8 Hi Subscribers, Does anybody know how to stop writing to a rasmol script?? I start the script with: write sript example.spt How do I stop writing without leaving the programm? Thanks in advance Frank --------------10D4397AECF87E2149BB72F8 Hi Subscribers,

Does anybody know how to stop writing to a rasmol script??

I start the script with: write sript example.spt

How do I stop writing without leaving the programm?

Thanks in advance

                    Frank --------------10D4397AECF87E2149BB72F8-- ++++------+------+------+------+------+------+------+------+------+------+ From: "Patrick Flash" Subject: Re: transparent gifs? Date: Mon, 1 Mar 1999 09:46:57 EST To: rasmol@dhcp-srv2.oit.umass.edu Frank, I've just been saving the script after the last instruction: save script filename.spt Pat Flash Kent-Ashtabula flash@ashtabula.kent.edu ++++------+------+------+------+------+------+------+------+------+------+ From: lynna@cgl.ucsf.EDU Subject: Re: transparent gifs? Date: Mon, 1 Mar 1999 16:05:29 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu On Thu, 25 Feb 1999 15:38:52 -0800 (PST), I wrote: > > On Thu, 25 Feb 1999 17:03:26 -0500 (EST), Dr. Don Harden wrote: > > > > > I've been trying to save gifs from Rasmol with transparent backgrounds. > > > All I've gotten have been black backgrounds with "set transparent on", > > > then "write gif file.gif". What am I missing? > > > > > > background color # set the background to the color you want. > > background white # white, for example > > > > Then Export >> GIF > > > > Use an image editor (I like PaintShop Pro from Jasc software > > http://www.jasc.com/) to re-save the file with a transparent backgroundB > > > > This is not what I was looking for. I have several thousand gifs that I > need to make with transparent backgrounds, and this will just not work. > (Okay, it will work, but I'm unwilling to do this.) From reading the > Rasmol manual at: > > http://www.umass.edu/microbio/rasmol/distrib/rasman.htm#settransparent > > I believe Rasmol is capable of writing gifs with a transparent > background, but following the directions does not give me a > transparent background. > > If it makes a difference, I'm running Rasmol 2.6 under Linux. > No one wrote to tell me if RasMol is capable (or if it isn't capable) of outputting transparent GIFs. I found a utility that can perform batch conversions of GIFs so that they have a transparent background, and I thought that others might be interested. The program is 'gifsicle' and runs under most unix-like operation systems. You can find it at: http://www.pdos.lcs.mit.edu/~eddietwo/gifsicle/ If the GIFs are saved with black backgrounds, the black can be converted into transparent by: gifsicle --batch --transparent #000000 *.gif This made it much easier to process my ~2000 GIFs. -Aenoch ++++------+------+------+------+------+------+------+------+------+------+ From: lynna@cgl.ucsf.EDU Subject: the opposite of 'restrict'? Date: Mon, 1 Mar 1999 17:59:27 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu Cc: lynna@cgl.ucsf.EDU Hello. I was wondering if there was a command in Chime (or RasMol) to do the converse of 'restrict'. The command I'm looking for would select the spcified region, then turn the display of those atoms on, remembering previous formatting commands so that the atoms/molecules would be displayed with their former characteristics. For example, say I have a four chain structure and I do something like: select all wireframe 1 select arg wireframe 50 Then I want to display each chain individually, with the arginines as sticks. If I do: restrict :A this will make chains B, C, and D invisable, and chain A will be left on the screen. This is what I want. However, if I then do: restrict :B The screen is blank. While the atoms of chain B are selected, their display was not turned on. Since I want to maintain the arginies as sticks, I cannot just do: wireframe 1 as this would change the arginies to wireframe as well. The reason I would like this feature is because I would like to have a series of buttons that restricts the display to pre-determined sub-sets of the structures and allows the user to change the display/ color/wireframe/labels of the atoms and have these changes maintained as each sub-set is selected for display. I cannot find any such command in the RasMol manual, the Chime manual, or the mailing list archives. If no such command exists, can I petition for such a beast in the next version of Chime? Thanks. -Aenoch ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: Re: transparent gifs? Date: Mon, 1 Mar 1999 21:23:32 -0500 To: rasmol@dhcp-srv2.oit.umass.edu On Thu, 25 Feb 1999 15:38:52 -0800 (PST), I wrote: > > On Thu, 25 Feb 1999 17:03:26 -0500 (EST), Dr. Don Harden wrote: > > > > > I've been trying to save gifs from Rasmol with transparent backgrounds. > > > All I've gotten have been black backgrounds with "set transparent on", > > > then "write gif file.gif". What am I missing? > > > > > > background color # set the background to the color you want. > > background white # white, for example > > > > Then Export >> GIF > > > > Use an image editor (I like PaintShop Pro from Jasc software > > http://www.jasc.com/) to re-save the file with a transparent backgroundB > > > > This is not what I was looking for. I have several thousand gifs that I > need to make with transparent backgrounds, and this will just not work. > (Okay, it will work, but I'm unwilling to do this.) From reading the > Rasmol manual at: > > http://www.umass.edu/microbio/rasmol/distrib/rasman.htm#settransparent > > I believe Rasmol is capable of writing gifs with a transparent > background, but following the directions does not give me a > transparent background. > > If it makes a difference, I'm running Rasmol 2.6 under Linux. > No one wrote to tell me if RasMol is capable (or if it isn't capable) of outputting transparent GIFs. I found a utility that can perform batch conversions of GIFs so that they have a transparent background, and I thought that others might be interested. The program is 'gifsicle' and runs under most unix-like operation systems. You can find it at: http://www.pdos.lcs.mit.edu/~eddietwo/gifsicle/ If the GIFs are saved with black backgrounds, the black can be converted into transparent by: gifsicle --batch --transparent #000000 *.gif This made it much easier to process my ~2000 GIFs. -Aenoch ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: the opposite of 'restrict'? Date: Mon, 1 Mar 1999 21:23:39 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Cc: lynna@cgl.ucsf.EDU Hello. I was wondering if there was a command in Chime (or RasMol) to do the converse of 'restrict'. The command I'm looking for would select the spcified region, then turn the display of those atoms on, remembering previous formatting commands so that the atoms/molecules would be displayed with their former characteristics. For example, say I have a four chain structure and I do something like: select all wireframe 1 select arg wireframe 50 Then I want to display each chain individually, with the arginines as sticks. If I do: restrict :A this will make chains B, C, and D invisable, and chain A will be left on the screen. This is what I want. However, if I then do: restrict :B The screen is blank. While the atoms of chain B are selected, their display was not turned on. Since I want to maintain the arginies as sticks, I cannot just do: wireframe 1 as this would change the arginies to wireframe as well. The reason I would like this feature is because I would like to have a series of buttons that restricts the display to pre-determined sub-sets of the structures and allows the user to change the display/ color/wireframe/labels of the atoms and have these changes maintained as each sub-set is selected for display. I cannot find any such command in the RasMol manual, the Chime manual, or the mailing list archives. If no such command exists, can I petition for such a beast in the next version of Chime? Thanks. -Aenoch ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Disabling Chime's Menu Date: Wed, 03 Mar 1999 09:15:18 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Cc: tdriscoll@amherst.edu, jch@mdli.com Jean Holt at MDLI just pointed out to me a list of embed tags which are new in Chime 2. You can see it by going to the Chime support page at MDL, http://www.mdli.com/support/chime/chimefree.htm, clicking on 'embed tags' (this link should be labeled 'embed tags and script commands'), then notice the inconspicuous link near the lower left, 'new embed tags'. Some of us are developing javascript which keeps the state of chime in javascript variables. A problem is that when the color scheme or the display rendering is changed from Chime's menu, no message is sent back to Chime, so the state values become incorrect. In this regard, I notice the new embed tag 'nomenus' (read No Menus). 'nomenus=true' disables all menus except 'About'. Unfortunately this and some other embed tags don't have script command counterparts such as 'nomenus false' or 'set nomenus off' so they can't be changed dynamically -- only when Chime is invoked. Anyway, at the expense of having no menus at all, one can ensure that the state of Chime is known to javascript. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - UMass Chime Resources: www.umass.edu/microbio/chime Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Keeping Chime's menu from popping up unwanted on the Mac Date: Wed, 03 Mar 1999 09:29:38 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Cc: jch@mdli.com I note that the Chime 2 embed tag documentation at MDLI omits one new tag said by Tim Maffett to exist in the Macintosh version only: menudelay= The purpose of this is to prevent the menu from popping up unwanted during presentations. By setting the delay to a high value, it won't pop up unwanted. You can always pop it up immediately when wanted by clicking on the MDL frank. I would appreciate knowing from some Macintosh users if this works. The problem with it is that it requires a change in the html embed tag. This means that existing sites will continue to have this very annoying problem unless and until they are changed. In my opinion a much better method would be to have a toggle on the menu (no reason not to have it on Windows also) "Menu from MDL only". When checked, you could only get the menu by clicking on the frank -- which would allow you to uncheck the toggle if wanted. If you agree that this is a desirable enhancement, please let MDL know this (http://www.mdli.com/support/chime/supporting.htm) -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - UMass Chime Resources: www.umass.edu/microbio/chime Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Please gzip your Chime PDB's! Date: Wed, 03 Mar 1999 09:58:07 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Most people who are authoring Chime sites on the web are not bothering to gzip their PDB files. Gzipping the PDB files reduces file size and therefore web transfer time by about 3.5-fold which is a boon to those using modems and wishing to view e.g. a 400K (or worse, a 2 megabyte NMR) PDB file. Chime will recognize and automatically decompress gzipped PDB files which it receives. Gzipped PDB files are no slower to appear in Chime than plain text ones -- probably faster. The only action you need to take is to gzip the copy of the PDB file on the server. No changes to the html (or javascript) are needed on the server. The gzipped PDB file must typically be renamed to end in '.pdb' (for MIME type compatibility) and for ftp to the server, must be transferred in BINARY mode. I have added a section to my FAQ which gives full details, including where you can get the gzip program. Note that gzip uses a different compression method (quite a good one by the way) than do pkzip, winzip, unix compress, etc. You must use the gzip program to see the PDB file in Chime. Please see http://www.umass.edu/microbio/rasmol/faq_em.htm#gzip for all details and to download the gzip freeware. Thanks to Jean-loup Gailly and Mark Adler who gave gzip, free of patents and encumbrances, to the world! www.gzip.org -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Alexander Garcia Subject: inquiry Date: Wed, 03 Mar 1999 02:15:43 -0500 To: "rasmol@lists.umass.edu" having an aminoacid seq how can I get the aproximate pdb file, is there any software for this? cheers ++++------+------+------+------+------+------+------+------+------+------+ From: lynna@cgl.ucsf.EDU Subject: Re: Keeping Chime's menu from popping up unwanted on the Mac Date: Wed, 3 Mar 1999 07:46:06 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu On Wed, 03 Mar 1999 09:29:38 -0500, Eric Martz wrote: > > I note that the Chime 2 embed tag documentation at MDLI omits one new tag > said by Tim Maffett to exist in the Macintosh version only: > > menudelay= > > The purpose of this is to prevent the menu from popping up unwanted during > presentations. By setting the delay to a high value, it won't pop up > unwanted. You can always pop it up immediately when wanted by clicking on > the MDL frank. > > I would appreciate knowing from some Macintosh users if this works. > This is good. I've been annoyed at how quickly the menu pops up on the Macs. However, the delay is not in seconds. A value of 100 gives an approximately 1.5 second delay. I like the delay that this value gives. This is on a PB3400 and an 8100. -Aenoch ++++------+------+------+------+------+------+------+------+------+------+ From: Albion Baucom Subject: Re: inquiry Date: Wed, 3 Mar 1999 09:23:18 -0800 (PST) To: Alexander Garcia Cc: "rasmol@lists.umass.edu" Alexander Try a BLAST search at: http://www.ncbi.nlm.nih.gov/BLAST/ This will search for homologs in number of databases (the PDB included) and return a list of likely matches. Albion Albion E. Baucom '71 R75/5 '74 R75/5 http://tito.ucsc.edu/baucom http://c4.cabrillo.cc.ca.us On Wed, 3 Mar 1999, Alexander Garcia wrote: > having an aminoacid seq how can I get the aproximate pdb file, is there > any software for this? cheers > References: <199903020159.RAA03905@socrates.cgl.ucsf.EDU> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: the opposite of 'restrict'? Date: Wed, 03 Mar 1999 17:57:12 +0000 To: rasmol@dhcp-srv2.oit.umass.edu lynna@cgl.ucsf.EDU wrote: > > Hello. > > I was wondering if there was a command in Chime (or RasMol) to do > the converse of 'restrict'. The command I'm looking for would > select the spcified region, then turn the display of those atoms > on, remembering previous formatting commands so that the atoms/molecules > would be displayed with their former characteristics. > > For example, say I have a four chain structure and I do something like: > > select all > wireframe 1 > select arg > wireframe 50 > > Then I want to display each chain individually, with the arginines > as sticks. If I do: > > restrict :A > > this will make chains B, C, and D invisable, and chain A will be left > on the screen. This is what I want. However, if I then do: > > restrict :B > > The screen is blank. While the atoms of chain B are selected, their > display was not turned on. Since I want to maintain the arginies as > sticks, I cannot just do: > > wireframe 1 > > as this would change the arginies to wireframe as well. > > The reason I would like this feature is because I would like to > have a series of buttons that restricts the display to pre-determined > sub-sets of the structures and allows the user to change the display/ > color/wireframe/labels of the atoms and have these changes maintained > as each sub-set is selected for display. > > I cannot find any such command in the RasMol manual, the Chime manual, > or the mailing list archives. > > If no such command exists, can I petition for such a beast in the > next version of Chime? > > Thanks. > > -Aenoch Hi All, hm ..., I tried some stuff in RasMol to figure out a good way to solve the problem but it seems to me that the only way is to handle is is a sort of work around using a script. maybe the following works: view.script is a file and conatins: wireframe 1 select selected and arg wireframe 50 in rasmol do the following (as you wrote above): wireframe 1 select arg wireframe 50 restrict :A restrict :B # after that the screen is blank ... script 'view.script' # put chain B on the screen ( with ARGs in wireframe 50) restrict :A script 'view.script' # switches to chain A agisn ... I'm not sure if this helps ... . I realy agree with that 'reverse restrict' you suggest. But try the following: select all color green select arg color red # molecule in green expect arginin (in red) restrict :A # only chain A displayed ... restrict :B # blank screen wireframe # chain B displayed (green and arginin in red ...) So it works with colours but not with other representations! This is because you HAVE to choose one of the available representations (like wireframe) to redisplay hidden part of your molecule. So the 'only thing' we need in RasMol is a kind of dummy or default representation which could work like this: select all wireframe 1 select arg wireframe 50 restrict A: restrict B: default which will do what you expect. 'default' uses the last representation for each of the redisplayed part of the molecule or say 'wireframe' if no default has been set. Ok, actually that doens't help anyone but may inspire future developement. Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)171 2693405 | Fax : +44-(0)171 269 3258 email : a.mueller@icrf.icnet.uk | http://www.icnet.uk/bmm/ References: <199903031456.JAA05026@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: " Dr. Frank Eblinger" Subject: Re: Please gzip your Chime PDB's! Date: Thu, 04 Mar 1999 09:36:54 +0100 To: rasmol@dhcp-srv2.oit.umass.edu --------------7EBA41481D7F6D722FFC67D3 Hi, gzipping pdb files is an excellent idea in terms of diskspace and transferring rates! Under windows its very easy to do this for all your pdb files in one step! 1. Copy (transfer by ftp) all your pdb fils in a new directory containing gzip.exe 2. go to dos ; cd directory ; gzip *.pdb 3. ren *.pdz *.pdb 4. transfer all the resulting pdb files (much smaller now) back to the server very easy! cheers --------------7EBA41481D7F6D722FFC67D3 Hi,

gzipping pdb files is an excellent idea in terms of diskspace and transferring rates!
Under windows its very easy to do this for all your pdb files in one step!

1. Copy (transfer by ftp) all your pdb fils in a new directory containing gzip.exe
2. go to dos ; cd directory  ; gzip *.pdb
3. ren  *.pdz   *.pdb
4. transfer all the resulting pdb files (much smaller now) back to the server

very easy!

cheers
  --------------7EBA41481D7F6D722FFC67D3-- charset="koi8-r" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 ++++------+------+------+------+------+------+------+------+------+------+ From: "Sergey Vasil'ev" Subject: Your can RAR your Chime PDB's! Date: Thu, 4 Mar 1999 13:44:08 +0300 To: Hi all! If you use a lot of PDB files (like me) I think it'll be interesting for you to read about RAR archiver. You can use it on many platforms (DOS, Win32 console, Win32 GUI, Macintosh, OS/2, SCO, BSD, Linux, Sparc and HP-UX) and I can say that it is very useble in terms of diskspace and transferring rates :) http://www.rarsoft.com/rar_archiver.htm Sergey Vasil'ev /*------------------------------------------------ DNA-Protein Interaction DataBase project team. Belozersky Institute of Physico-Chemical Biology, Moscow State University & Inst. of Agricultural BioTechnology RAAS. 42 Timiryazevskaya St., Moscow 127550, RUSSIA email vasil@iab.ac.ru vasil@biocom.genebee.msu.su fax +7-095-9770947 ------------------------------------------------*/ References: <000401be662b$ee8f05d0$5b1c22c3@sergey> ++++------+------+------+------+------+------+------+------+------+------+ From: " Dr. Frank Eblinger" Subject: Re: Your can RAR your Chime PDB's! Date: Thu, 04 Mar 1999 12:17:44 +0100 To: rasmol@dhcp-srv2.oit.umass.edu Hi, don't think that chime will read RAR-archives! Frank Sergey Vasil'ev wrote: > Hi all! > > If you use a lot of PDB files (like me) I think it'll be interesting for you > to read about RAR archiver. > You can use it on many platforms (DOS, Win32 console, Win32 GUI, Macintosh, > OS/2, SCO, BSD, Linux, Sparc and HP-UX) and I can say that it is very > useble in terms of diskspace and transferring rates :) > > http://www.rarsoft.com/rar_archiver.htm > > Sergey Vasil'ev > > /*------------------------------------------------ > DNA-Protein Interaction DataBase project team. > Belozersky Institute of Physico-Chemical Biology, > Moscow State University & > Inst. of Agricultural BioTechnology RAAS. > 42 Timiryazevskaya St., > Moscow 127550, RUSSIA > email vasil@iab.ac.ru > vasil@biocom.genebee.msu.su > fax +7-095-9770947 > ------------------------------------------------*/ References: <199903031456.JAA05026@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: Re: Please gzip your Chime PDB's! Date: Thu, 04 Mar 1999 10:54:40 -0800 To: rasmol@dhcp-srv2.oit.umass.edu At 09:36 AM 3/4/99 +0100, you wrote: > Hi, gzipping pdb files is an excellent idea in terms of diskspace and >transferring rates! >Under windows its very easy to do this for all your pdb files in one step! >1. Copy (transfer by ftp) all your pdb fils in a new directory containing >gzip.exe >2. go to dos ; cd ; gzip *.pdb > *.pdb >4. transfer all the resulting pdb files (much smaller now) back to the >server very easy! cheers > Thanks to both you & Eric for the reminder - this doesn't matter too much for small molecules, but what a difference for enzymes & other biomolecules!! References: <0F6L00K4V1WH5Q@pobox1.oit.umass.edu> <36C2FAF4.327E4699@rorqual.cc.metu.edu.tr> ++++------+------+------+------+------+------+------+------+------+------+ From: Eugene Leitl Subject: Rasmol on SuSE Linux Date: Thu, 4 Mar 1999 21:42:53 +0100 (CET) To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu Hi. I'm trying to build RasMol26b2 (for MMTK/MDTools/OpenChem) using just-built gcc version egcs-2.91.60 19981201 (egcs-1.1.1 release) under some Apr 1998..Jan 1999 SuSE Linux (the non-egcs gcc showed the same behaviour, btw). According to the procedure described in INSTALL, I use xmkmf to generate the Makefile, then invoke make. The build bails out with gcc -O2 -fno-strength-reduce -I/usr/X11R6/include -I/include -Dlinux -D__i386__ -D_POSIX_SOURCE -D_BSD_SOURCE -D_SVID_SOURCE -DX_LOCALE -DFUNCPROTO=15 -DNARROWPROTO -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DEIGHTBIT -c rasmol.c -o rasmol.o rasmol.c: In function `FetchCharacter': rasmol.c:497: `WaitSet' has an incomplete type rasmol.c:503: warning: passing arg 2 of `select' from incompatible pointer type rasmol.c:503: warning: passing arg 3 of `select' from incompatible pointer type rasmol.c:503: warning: passing arg 4 of `select' from incompatible pointer type rasmol.c: At top level: rasmol.c:112: storage size of `OrigWaitSet' isn't known rasmol.c:113: storage size of `WaitSet' isn't known make: *** [rasmol.o] Error 1 Though I may be confabulating things, I think some previous RasMol version (alas, purged) compiled allright. OrigWaitSet and WaitSet are defined in rasmol.c as static struct fd_set OrigWaitSet; static struct fd_set WaitSet; I grepped the sourcetree for fd_set with the following results: lrz:/usr4/model/RasMol/RasMol2 # grep -i fd_set * ChangeLog.2: defined to allow struct fd_set to be properly defined. [...] rasmol.c:static struct fd_set OrigWaitSet; rasmol.c:static struct fd_set WaitSet; rasmol.c: { FD_SET(socket,&OrigWaitSet); rasmol.c: FD_SET(FileNo,&OrigWaitSet); rasmol.c: { FD_SET(SocketNo,&OrigWaitSet); rasmol.c: FD_SET(i,&OrigWaitSet); rasmol.c: status = select( WaitWidth, &WaitSet, (struct fd_set*)NULL, rasmol.c: (struct fd_set*)NULL, &TimeOut ); [...] The according lines in ChangeLog.2 are: [15/10/93] rasmol.c Added #include to rasmol.c, when _SEQUENT_ is defined to allow struct fd_set to be properly defined. Which doesn't seem to be relevant, the more so that according to locate select.h doesn't dwell anywhere in my system. Any ideas what is going on? Thanks! Regards, Eugene Leitl ++++------+------+------+------+------+------+------+------+------+------+ From: lynna@cgl.ucsf.EDU Subject: Re: Rasmol on SuSE Linux Date: Thu, 4 Mar 1999 12:55:14 -0800 (PST) To: rasmol@dhcp-srv2.oit.umass.edu, rasmol@dhcp-srv2.oit.umass.edu On Thu, 4 Mar 1999 21:42:53 +0100 (CET), Eugene Leitl wrote: > > Hi. I'm trying to build RasMol26b2 (for MMTK/MDTools/OpenChem) using just-built > gcc version egcs-2.91.60 19981201 (egcs-1.1.1 release) under some Apr > 1998..Jan 1999 SuSE Linux (the non-egcs gcc showed the same behaviour, btw). > According to the procedure described in INSTALL, I use xmkmf to > generate the Makefile, then invoke make. The build bails out with > > gcc -O2 -fno-strength-reduce -I/usr/X11R6/include -I/include -Dlinux -D__i386__ -D_POSIX_SOURCE -D_BSD_SOURCE -D_SVID_SOURCE -DX_LOCALE -DFUNCPROTO=15 -DNARROWPROTO -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DEIGHTBIT -c rasmol.c -o rasmol.o > rasmol.c: In function `FetchCharacter': > rasmol.c:497: `WaitSet' has an incomplete type > rasmol.c:503: warning: passing arg 2 of `select' from incompatible pointer type > rasmol.c:503: warning: passing arg 3 of `select' from incompatible pointer type > rasmol.c:503: warning: passing arg 4 of `select' from incompatible pointer type > rasmol.c: At top level: > rasmol.c:112: storage size of `OrigWaitSet' isn't known > rasmol.c:113: storage size of `WaitSet' isn't known > make: *** [rasmol.o] Error 1 > I believe this is covered in the mailing list archive; you can find it at: ftp://marlin.bio.umass.edu/pub/shareware/rasmol/email-history/all Search for 'fd_set'. The solution described there worked for me. -Aenoch References: <0F6L00K4V1WH5Q@pobox1.oit.umass.edu> <36C2FAF4.327E4699@rorqual.cc.metu.edu.tr> <14046.59806.51728.609722@lrz.uni-muenchen.de> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: Rasmol on SuSE Linux Date: Thu, 04 Mar 1999 21:04:59 +0000 To: rasmol@dhcp-srv2.oit.umass.edu Eugene Leitl wrote: > > Hi. I'm trying to build RasMol26b2 (for MMTK/MDTools/OpenChem) using just-built > gcc version egcs-2.91.60 19981201 (egcs-1.1.1 release) under some Apr > 1998..Jan 1999 SuSE Linux (the non-egcs gcc showed the same behaviour, btw). > According to the procedure described in INSTALL, I use xmkmf to > generate the Makefile, then invoke make. The build bails out with > > gcc -O2 -fno-strength-reduce -I/usr/X11R6/include -I/include -Dlinux -D__i386__ -D_POSIX_SOURCE -D_BSD_SOURCE -D_SVID_SOURCE -DX_LOCALE -DFUNCPROTO=15 -DNARROWPROTO -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DEIGHTBIT -c rasmol.c -o rasmol.o > rasmol.c: In function `FetchCharacter': > rasmol.c:497: `WaitSet' has an incomplete type > rasmol.c:503: warning: passing arg 2 of `select' from incompatible pointer type > rasmol.c:503: warning: passing arg 3 of `select' from incompatible pointer type > rasmol.c:503: warning: passing arg 4 of `select' from incompatible pointer type > rasmol.c: At top level: > rasmol.c:112: storage size of `OrigWaitSet' isn't known > rasmol.c:113: storage size of `WaitSet' isn't known > make: *** [rasmol.o] Error 1 > > Though I may be confabulating things, I think some previous RasMol version (alas, > purged) compiled allright. > > OrigWaitSet and WaitSet are defined in rasmol.c as > > static struct fd_set OrigWaitSet; > static struct fd_set WaitSet; > > I grepped the sourcetree for fd_set with the following results: > > lrz:/usr4/model/RasMol/RasMol2 # grep -i fd_set * > ChangeLog.2: defined to allow struct fd_set to be properly defined. > [...] > rasmol.c:static struct fd_set OrigWaitSet; > rasmol.c:static struct fd_set WaitSet; > rasmol.c: { FD_SET(socket,&OrigWaitSet); > rasmol.c: FD_SET(FileNo,&OrigWaitSet); > rasmol.c: { FD_SET(SocketNo,&OrigWaitSet); > rasmol.c: FD_SET(i,&OrigWaitSet); > rasmol.c: status = select( WaitWidth, &WaitSet, (struct fd_set*)NULL, > rasmol.c: (struct fd_set*)NULL, &TimeOut ); > [...] > > The according lines in ChangeLog.2 are: > > [15/10/93] rasmol.c > Added #include to rasmol.c, when _SEQUENT_ is > defined to allow struct fd_set to be properly defined. > > Which doesn't seem to be relevant, the more so that according to > locate select.h doesn't dwell anywhere in my system. > > Any ideas what is going on? Thanks! > > Regards, > Eugene Leitl Hi, 'struct fd_set' is 'typedef'ed now (in newer linux-kernels). Get a fixed version from ftp://ftp.roko.goe.net/pub/rasmol/ and uncomment '#define USE_FD_SET_TYPE' in rasmol.h. Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)171 2693405 | Fax : +44-(0)171 269 3258 email : a.mueller@icrf.icnet.uk | http://www.icnet.uk/bmm/ ++++------+------+------+------+------+------+------+------+------+------+ From: Boris Matthew Puhanic Subject: Re: Rasmol on SuSE Linux Date: Fri, 5 Mar 1999 19:50:39 +1100 (EST) To: rasmol@dhcp-srv2.oit.umass.edu > > Hi. I'm trying to build RasMol26b2 (for MMTK/MDTools/OpenChem) using just-built > gcc version egcs-2.91.60 19981201 (egcs-1.1.1 release) under some Apr > 1998..Jan 1999 SuSE Linux (the non-egcs gcc showed the same behaviour, btw). > According to the procedure described in INSTALL, I use xmkmf to > generate the Makefile, then invoke make. The build bails out with > > gcc -O2 -fno-strength-reduce -I/usr/X11R6/include -I/include -Dlinux -D__i386__ -D_POSIX_SOURCE -D_BSD_SOURCE -D_SVID_SOURCE -DX_LOCALE -DFUNCPROTO=15 -DNARROWPROTO -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DEIGHTBIT -c rasmol.c -o rasmol.o > rasmol.c: In function `FetchCharacter': > rasmol.c:497: `WaitSet' has an incomplete type > rasmol.c:503: warning: passing arg 2 of `select' from incompatible pointer type > rasmol.c:503: warning: passing arg 3 of `select' from incompatible pointer type > rasmol.c:503: warning: passing arg 4 of `select' from incompatible pointer type > rasmol.c: At top level: > rasmol.c:112: storage size of `OrigWaitSet' isn't known > rasmol.c:113: storage size of `WaitSet' isn't known > make: *** [rasmol.o] Error 1 > > Though I may be confabulating things, I think some previous RasMol version (alas, > purged) compiled allright. > > OrigWaitSet and WaitSet are defined in rasmol.c as > > static struct fd_set OrigWaitSet; > static struct fd_set WaitSet; > > I grepped the sourcetree for fd_set with the following results: > > lrz:/usr4/model/RasMol/RasMol2 # grep -i fd_set * > ChangeLog.2: defined to allow struct fd_set to be properly defined. > [...] > rasmol.c:static struct fd_set OrigWaitSet; > rasmol.c:static struct fd_set WaitSet; > rasmol.c: { FD_SET(socket,&OrigWaitSet); > rasmol.c: FD_SET(FileNo,&OrigWaitSet); > rasmol.c: { FD_SET(SocketNo,&OrigWaitSet); > rasmol.c: FD_SET(i,&OrigWaitSet); > rasmol.c: status = select( WaitWidth, &WaitSet, (struct fd_set*)NULL, > rasmol.c: (struct fd_set*)NULL, &TimeOut ); > [...] > > The according lines in ChangeLog.2 are: > > [15/10/93] rasmol.c > Added #include to rasmol.c, when _SEQUENT_ is > defined to allow struct fd_set to be properly defined. > > Which doesn't seem to be relevant, the more so that according to > locate select.h doesn't dwell anywhere in my system. > > Any ideas what is going on? Thanks! > > Regards, > Eugene Leitl I encountered the same error recently after switching to linux kernel 2.0.29 from 2.0.0, with which the same rasmol source files would complie without a problem. Similarly the pre-compiled binary which used to work fine with 2.0.0 now returns a "cannot execute binary file" error. I don't know for sure but it seems that something in the recent distributions of gcc is missing or has changed, since it's not the only program I had this problem with. Eventually I managed to successfully compile by undefining "TERMIOS" in rasmol.h, since that's where the 'static struct' instructions which cause the error seem to be. Everything seems to be working as usual now, though this was only with the Rasmol2.6.tgz archive and not Rasmol2.6beta2.tgz. I haven't tried any of the things that others have mentioned. Cheers, Boris. ++++------+------+------+------+------+------+------+------+------+------+ From: Subject: Re: Please gzip your Chime PDB's! Date: Fri, 5 Mar 1999 14:31:36 +0000 (GMT) To: rasmol@dhcp-srv2.oit.umass.edu Dear All, (I wrote this after seeing all the messages about gziping pdb files. On rereading it I am worried that it sounds far more antagonistic than was my intention. Rather than try to tone it down, I'm sending it as it is, with a plea for it to be taken as a positive contribution rather than wholly negative!) Eric Martz wrote: > Most people who are authoring Chime sites on the web are not bothering to > gzip their PDB files. Gzipping the PDB files reduces file size ... > etc. However, most other molecular graphics software *doesn't* know how to un-gzip files on the fly. Doing this for any file of MIME type chemical/x-pdb would prevent anyone but Chime users (and of course RasMol users which is presumably where Chime inherits this ability from) from using your information, which seems a little unhelpful. Also, strictly speaking, a gzipped pdb file does not comply with *any* MIME-type any more, because you have turned it into binary and MIME-types use a more limited set of characters for the sake of portability. For Chime/Rasmol-specific MIME-types this would be fair enough though, and I understand that the files referenced by a Chime-focused web-page might not be easily followed by a non-Chime client any way. I didn't think the relevant MIME-types were specific to Chime and RasMol though and do we really want to hide our information from people who don't choose (or can't - see my earlier postings on my problems using Chime or RasMac on a Mac) to use the same software that we do. I don't mean to sound too picky though! I understand and applaud the motivation here. What else could we do instead? What I do is to edit the pdb file so that only the atoms that I actually want to display are present. Thats usually a lot less than the full Brookhaven entry and will have a corresponding effect on transfer time. Finally, with my NMR spectroscopists hat on, there really is no point using a pdb file containing a 30-model ensemble of strutures, gzipped or otherwise, if you only want to display a single structure. You'd be much better off picking one of the models as representative and putting that in a seperate file. Common practice used to be to submit a minimised average structure as a separate entry to the PDB. Better, and more modern practice is to identify within the REMARKS of an ensemble which member is the "closest to the mean" or best representative in some other way. If you *do* want to display multiple models (to demonstrate convergence, perhaps) then you probably only want to show CAs, or at the most backbone atoms, so again editing the file will almost always bring improvements in transfer rates. Andrew -------------------------------------------------------------------------------- Dr. Andrew Raine Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, United Kingdom Telephone: +44 223 333744 or 333499, email: A.R.C.Raine@bioc.cam.ac.uk -------------------------------------------------------------------------------- X-Authenticated: wm0p by cyrus.andrew.cmu.edu X-Licensed-To: Site License ++++------+------+------+------+------+------+------+------+------+------+ From: "Will McClure" Subject: Re: Please gzip your Chime PDB's! Date: Fri, 05 Mar 1999 10:11:59 -0500 To: A.R.C.Raine@bioc.cam.ac.uk, rasmol@dhcp-srv2.oit.umass.edu A solution to the point raised by Andrew's comments is to use a different suffix on the Gzipped PDB files. We use "filename.pdbgz", for example. We then set the server preferences to send out that file in the correct format. Chime receives it fine and unzips it when the EMBED SRC="filename.pdbgz" is used. Moreover, if the viewer chooses to "Save as..." from the Chime File menu, the coordinates are transferred as a plain text file. (On Macs, the file appears with the RasMol icon, i.e. a RSML filetype.) In other words, the viewer would never know that the file was Gzipped, except that the page loads about 4x faster than otherwise. -Will McClure --On Fri, Mar 5, 1999 2:31 PM +0000 A.R.C.Raine@bioc.cam.ac.uk wrote: > Eric Martz wrote: > >> Most people who are authoring Chime sites on the web are not bothering to >> gzip their PDB files. Gzipping the PDB files reduces file size ... > >> etc. > > However, most other molecular graphics software *doesn't* know how to > un-gzip files on the fly. Doing this for any file of MIME type > chemical/x-pdb would prevent anyone but Chime users (and of course > RasMol users which is presumably where Chime inherits this ability > from) from using your information, which seems a little unhelpful. > > Also, strictly speaking, a gzipped pdb file does not comply with *any* > MIME-type any more, because you have turned it into binary and > MIME-types use a more limited set of characters for the sake of > portability. > etc. References: <000401be662b$ee8f05d0$5b1c22c3@sergey> ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: Your can RAR your Chime PDB's! Date: Fri, 05 Mar 1999 09:44:51 -0800 To: rasmol@dhcp-srv2.oit.umass.edu At 12:17 PM 3/4/99 +0100, you wrote: >Hi, > >don't think that chime will read RAR-archives! > Indeed. While the RAR archiver looks interesting, and may have many useful features, it is not a *free*, *source code available*, *shared library available* archiving program like gzip. Gzip attains very good compression ratios for chemical files, and there is commonly available (free) executables for most platforms, and there is also source for both the programs and for shared library versions of the executables. In addition to that the Java language has built in support for gzip compress/uncompress, making it a very easy compression algorithm to support. Sergey Vasil'ev - Thanks for the pointer on RAR through, I will have to try and download it and have a look. It looks like it's ability to compress *across* files within the archive would be very, very useful for archives of many source files. -tim >Frank > >Sergey Vasil'ev wrote: > >> Hi all! >> >> If you use a lot of PDB files (like me) I think it'll be interesting for you >> to read about RAR archiver. >> You can use it on many platforms (DOS, Win32 console, Win32 GUI, Macintosh, >> OS/2, SCO, BSD, Linux, Sparc and HP-UX) and I can say that it is very >> useble in terms of diskspace and transferring rates :) >> >> http://www.rarsoft.com/rar_archiver.htm >> >> Sergey Vasil'ev >> >> /*------------------------------------------------ >> DNA-Protein Interaction DataBase project team. >> Belozersky Institute of Physico-Chemical Biology, >> Moscow State University & >> Inst. of Agricultural BioTechnology RAAS. >> 42 Timiryazevskaya St., >> Moscow 127550, RUSSIA >> email vasil@iab.ac.ru >> vasil@biocom.genebee.msu.su >> fax +7-095-9770947 >> ------------------------------------------------*/ > > > ++++------+------+------+------+------+------+------+------+------+------+ From: Tom Manderfield Subject: Re: Your can RAR your Chime PDB's! Date: Fri, 05 Mar 1999 12:57:59 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Excerpts from mail: 5-Mar-99 Re: Your can RAR your Chime.. by Tim Maffett@mdli.com > Indeed. While the RAR archiver looks interesting, and may have > many useful features, it is not a *free*, *source code available*, > *shared library available* archiving program like gzip. Has MDLI released Chime source code and/or shared libraries? Tom charset="koi8-r" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 ++++------+------+------+------+------+------+------+------+------+------+ From: "Sergey Vasil'ev" Subject: You can RAR your PDB's! Date: Fri, 5 Mar 1999 21:52:23 +0300 To: > Thanks for the pointer on RAR through, I will have to try and > download it and have a look. It looks like it's ability to compress > *across* files within the archive would be very, very useful for > archives of many source files. As our team work with many and many files of source code and files in PDB format, we tried for to find the best archiver for such kind of data files. After some experiments we stopped on RAR. If you work under Win32 (Win95/98/NT), I strongly recommended you to try WinRAR 2.50b5 (soon will be the final release). One more thing: you can compile UnRAR program (or UnRAR.dll) on any platform from free source code SY --- Sergey Vasil'ev References: <36DE4626.90CEDA01@rz.uni-sb.de> <000401be662b$ee8f05d0$5b1c22c3@sergey> ++++------+------+------+------+------+------+------+------+------+------+ From: Eugene Leitl Subject: Your can RAR your Chime PDB's! Date: Thu, 4 Mar 1999 22:50:40 +0100 (CET) To: rasmol@dhcp-srv2.oit.umass.edu Cc: Sergey Vasil'ev writes: > Hi all! > > If you use a lot of PDB files (like me) I think it'll be interesting for you > to read about RAR archiver. [...] Though this is off-topic, probably the hitherto best archiver is bzip2 ( .Z < .gz < .bz2 ). lrz:/usr4/vault/pub/pdb # head r14-ico.pdb ATOM 126 CA THR A1017 34.927 31.828 97.416 ATOM 133 CA VAL A1018 33.913 35.302 98.526 ATOM 140 CA ALA A1019 34.524 36.207 102.146 ATOM 145 CA SER A1020 32.670 39.482 101.745 ATOM 151 CA ILE A1021 30.687 40.859 98.851 ATOM 159 CA SER A1022 30.588 44.510 97.856 ATOM 165 CA SER A1023 27.593 46.273 99.455 ATOM 171 CA GLY A1024 26.637 50.008 99.547 ATOM 175 CA PRO A1025 24.271 52.365 101.388 ATOM 182 CA LYS A1026 20.879 50.817 102.496 lrz:/usr4/vault/pub/pdb # l r14-ico.pdb -rw-r--r-- 1 root 50 2666400 Jan 25 1998 r14-ico.pdb ^^^^^^^ original size lrz:/usr4/vault/pub/pdb # gzip --best r14-ico.pdb lrz:/usr4/vault/pub/pdb # l r14-ico.pdb.gz -rw-r--r-- 1 root 50 849199 Jan 25 1998 r14-ico.pdb.gz ^^^^^^ gzip --best size lrz:/usr4/vault/pub/pdb # gunzip r14-ico.pdb.gz lrz:/usr4/vault/pub/pdb # bzip2 r14-ico.pdb lrz:/usr4/vault/pub/pdb # l r14-ico.pdb.bz2 -rw-r--r-- 1 root root 494961 Jan 25 1998 r14-ico.pdb.bz2 ^^^^^^ bzip2 size Wow! Now I'm myself quite impressed. bzip2 is lots faster than gzip --best, too. As you can combine it with tar (gtar), it looks like a total winner to me. Regards, Eugene Leitl References: <0F6L00K4V1WH5Q@pobox1.oit.umass.edu> <36C2FAF4.327E4699@rorqual.cc.metu.edu.tr> ++++------+------+------+------+------+------+------+------+------+------+ From: Eugene Leitl Subject: compilation successful Date: Sun, 7 Mar 1999 00:44:36 +0100 (CET) To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu Thanks to everybody who responded. (Whew!). The Rasmol 2.6.4 from ftp://ftp.dcs.ed.ac.uk/pub/rasmol/ compiled smoothly, while crusty old RasMol26b2 did not. The only thing short of attaining nirvana: is there a 24-bit RasMol version out there? Having just 4 MByte video RAM, I'd hate to abandon my virtual 1280x1024 24 bit mode, you see... Regards, Eugene Leitl ++++------+------+------+------+------+------+------+------+------+------+ From: Barak Subject: Selecting functional groups Date: Sun, 07 Mar 1999 15:28:30 -0600 To: rasmol@dhcp-srv2.oit.umass.edu I have a moderately large organic molecule (>900 atoms) for which I'd like to be able select and highlight various functional groups--carboxyls, methoxys, quinones, aromatic rings, etc.--in that molecule without having to call them out by atomno or identify them all in the pdb file. Anyone have any experience or suggestions as to how to retrieve these groups generically, perhaps by using carefully crafted "select within" script? Phillip Barak, Assoc. Prof. Soil Science Univ of Wisconsin-Madison pwbarak@facstaff.wisc.edu http://www.soils.wisc.edu/~barak/ X-pmrqc: 1 ++++------+------+------+------+------+------+------+------+------+------+ From: "Michael Meredith" Subject: Newbie Question Date: Mon, 8 Mar 1999 15:31:39 -0000 To: rasmol@dhcp-srv2.oit.umass.edu Dear all, Two very basic questions for you all: 1. I am attempting to run scripts, generated in RasMol, using Netscape with the chime plugin. I know it is basic, but what is the simplest html I can use to call the script? 2. Is there a technical FAQ that I could use to avoid pestering the list? Thank you for all you help in advance. Michael Meredith **************************************** Dr Michael Meredith Course Designer (Immunology), University of Oxford, Department for Continuing Education, Rewley House, 1 Wellington Square, Oxford. OX1 2JA Tel: +44(01865)270 284 Fax: +44(01865)270 309 **************************************** ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: Identifying H-bonds (bug?) Date: Wed, 10 Mar 1999 11:04:10 +0200 To: RasMol list If you download the structure 2PAD and do the following commands: restrict 183-186 hbonds you see a hydrogen bond between Glu183.N (atom 1420) and Tyr186.O (atom 1444) However, if you cut just these four residues out of the file and try to display the H-bond, it doesn't show up: http://inn-prot.weizmann.ac.il/tutorials/secstr/pdb/2pad_turn.pdb (application/x-rasmol MIME) Does anyone have any idea why/how this is happening? Kurt -- --------------------------------------------------------------- Dr. Kurt Giles kurt@inn-prot.weizmann.ac.il Israeli National Node Biological Computing Unit Tel: +-972-8-9342614 Weizmann Institute of Science Fax: +-972-8-9466269 Rehovot 76100, Israel http://inn-prot.weizmann.ac.il/ --------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: James Milner-White Subject: Re: Identifying H-bonds (bug?) Date: Wed, 10 Mar 1999 10:11:11 +0000 To: rasmol@dhcp-srv2.oit.umass.edu The reason is probably that the calculation for placing the NH hydrogen atom needs the coordinates of the C, O and N atoms, where the C and O atoms come from the residue before. If the coordinates aren't there you get no hydrogen bond. James >If you download the structure 2PAD and do the following commands: > >restrict 183-186 >hbonds > >you see a hydrogen bond between Glu183.N (atom 1420) and Tyr186.O (atom >1444) > >However, if you cut just these four residues out of the file and try to >display the H-bond, it doesn't show up: > >http://inn-prot.weizmann.ac.il/tutorials/secstr/pdb/2pad_turn.pdb > >(application/x-rasmol MIME) > > >Does anyone have any idea why/how this is happening? > >Kurt > >-- >--------------------------------------------------------------- >Dr. Kurt Giles kurt@inn-prot.weizmann.ac.il >Israeli National Node >Biological Computing Unit Tel: +-972-8-9342614 >Weizmann Institute of Science Fax: +-972-8-9466269 >Rehovot 76100, Israel http://inn-prot.weizmann.ac.il/ >--------------------------------------------------------------- Dr E. James Milner-White Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, G128QQ, UK. E-mail: E.J.Milner-White@bio.gla.ac.uk FAX: +44(0)141-330-4620 Tel.: +44(0)141-330-5283 Research Interests: http://www.enzyme.gla.ac.uk/Biostructures/discoveries.html http://www.biochem.gla.ac.uk/BMB/Res/BSA/EJM.html Teaching Interests: http://www.enzyme.gla.ac.uk/Biostructures/teaching.html References: ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: Re: Identifying H-bonds (bug?) Date: Wed, 10 Mar 1999 12:39:38 +0200 To: rasmol@dhcp-srv2.oit.umass.edu James Milner-White wrote: > > The reason is probably that the calculation for placing the NH hydrogen > atom needs the coordinates of the C, O and N atoms, where the C and O atoms > come from the residue before. If the coordinates aren't there you get no > hydrogen bond. > James > Yes, this solved the problem. Thanks, Kurt -- --------------------------------------------------------------- Dr. Kurt Giles kurt@inn-prot.weizmann.ac.il Israeli National Node Biological Computing Unit Tel: +-972-8-9342614 Weizmann Institute of Science Fax: +-972-8-9466269 Rehovot 76100, Israel http://inn-prot.weizmann.ac.il/ --------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: hbonds in RasMol & Chime: CAUTION! Date: Wed, 10 Mar 1999 11:16:21 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Since Kurt Giles brought up hbonds in RasMol, it may be worth reminding/cautioning the subscribers to the RasMol list about the severe limitations of RasMol's hbond mechanism. In contrast to some other software (e.g. SwissPDB Viewer) and to what you might expect were you not informed otherwise, RasMol (also Chime) does not scan interatomic donor/acceptor distances to decide where hbonds should be drawn. Rather, it uses very simplistic rules about backbone hbonds in helices and strands, and between nucleotide base pairs ONLY. There are several consequences: 1. The majority of hbonds are never shown (all non-backbone hbonds!). 2. The hbonds shown are not always reasonable or correct. It is possible to show arbitrary hbonds with the 'set picking monitor' command. You can find hbonds in the Noncovalent Bond Finder at www.umass.edu/microbio/chime/find-ncb but one at a time. It would be very useful if there were a way to automatically generate a list of hbonded pairs as a script which could be run in RasMol/Chime to display all, or selected categories, of hbonds. The script could use a series of commands of the form 'monitor 1279 322', where the numbers are atom serial numbers, to draw monitor lines. Alternatively, in Chime only, it is possible to specify where some arbitrary bonds should be added (I forget the details but it is in the email history of this list), which allows them to have different thicknesses as with any other bonds (vs. the monitor line which can only be a single-pixel dotted line). Perhaps some of our subscribers can suggest freeware which will emit a list of hbonded pairs? The output could then be cast easily enough into the requisite script for RasMol/Chime. An example of case #2 above results from an error in file 1d66 in which one base pair was inadvertantly left out of Watson-Crick position (personal communication with the author). RasMol draws an hbond between the canonical WC atom pair regardless, producing a line which crosses several intervening atoms and covalent bonds!! I leave it as an interesting exercise for the reader to find this base pair out of the 19 present in this structure. An easy way to view it is to go to http://www.umass.edu/microbio/chime/dna/index.htm where the initial view shows RasMol's hbonds. Or for more flexibility (ability to click on atoms and report identities), you can go to http://www.umass.edu/microbio/chime/explorer/ type '1d66' in the PDB ID slot and press 'Load' (the coordinates will come directly from the PDB). The following commands will quickly produce a useful hbonds display. The aliases are given followed by the full commands as automatically expanded from the aliases by the Explorer: r dna # restrict dna [press Bkg button to change background from white to black] wf # wireframe coe # color cpk (COlor by Element) hb # hbonds 0.4;color hbonds white;set hbonds sidechain; cs # center selected Now press the Zoom button a few times and rotate to see the "long" hbond. Apologies to Roger Sayle -- this is not meant as a criticism but just a caution to users. As Roger knows I am one of RasMol's greatest enthusiasts and advocates! -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id OAA26904 ++++------+------+------+------+------+------+------+------+------+------+ From: Gerard Pujadas Subject: Re: hbonds in RasMol & Chime: CAUTION! Date: Wed, 10 Mar 1999 20:31:27 +0100 To: rasmol@dhcp-srv2.oit.umass.edu Hi to all, > >Perhaps some of our subscribers can suggest freeware which will emit a list >of hbonded pairs? The output could then be cast easily enough into the >requisite script for RasMol/Chime. > I use HBPLUS (http://www.biochem.ucl.ac.uk/~mcdonald/hbplus/home.html) and LIGPLOT (http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html) to obtain the list of hydrogen bond pairs. When you know them, then you can use the monitor command to visualize the hbonds. Unfortunately the thicknesses of the "hbond" cannot be modified. Perphaps, a good implementation of hbond representation could be a great improve for the next rasmol releases ... (I'm thinking in the message of Herbert J. Bernstein some weeks ago ...): ============================================================================== > After discussion with Roger Sayle, we have decided to bring at least >three of the current RasMol variants together into a common version. >Anyone using any of the following variants of RasMol is invited to submit >bug reports over the next couple of weeks to rasmol@bernstein-plus-sons.com: > > RasMol_2.6.4 (Roger Sayle's February 1999 version) > from ftp://ftp.dcs.ed.ac.uk/pub/rasmol/RasMol2.tar.gz > RasMol_2.6b2x1 (Arne Mueller's May 1998 variant) > from ftp://nexus.roko.goe.net/pub/rasmol/RasMol26b2x1.tar.gz > RasMol_2.6_CIF.1 (Herbert Bernstein's January 1999 variant) > from http://www.bernstein-plus-sons.com/software/rasmol > >If you are using any other versions and having a problem, please get one of >these three versions and check if your problem is reproducible with one of >these three versions. > > Sometime in mid-March, we will release version 2.7.0 of RasMol containing >as many of the features and bug fixes related to these three versions as we >can get to work in a single version in such a short time-frame, and will >then create versions 2.7.1, 2.7.2, etc. as problems are reported. Features >from other variants of RasMol will be considered for inclusion in RasMol >2.7.n if the features are particularly popular and if available resources >(or helpful colleagues) make inclusion of those features feasible. When we >are done, probably in the early fall, the resulting best version should be >a reasonably stable and reliable single version combining most of the >features of the major current variants of RasMol. > > -- Herbert J. Bernstein > ============================================================================== Best regards !!! Gerard. =========================================================================== DR. GERARD PUJADAS BIOTECNOLOGIA COMPUTACIONAL DEPT. BIOQUIMICA I BIOTECNOLOGIA E-MAIL: pujadas@quimica.urv.es UNIV. ROVIRA I VIRGILI PHONE: 34-977 559565 PLAÇA IMPERIAL TARRACO 1 FAX: 34-977 559597 43005 TARRAGONA (CATALONIA) STATE: SPAIN (EUROPEAN UNION) =========================================================================== ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Presenting RasMol-Saved Scripts in Chime Date: Mon, 15 Mar 1999 11:36:26 -0500 To: michael.meredith@continuing-education.oxford.ac.uk Cc: rasmol@dhcp-srv2.oit.umass.edu Dear Michael: Are you aware of the template I provide, downloadable, with lots of bells and whistles, to do exactly this? http://www.umass.edu/microbio/chime/prsswc/template.htm I don't recommend writing your own from scratch as it takes too long to do a good job. Better to take my template and modify whatever you wish. But only make one change at a time or debugging can be horrendous! There is lots of info at my site on how to build Chime presentations. You should also take a look at the Protein Explorer http://www.umass.edu/microbio/chime/explorer/ which you can download and modify if you wish. It includes a command line interface and much much more not in the template mentioned above. At 3/8/99, you wrote: >Dear all, > >Two very basic questions for you all: > >1. I am attempting to run scripts, generated in RasMol, using >Netscape with the chime plugin. I know it is basic, but what is the >simplest html I can use to call the script? > >2. Is there a technical FAQ that I could use to avoid pestering the >list? > >Thank you for all you help in advance. > >Michael Meredith > > >**************************************** >Dr Michael Meredith >Course Designer (Immunology), >University of Oxford, >Department for Continuing Education, >Rewley House, >1 Wellington Square, >Oxford. >OX1 2JA > >Tel: +44(01865)270 284 >Fax: +44(01865)270 309 >**************************************** > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by dhcp-srv2.oit.umass.edu id DAA02270 ++++------+------+------+------+------+------+------+------+------+------+ From: Jean Richelle Subject: MDL format of files created by RasMol Date: Thu, 18 Mar 1999 09:39:07 +0100 (MET) To: rasmol@dhcp-srv2.oit.umass.edu Dear all, First I noted that the file created with the option "Save As" (under Mac), choosing MDL Mol format, is in PDB format, ... :-(. Next I saved my molecule using the command "save mdl blabla.mol" and tried to read (unsuccessfuly) the file in ISISDraw. Looking at the file and comparing with a MOL file created by ISIDraw, even if the formats look similar, there are many differences. Could somebody give me some tips ? (well I can imagine that what I'm trying to do is completely senseless, going from 2D <-> 3D graphic programs, but I'm not completely sure - why so having the same format in both applications ?) Thanx in advance, Jean _____________________________________________________________________________ Jean Richelle Unité de Conformation des Macromolécules Biologiques Tel: +32 (0)2 650 3587 Université libre de Bruxelles FAX: +32 (0)2 648 8954 av. FD Roosevelt 50 - CP160/16, B-1050 Bruxelles, Belgium _____________________________________________________________________________ X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by dhcp-srv2.oit.umass.edu id FAA02467 ++++------+------+------+------+------+------+------+------+------+------+ From: Jean Richelle Subject: Re: MDL format of files created by RasMol Date: Thu, 18 Mar 1999 10:57:10 +0100 (MET) To: rasmol@dhcp-srv2.oit.umass.edu Dear all, This is a correction to my previous message, I apologize for the "noise" on the list. The first point (saving in MDL format from the Mac menu) still holds. But now concerning the second point. In the meantime, I found the complete format specification, and the file from RasMol (and of course from ISISDraw) is complient (my mistake: I didn't figure out that absence of data was meaning 0). The error I got in reading the RasMol generated file seems to come from a minor problem of bond order, possibly in an aromatic ring. Thanks for your patience, Jean On Thu, 18 Mar 1999, Jean Richelle wrote: > Dear all, > > First I noted that the file created with the option "Save As" (under Mac), > choosing MDL Mol format, is in PDB format, ... :-(. > > Next I saved my molecule using the command "save mdl blabla.mol" and tried > to read (unsuccessfuly) the file in ISISDraw. Looking at the file and > comparing with a MOL file created by ISIDraw, even if the formats > look similar, there are many differences. Could somebody give me some > tips ? (well I can imagine that what I'm trying to do is completely > senseless, going from 2D <-> 3D graphic programs, but I'm not completely > sure - why so having the same format in both applications ?) > > Thanx in advance, > > Jean > > _____________________________________________________________________________ > Jean Richelle > Unité de Conformation des Macromolécules Biologiques Tel: +32 (0)2 650 3587 > Université libre de Bruxelles FAX: +32 (0)2 648 8954 > av. FD Roosevelt 50 - CP160/16, B-1050 Bruxelles, Belgium > _____________________________________________________________________________ > > _____________________________________________________________________________ Jean Richelle Unité de Conformation des Macromolécules Biologiques Tel: +32 (0)2 650 3587 Université libre de Bruxelles FAX: +32 (0)2 648 8954 av. FD Roosevelt 50 - CP160/16, B-1050 Bruxelles, Belgium _____________________________________________________________________________ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer beta 0.98 available Date: Thu, 18 Mar 1999 09:57:27 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Version 0.98 of the Protein Explorer is now available at www.umass.edu/microbio/chime/explorer. Several Macintosh problems have been fixed in this version, thanks to feedback from several colleagues, especially Tim Driscoll. A new feature has been added: verbose explanations of the RasMol-style atom identifications reported when you click on an atom (can be disabled in the Preferences). This was an interesting challenge and I'm sure I haven't done it terribly well, but hopefully it is better than nothing. For example "2HH1" is explained as "Element: H 2nd on eta (7th) #1". Try it on the unusual atoms in your favorite molecule and let me know how I can improve it. "CD" is reported as "Element: Cd" when group is "CD", else "Element: C delta (4th)". Check the list of two-letter elements in shared/pick2.js to see if your favorites are there (or just click on them). Greek letters are explained out to eta; are there any cases of theta positions or beyond? If a Hetero residue name contains a digit, the explanation shows it in brackets, e.g. [B7G] with a reminder to use the brackets when searching by residue name. The PE can be downloaded for local use or to adapt its html/javascript to other purposes. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas Gunda" Subject: Re: MDL format of files created by RasMol Date: Thu, 18 Mar 1999 15:56:53 +1 To: rasmol@dhcp-srv2.oit.umass.edu Jean Richelle wrote: > Dear all, > > First I noted that the file created with the option "Save As" (under Mac), > choosing MDL Mol format, is in PDB format, ... :-(. > > Next I saved my molecule using the command "save mdl blabla.mol" and tried > to read (unsuccessfuly) the file in ISISDraw. Looking at the file and > comparing with a MOL file created by ISIDraw, even if the formats > look similar, there are many differences. Could somebody give me some > tips ? (well I can imagine that what I'm trying to do is completely > senseless, going from 2D <-> 3D graphic programs, but I'm not completely > sure - why so having the same format in both applications ?) > > Thanx in advance, > > Jean > The structure of the molfile in nutshell is as follows: At first 3 lines (may be empty) 4th line: no. of atoms and bonds is mandatory, at the end 1 - lines after the bonds (now M END), V2000 version stamp next 7 lines: coordinates, atom symbol, 0s: charges, etc info, if any next 7 lines: bonds: from atom - to atom, bond type. 0s: stereochemistry etc if any. after: extra infos, ends with M END if version is V2000 ................................ -ISIS- 03189915342D 7 7 0 0 0 0 0 0 0 0 1 V2000 -0.7583 -0.3417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7583 -1.1667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6657 -1.1667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6657 -0.3417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0463 -1.5750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0463 0.0750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0463 0.9000 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 3 4 1 0 0 0 0 1 6 1 0 0 0 0 2 5 1 0 0 0 0 5 3 2 0 0 0 0 4 6 2 0 0 0 0 1 2 2 0 0 0 0 6 7 1 0 0 0 0 M END ; only if V2000 ----------------------------------------------- Mol files may contain many other data beyond pure coordinates, therefore the outlook of the molfile can differ from program to program, and some programs do not print the zeros, if there are no extra info. The absolut minimum is: 3 lines at the beginning, number of atoms and bonds, coordinates and atom symbol bonds and bond types. E-mail me a problematic file, let me have a look into it. regards Tamas ************************************************************************ Dr Tamas E. Gunda phone: (+36-52) 316666-2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 http://dragon.klte.hu/~gundat H-4010 Debrecen Hungary ************************************************************************ boundary="------------B9D9A4A76178676322FF44CF" X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: "Jeffrey J. Ayres" Subject: Using Adobe PageMill Date: Sat, 20 Mar 1999 19:13:18 -0700 To: rasmol@dhcp-srv2.oit.umass.edu This is a multi-part message in MIME format. --------------B9D9A4A76178676322FF44CF Hello, I would like to view and build web pages using CHIME. I have already produced several CHIME web pages using Netscape Navigator 4.0. I would like to use Adobe PageMill to produce them. I attempted installation of CHIME 2.0 in PageMill by downloading the .zip file in Browser Plugins, however the installation halted itself, giving the error message that a browser was not located. Chime 1.02 installation did go to completion, however PageMill displayed a missing plugin message. Does anyone know of a way to install Chime into PageMill 2.0? Jeff Ayres --------------B9D9A4A76178676322FF44CF name="jayres.vcf" Content-Description: Card for Jeffrey J. Ayres Content-Disposition: attachment; filename="jayres.vcf" begin:vcard n:Ayres;Jeffrey x-mozilla-html:FALSE url:http://www.mc.maricopa.edu/users/jayres/org_molecules http://www.geocities.com/yosemite/trails/5681 org:Yavapai Community College;Math Sciences/ Learning Center adr:;;;Prescott;AZ;; version:2.1 email;internet:jayres@ycpo.yavapai.cc.az.us jeffayres@hotmail.com title:Adjunct Faculty Chemistry, Tutor Math/Chemistry note:Views taken are not necessarily those of Yavapai College. x-mozilla-cpt:;0 fn:Jeffrey Ayres end:vcard --------------B9D9A4A76178676322FF44CF-- boundary="----=_NextPart_000_0004_01BE7541.112DF0A0" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 X-Warn: Sender was arist@debitel.net ++++------+------+------+------+------+------+------+------+------+------+ From: "Arist Engelmann" Subject: chimescript and rasmol commands Date: Tue, 23 Mar 1999 15:23:13 +0100 To: This is a multi-part message in MIME format. ------=_NextPart_000_0004_01BE7541.112DF0A0 charset="iso-8859-1" Hello everybody I am currently using chime 2.0 to view molecules in websites for my pupils. I would like to do a script with a button for the chime = plugin=20 like chime menue . How can I do so? =20 Thanks a lot in advance Arist Engelmann Max Born Gymnasium Germering ------=_NextPart_000_0004_01BE7541.112DF0A0 charset="iso-8859-1"

Hello everybody
I am currently using chime 2.0  to view = molecules=20 in websites
for my pupils. I would like to do a script with a button=20 for the chime plugin
like chime menue <Options Sprout Hydrogens>.
How can I do so? 
Thanks a lot in advance
 
Arist Engelmann
Max Born Gymnasium Germering
------=_NextPart_000_0004_01BE7541.112DF0A0-- ++++------+------+------+------+------+------+------+------+------+------+ From: John Tweedie Subject: Select None in Chime 2 Date: Thu, 25 Mar 1999 14:09:05 +1200 To: rasmol@dhcp-srv2.oit.umass.edu Is there a way to deselect all atoms in Chime 2 without "Selecting All" and then "Inverting Selection"? Thanks John Tweedie John W. Tweedie Phone (Office): (64) (6) 350 4804 Associate Professor in Biochemistry Phone (Home): (64) (6) 358 0150 Institute of Molecular BioScience Fax: (64) (6) 350 5688 College of Science E-mail: j.tweedie@massey.ac.nz Massey University PO Box 11-222 Palmerston North New Zealand ++++------+------+------+------+------+------+------+------+------+------+ From: "Jesus M. Sanz" Subject: New page in Spanish Date: Thu, 25 Mar 1999 12:48:49 +0100 To: rasmol@dhcp-srv2.oit.umass.edu Dear all, Finally, I have overcome most of the problems with my server and I'm able to present the following Chime-based page: http://cbmc.umh.es/jmsanz/est2/est3/estructuras.htm I hope there are no technical problems anymore. At the moment, only the version in Spanish is available, although I think that most Chime users will not have problems in using it. It is based on the good old templates provided by Eric Martz, and since I'm not an expert in HTML, Javascript or those kind of things, I have not improved anything with respect to such templates. Thus, the optimal configuration seems to be Netscape 3.04 and Chime 1.0, but using Netscape 4.5 or Internet Explorer 4.0 with Chime 2.0 yields relatively good results. I have included some of Eric's scripts, but translated to Spanish. This is especially good for Spanish-speaking students whose level of English is not terribly high. There's an Acknowledgments page that I hope will be enough, but if some of you feel that you're under-represented, or have any sort of suggestions, please let me know. Dr. Jesus Sanz -------------------------------------------------------------------------- Prof. Jesus M. Sanz Tel:(34) 966 658 761 Dep. Bioquimica y Biologia Molecular Fax:(34) 966 658 780 Universidad Miguel Hernandez E-mail: jmsanz@umh.es c/ Monovar s/n, Poligono Carrus, ELCHE, 03206-Alicante, SPAIN "Asombrarse es la esencia de la vida" M. C. Escher -------------------------------------------------------------------------- References: <3.0.3.32.19990325124849.006952d8@mussol.umh.es> ++++------+------+------+------+------+------+------+------+------+------+ From: " Dr. Frank Eblinger" Subject: Re: New page in Spanish Date: Thu, 25 Mar 1999 13:03:19 +0100 To: rasmol@dhcp-srv2.oit.umass.edu Dear Jesus, tried to open your page (e.g. beta turn peptide). The page is loaded but the structur not! I use Netsc. 4.05 and Chime 2 for windows. Any suggestons? Frank References: x-mac-creator="4D4F5353" ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Select None in Chime 2 Date: Thu, 25 Mar 1999 07:31:19 +0000 To: rasmol@dhcp-srv2.oit.umass.edu John Tweedie wrote: > Is there a way to deselect all atoms in Chime 2 without "Selecting All" and > then "Inverting Selection"? > > Thanks > > John Tweedie > > John W. Tweedie Phone (Office): (64) (6) 350 4804 > Associate Professor in Biochemistry Phone (Home): (64) (6) 358 0150 > Institute of Molecular BioScience Fax: (64) (6) 350 5688 > College of Science E-mail: j.tweedie@massey.ac.nz > Massey University > PO Box 11-222 > Palmerston North > New Zealand John, You can use "restrict none" to deselect all atoms in Chime & Rasmol; although this makes them all disappear from view, that's the only reason I've come across for wanting to deselect everything. Tim -- ******************** Timothy Driscoll UMass Amherst Molecular and Cellular Biology Chemistry-Biology Interface Program * Department of Chemistry Amherst College Amherst, MA 01002 413 542 2738 * http://merckx.chem.amherst.edu/tdriscoll/ ******************** References: <002501be7538$cce91bc0$87d1a8c1@arist> x-mac-creator="4D4F5353" ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: chimescript and rasmol commands Date: Thu, 25 Mar 1999 08:13:36 +0000 To: rasmol@dhcp-srv2.oit.umass.edu Arist, The quickest answer to your question is probably for you to check out http://www.mdli.com/download/chime/csdocs/chimehelp2.html#Dev1 This is MDLI's brief intro to writing your own web pages that incorporate Chime. It is fairly limited but a good place to start, and it does point to other, more comprehensive resources (like Eric Martz's Rasmol and Chime pages - http://www.umass.edu/microbio/rasmol) which are also a great place to get info on this topic. If you come up with more specific questions along the way, don't hesitate to post them. To get your started, I've also pasted at the bottom of this message the html code for a simple Chime page. Copy everything between and (inclusive) to a text document, put the name of your favorite pdb file in place of the text in CAPS, save it in the same dir as this pdb file, then open it using Netscape's File/Open. ******************** Timothy Driscoll UMass Amherst Molecular and Cellular Biology Chemistry-Biology Interface Program * Department of Chemistry Amherst College Amherst, MA 01002 413 542 2738 * http://merckx.chem.amherst.edu/tdriscoll/ ******************** Arist Engelmann wrote: > Hello everybody > I am currently using chime 2.0 to view molecules in websitesfor my > pupils. I would like to do a script with a button for the chime > pluginlike chime menue .How can I do > so?Thanks a lot in advance Arist EngelmannMax Born Gymnasium Germering A simple Chime page, with a button: A Simple Chime Page This button renders a cartoon view, colored by secondary structure with hetero atoms spacefilled and in CPK. !!!You can also attach a button to an spt file (i.e., one saved from Rasmol or written by hand). Just replace the script = "..." with src="YOUR_SCRIPT_NAME.spt" Enjoy! charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.0810.800 ++++------+------+------+------+------+------+------+------+------+------+ From: "Tjaard Pijning" Date: Fri, 26 Mar 1999 08:22:28 +0100 To: Hello I am writing some chime pages and would like to know the meaning of the numbers in the "move" instruction e.g. move 30 0 0 +100 100 50 0 0 5 30 This command seems very useful, but I can't find it in the RasMol help. Regards, Ing. Tjaard Pijning Protein Crystallography Group University of Groningen Nijenborgh 4 9747 AG Groningen tel : (31)(0)50 3634385 email : pijning@chem.rug.nl References: <199901170503.AAA20324@dhcp-srv2.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Robert M. Horton" Subject: Chime/Rasmol Scripting Wizards Date: Thu, 25 Mar 1999 23:49:39 -0800 To: rasmol@dhcp-srv2.oit.umass.edu Dear Chime/RasMol users; I have just uploaded a prototype of my Chime/RasMol Scripting Wizard to http://www.attotron.com/pub/CS/ChScript.htm This is a collection of Javascript pages that call and respond to one another. Here is an outline of their hierarchy: === Chime Scripter / \ Add Molecule Wizard Add Button Wizard \ / Script Wizard | Expression Wizard === Each Wizard contains a form that lets you pick from available options. When you open the Chime Scripter and click "Add Molecule", a new window is opened containing the Add Molecule Wizard, which assists in creating an EMBED tag for a new molecule. If you want to add a RasMol script to the tag, the Script Wizard is called in yet another window. If you need to add an atom expression to a script command, the Expression Wizard is called. Each window returns its results back to a text area of the window that called it. This works OK on the Mac, but it has a few bizarre behaviors on Win95. It requires NS4; 4.03 seems to give some non lethal error messages that 4.5 does not (haven't tried IE4 yet) Features: - "verbose" mode includes comments in the script. Comments from expressions are added to comments from the command that uses the expression. Comments are the same phrases used on the pull-down menus. Sometimes the grammar comes out better than other times. :) - option expansion fills in variable values using find/replace with regular expressions (new capability of 4th generation browsers). - the list of available target molecules in the Add Button wizard is created dynamically based on the current set of molecule EMBED tags. - some input validations are in place (try adding a button without picking a target.) - the copies of the help files it refers you to (it just references the appropriate anchor in either the rasmol manual or the Chime embedded tags page) depend on whether you are using the Wizard from the Net or from a local file. - nested "within" commands are created by the Expression Wizard invoking copies of itself. I would greatly appreciate your feedback on the potential usefulness of this approach. If there is an audience for it, I'll try to polish up the bugs, make the interface more consistent, work on more descriptive descriptions, etc. If anyone would like a local copy, I can zip the folder together to facilitate downloading. -- Robert M. Horton, Ph.D. 0 []~ ~ ~ ~ http://www.attotron.com ~ ~ ~ ~[] 0 |-/_| rmhorton@attotron.com |_\-| -\_|| He travels swiftest who telecommutes. ||_/- ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas Gunda" Subject: Re: move/chime Date: Fri, 26 Mar 1999 09:37:06 +1 To: rasmol@dhcp-srv2.oit.umass.edu Cc: T.Pijning@chem.rug.nl Ing. Tjaard Pijning wrote: > Hello > > I am writing some chime pages and would like to know > the meaning of the numbers in the "move" instruction > e.g. > > move 30 0 0 +100 100 50 0 0 5 30 > > This command seems very useful, but I can't find it in the > RasMol help. Regards, > The Move command exists only in Chime, but not in Rasmol: Here it is, as copied from Chime help found at umass: --- Move Syntax: move {} Xrot YRot ZRot Zoom XTrans YTrans ZTrans Slab TotalTime FPS MaxAccel The Chime move command allows the user to specify RELATIVE values for various view parameters, and Chime will 'animate' the structure in steps over 'TotalTime' to reach the targets implied by the relative arguments. Each of the arg (Xrot through Slab) is the RELATIVE CHANGE over the entire move. Total time is the 'target' total time for the entire animation FPS is the 'target' frames per second for the animation. If the machine cannot keep up then the movement is accelerated, in integral steps, depending on how far behind it is (in order to keep up with the target times) The MaxAccel argument is the maximum rate that you will allow the move to be accelerated on slow machines. MaxAccel default is maximum amount you will allow the acceleration to go is 5, and you may LEAVE THIS ARG OFF The default FPS is 30, and you may also LEAVE THIS ARG OFF All other args are required. [observations from Eric Martz:] -Actual time will never be less than total time. -Actual time will exceed total time only when (accel > MaxAccel) is needed. -Actual FPS (aFPS) will never exceed target FPS (tFPS). -aFPS can be less than tFPS up to tFPS/aFPS=MaxAccel. Acceleration is an integral divisor for tFPS. Thus, the if MaxAccel=5 and tFPS=30, the largest jumps possible would be 30/5 = 6 = max aFPS. -The acceleration occurs at more than one point during the move. Thus the first few frames can be at 30 FPS (hence small rotations), then it can drop to 15 FPS (twice as much rotation per frame, accel=2), then to 10 FPS (accel=3), then to 7 FPS (accel=4), then to 6 FPS (accel=5), but no lower if MaxAccel=5. ----- Hope this helps Tamas Gunda ************************************************************************ Dr Tamas E. Gunda phone: (+36-52) 316666-2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 http://dragon.klte.hu/~gundat H-4010 Debrecen Hungary ************************************************************************ References: <001301be7759$679400a0$66237d81@chem.rug.nl> x-mac-creator="4D4F5353" ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: move command in Chime Date: Fri, 26 Mar 1999 07:55:37 +0000 To: rasmol@dhcp-srv2.oit.umass.edu One place to find the answer to your question is in the old Chime 0.99 Manual Partial Draft (http://www.umass.edu/microbio/chime/manual/chimeman.htm#move), located at Eric Martz's Chime homepage. -- ******************** Timothy Driscoll UMass Amherst Molecular and Cellular Biology Chemistry-Biology Interface Program * Department of Chemistry Amherst College Amherst, MA 01002 413 542 2738 * http://merckx.chem.amherst.edu/tdriscoll/ ******************** Tjaard Pijning wrote: > Hello > > I am writing some chime pages and would like to know > the meaning of the numbers in the "move" instruction > e.g. > > move 30 0 0 +100 100 50 0 0 5 30 > > This command seems very useful, but I can't find it in the > RasMol help. Regards, > > Ing. Tjaard Pijning > Protein Crystallography Group > University of Groningen > Nijenborgh 4 > 9747 AG Groningen > tel : (31)(0)50 3634385 > email : pijning@chem.rug.nl pdb-l@rcsb.org ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Feedback from Chime Resources Date: Fri, 26 Mar 1999 09:13:24 -0500 To: "Raymond Costantini" Cc: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu, On 3/24/99, Raymond Costantini wrote to the RasMol email list:
Eric-
Can I run chime on Internet Explorer or do I have to have Netscape?
Thanks!
Ray
x_ray@email.msn.com

Chime will work partially, sometimes, and sort-of on MSIE. See www.mdli.com/support/chime for details.
On MSIE, if you get it to work at all, you'll get some images.  This often misleads people -- they see molecules so they assume Chime is "working" in MSIE.  The images often will not be the correct images, and many functions which work in Netscape won't work at all in MSIE.  So if you're going to use Chime, install Netscape 4.5. There is nothing to prevent you from having both Netscape and MSIE installed and using MSIE for everything else.

This dichotomy is because Netscape defined the plugin (Chime is a plugin) and MSIE has never felt it important to support plugins fully.  It is not within the control of MDL (authors of Chime) unless they were to write a completely different version for MSIE. Since they aren't even supporting SGI or linux Netscape due to limited resources for freeware development, supporting MSIE in this way is out of the question, I imagine.

-Eric
- - -
Eric Martz, Professor (Immunology), Dept Microbiology
U Mass, Amherst MA US 01003-5720

++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Documentation for Chime's 'move' command Date: Fri, 26 Mar 1999 09:59:10 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Documentation for freeware seems usually to get the short end of the stick. Due to MDL's limited resources for this freeware project, Chime documentation is really a mess. Frustrating, but we have to remember to be thankful that MDL has given us such a powerful and unique tool!! Anyway, at my Chime page http://www.umass.edu/microbio/chime/index.html you can find some of the things missing from MDL's site, including the move command at http://www.umass.edu/microbio/chime/manual/chimeman.htm At 3/26/99, you wrote: >Hello > >I am writing some chime pages and would like to know >the meaning of the numbers in the "move" instruction >e.g. > >move 30 0 0 +100 100 50 0 0 5 30 > >This command seems very useful, but I can't find it in the >RasMol help. Regards, > >Ing. Tjaard Pijning >Protein Crystallography Group >University of Groningen >Nijenborgh 4 >9747 AG Groningen >tel : (31)(0)50 3634385 >email : pijning@chem.rug.nl > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: reposting Re:chimescript and rasmol commands Date: Fri, 26 Mar 1999 10:24:02 +0000 To: Rasmol List This is a multi-part message in MIME format. --------------6B45FB77C3AEC99E6684F3F7 To the Rasmol List, I have just been told that a recent message that I posted to this list crashes Eudora email (this message contained a short piece of html code inline). My apologies if this has caused you problems. I am reposting the message with the html as a separate attachment. Tim Driscoll Arist, The quickest answer to your question is probably for you to check out http://www.mdli.com/download/chime/csdocs/chimehelp2.html#Dev1 This is MDLI's brief intro to writing your own web pages that incorporate Chime. It is fairly limited but a good place to start, and it does point to other, more comprehensive resources (like Eric Martz's Rasmol and Chime pages - http://www.umass.edu/microbio/rasmol) which are also a great place to get info on this topic. If you come up with more specific questions along the way, don't hesitate to post them. To get your started, I've also attached the html code for a simple Chime page. All you have to do is put the name of your favorite pdb file in place of the text in CAPS, save it in the same dir as this pdb file, then open it using Netscape's File/Open. ******************** Timothy Driscoll UMass Amherst Molecular and Cellular Biology Chemistry-Biology Interface Program * Department of Chemistry Amherst College Amherst, MA 01002 413 542 2738 * http://merckx.chem.amherst.edu/tdriscoll/ ******************** Arist Engelmann wrote: > Hello everybody > I am currently using chime 2.0 to view molecules in websitesfor my > pupils. I would like to do a script with a button for the chime > pluginlike chime menue .How can I do > so?Thanks a lot in advance Arist EngelmannMax Born Gymnasium Germering --------------6B45FB77C3AEC99E6684F3F7 name="untitled" Content-Description: Unknown Document Content-Disposition: inline; filename="untitled" A Simple Chime Page This button renders a cartoon view, colored by secondary structure with hetero atoms spacefilled and in CPK. --------------6B45FB77C3AEC99E6684F3F7-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Guestbook operational again Date: Fri, 26 Mar 1999 19:05:04 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Last June, we provided a guestbook at our Molecular Visualization Freeware/RasMol Home Page/UMass Chime Resources Site. This Guestbook allows visitors to the site to provide links to resources elsewhere on the web. In particular, links to new Chime tutorials or resources can be added to the "Education: Tutorials on Molecules" section of the Guestbook. In the longer range we are working to provide a 'visitor-maintained index' (VMI) which will allow visitors to insert new entries directly into the World Index of Animated Tutorials in Chime (www.umass.edu/microbio/rasmol/tutbymol.htm), but the guestbook is better than nothing until we have the VMI implemented. (The VMI idea was detailed in an earlier message to this list.) Due to circumstances beyond our control, the Guestbook was not operational between approximately November 1998 and today. Thanks to the generosity of Phil Bourne and the Research Collaboratory for Structural Bioinformatics (home of the new PDB, www.rcsb.org), the Guestbook is operational again. Thanks also to Srinivas Turaga who reinstalled it. The Guestbook (extensively linked into the RasMol and Chime sites mentioned above) is now at molvis.sdsc.edu/guestbk/guestbkc.htm -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ x-mac-creator="4D4F5353" ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Chime view show command Date: Mon, 29 Mar 1999 08:35:09 +0000 To: Rasmol List Can anyone provide any insight on how Chime positions a molecule in 3D space? I'm trying to restore a p-articular view using the move command. I can query Chime for the absolute position of the molecule using "view show" and get a series of numbers corresponding to rotX rotY rotZ zoom etc. Unfortunately, a simple move command based on those values does not always work. For example: starting: view set 0 0 0 # i.e., the default reset position new: view set 45 45 45 # a rotation about each axis 45 degrees \to get from new to starting position, the following DO NOT WORK (and I don't know why): move -45 -45 -45 0 0 0 0 0 1 # all in one move move 0 0 -45 0 0 0 0 0 1 #as per Chime manual, rotating about z then y then x then move 0 -45 0 0 0 0 0 0 1 then move -45 0 0 0 0 0 0 0 1 In addition, I can rotate about either the X OR the Z axis as much as I want and restore the original view with a move command (as long as the rotation is about ONLY ONE AXIS). I can do the same about the Y axis BUT ONLY UP TO 90! Anything greater than a "rotate y 90" yields strange "view set" values in which all three rotation values are changed: "rotate x 45" yields "view set 45 0 0" and can be fixed by "move -45 0 0 0 0 0 0 0 1" # okay so far "rotate y 45" yields "view set 0 45 0" and can be fixed by "move 0 -45 0 0 0 0 0 0 1" # still fine "rotate x 95" yields "view set 95 0 0" and can be fixed by "move -95 0 0 0 0 0 0 0 1" # great! "rotate y 95" yields "view set 180 85 -180" and can not be fixed with a simple move # uh oh :( Help? Tim Driscoll -- ******************** Timothy Driscoll UMass Amherst Molecular and Cellular Biology Chemistry-Biology Interface Program * Department of Chemistry Amherst College Amherst, MA 01002 413 542 2738 * http://merckx.chem.amherst.edu/tdriscoll/ ******************** ++++------+------+------+------+------+------+------+------+------+------+ From: REVET Bernard Subject: Rasmol under Linux Redhat 5.1-stb virgin Date: Mon, 29 Mar 1999 21:18:54 +0100 To: rasmol@dhcp-srv2.oit.umass.edu Dear Rasmol users While reading the problems encountered by rasmol users I found out that many had to pass through a similar difficulty while using Rasmol under Linux I have been using Rasmol under Windows 95 with no problem with a STB virgin graphic card. However on the same machine under Linux redHat 5.1 I have not yet succeeded. Last version 2.6.4 compiles correctly but I got the message no suitable display detected! Even if I modify DEPTHDEF = -DTWENTYFOURBIT in the Imakefile which was accepted at the compilation I got [8bit version] after the command rasmol If anyone has a solution to correctly modify, compile or use Rasmol under Linux, 24bit I will deeply appreciate to know it. By the way Rasmol is great ! Best regards Bernard Revet References: <9903292118.ZM17483@nardos.igr.fr> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: Rasmol under Linux Redhat 5.1-stb virgin Date: Mon, 29 Mar 1999 15:03:00 +0000 To: rasmol@dhcp-srv2.oit.umass.edu REVET Bernard wrote: > > Dear Rasmol users > > While reading the problems encountered by rasmol users I found out that > many had to pass through a similar difficulty while using Rasmol under Linux > > I have been using Rasmol under Windows 95 with no problem with a > STB virgin graphic card. However on the same machine under Linux redHat > 5.1 I have not yet succeeded. > Last version 2.6.4 compiles correctly but > I got the message no suitable display detected! > Even if I modify > DEPTHDEF = -DTWENTYFOURBIT in the Imakefile > which was accepted at the compilation > I got [8bit version] after the command rasmol > If anyone has a solution to correctly modify, compile or use Rasmol under > Linux, 24bit I will deeply appreciate to know it. > By the way Rasmol is great ! > Best regards > Bernard Revet Hi, run your X-Server with 32 bit and apply the follwing changes to the rasmol.h file: #define THIRTYTWOBIT /* #define SIXTEENBIT */ /* #define EIGHTBIT */ As far as I know there's no 'direct' support for 24 bit in rasmol, so your "-DTWENTYFOURBIT" may be without any effect ... . greetings, Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)171 2693405 | Fax : +44-(0)171 269 3258 email : a.mueller@icrf.icnet.uk | http://www.icnet.uk/bmm/ <"Re: Rasmol under Linux Redhat 5.1-stb virgin"@igr.fr> (Mar 29, 3:03pm) References: <9903292118.ZM17483@nardos.igr.fr> <36FF9624.16F165CB@icrf.icnet.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: REVET Bernard Subject: Re: Rasmol under Linux Redhat 5.1-stb virgin Date: Mon, 29 Mar 1999 21:46:40 +0100 To: rasmol@dhcp-srv2.oit.umass.edu, a.mueller@icrf.icnet.uk Dear Anne You are an angel First I would like to thank you to have reply so quickly and secondly to have effectively given the solution as immediately I got the Rasmol window after correcting the rasmol.h file accordingly. Qui peut le plus peut le moins Best regards Bernard ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Powerpoint vs. RasMol/Chime? Date: Wed, 31 Mar 1999 13:39:00 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Cc: mabrook@mcmaster.ca (I am forwarding this for Michael Brook. -- Eric) I looked without success for help on how to create either a chime presentation or Rasmol window INSIDE POWERPOINT. I want to have a protein pop up in a window on a powerpoint page and be able to do real time rotation. A rasmol or chime window would be perfect, but I can't figure out how to do it. Can one? thanks for any help you can offer. Best wishes, Mike Brook Michael A. Brook Phone: (905) 525-9140 ext. 23483 Department of Chemistry Fax: (905) 522-2509 McMaster University 1280 Main St. W. Hamilton, Ontario Canada, L8S 4M1. WWW: http://www.chemistry.mcmaster.ca/faculty/brook/brook.html X-Envelope-to: rasmol@lists.umass.edu X-VMS-To: IN%"rasmol@lists.umass.edu" X-VMS-Cc: WCOLEMAN ++++------+------+------+------+------+------+------+------+------+------+ From: FLICK COLEMAN Subject: Re: Powerpoint vs. RasMol/Chime? Date: Wed, 31 Mar 1999 15:42:33 -0500 (EST) To: rasmol@dhcp-srv2.oit.umass.edu There is a failry straightforward way to do this. If you are using a PC, go into Explorer (Windows Explorer, not IE) and click on view, file types. Make sure that .pdb and .mol (and any others you want) are associated with Rasmol - if not delete their association and make a new one (right click on a .pdb file and choose open with; then point the dialog box to your rasmol.exe file, and check always open with this program). In PowerPoint, insert object, and create from file, then point the dialog box to the molecular file you want to insert. This will create an icon in the PowerPoint page and clicking that icon will bring up Rasmol. I am sure you can do a similar thing on a Mac, but I don't know exactly how off of the top of my head. I hope this helps, Flick Coleman William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 email: wcoleman@wellesley.edu phone: 781-283-3129 fax: 781-283-3642 web: http://www.wellesley.edu/Chemistry/colemanw.html ++++------+------+------+------+------+------+------+------+------+------+ From: Tom Manderfield Subject: Re: Powerpoint vs. RasMol/Chime? Date: Wed, 31 Mar 1999 16:18:55 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Excerpts from mail: 31-Mar-99 Re: Powerpoint vs. RasMol/C.. by FLICK COLEMAN@WELLESLEY. > I am sure you can do a similar thing on a Mac, but I don't know > exactly how off of the top of my head. For PowerPoint 98, Go to the Slide Show menu and select Action Buttons->Custom, then draw a button and choose Hyperlink to->Other File. Select your pdb/script file from the open dialog box. Tom ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Powerpoint vs. RasMol/Chime? Date: Wed, 31 Mar 1999 16:53:24 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Thank you Powerpoint people for telling the rest of us how to spawn RasMol and a script from within a Powerpoint presentation in Windows or Mac. Suppose one wanted to use some features of Chime 2 scripts not available in RasMol, such as the hardware speed-independent move or delay commands, or surface renderings. Is there a way to have Powerpoint link to e.g. an html file for display in Netscape, where the html file invokes Chime with a script? -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - UMass Chime Resources: www.umass.edu/microbio/chime Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: <199903312150.QAA14464@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: Re: Powerpoint vs. RasMol/Chime? Date: Mon, 05 Apr 1999 10:40:26 +0200 To: rasmol@dhcp-srv2.oit.umass.edu When I've used hyperlinks in Powerpoint, especially with large PDB files, it takes a number of seconds for the structure to load, creating a break in the presentation. What I do is to have a Netscape window containing Chime (with the menu bars folded away to make it full screen) also open. I can then toggle instantly back and forth between PowerPoint and Chime using alt+-tab (an inherant feature of Windows, as I understand, and the 'Microsoft Office manager' control panel from MS Office98 for Mac). Once you've got the hang of it, the presentation becomes almost seemless. You can make the Chime presentation as complex as you like: I use a modified version of Eric's 'Viewing RasMol scripts in Chime' with buttons to press to give different views. The asdvantage of this is that once the molecule is loaded, changing views is very fast. MSI's WebLab viewer can be embeded into a powerpoint presentations, although I've never tried it. Kurt -- --------------------------------------------------------------- Dr. Kurt Giles kurt@inn-prot.weizmann.ac.il Israeli National Node Biological Computing Unit Tel: +-972-8-9342614 Weizmann Institute of Science Fax: +-972-8-9466269 Rehovot 76100, Israel http://inn-prot.weizmann.ac.il/ --------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Most popular PDB's Date: Mon, 05 Apr 1999 08:22:05 -0400 To: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu Dear Rasmoleans & Chimeleons: Recently, when I did an analysis of the Brookhaven PDB weblogs for the period Oct-Dec 1998, I was able to count the frequencies of access to information on each entry (namely the short table of information generated by pdb-bin/opdbshort in either PDB Lite or 3DB Browser). Here are those with frequencies >= 100, sorted by decreasing frequency of access. Dates at the end of each line are when the PDB file was published at the PDB. I pass this list on for those subscribers who find this as interesting as I did. 418 see cytochromes below 155c + 351C + 1A56 306 1AOI nucleosome, July 1997 234 see 2brd + 1brd below 207 1D66 Yeast Gal4 protein:dna used in Martz tutorials, 1992 193 155C cytochrome C, 1976 192 1TUB electron diffraction of tubulin, Sept 1997 168 1TNR TNF Receptor Complexed With TNF, 1994 159 1A4L Adenosine Deaminase, Jan 1998 155 1HEI Hepatitis C Virus Rna Helicase, Mar 1997 150 1BL8 Potassium Channel, July 1998, LAYER 1! 144 1LPE ApolipoproteinE3 (Ldl Receptor Binding Domain), 1991 140 3HHR Human Growth Hormone Complexed With Its Receptor, 1993 129 1ALK Alkaline Phosphatase, 1993 126 1Q21 C-H-Ras P21 Protein Catalytic Domain Complex With Gdp, 1991 125 1ATN Deoxyribonuclease I Complex With Actin, 1991 124 4CPA Carboxypeptidase A Complex With Inhibitor, 1982 122 351C Cytochrome C, 1981 120 2BRD electron diffraction of Bacteriorhodopsin, 1995 117 1A8O DIKETO-D-GLUCONIC ACID REDUCTASE WITH NADPH, ON HOLD!! 114 1PRC Photosynthetic Reaction Center (XRD), 1988 114 1BRD electron diffraction of Bacteriorhodopsin, 1990 113 2TCT Tetracycline Repressor, 1995 111 1RBC Ribonuclease S Mutant, 1992 110 1DLC B. thuringensis delta endotoxin, 1994 107 4INS Insulin, 1989 107 1ERE Estrogen Receptor + BetaEstradiol, Sep 1997 107 1AG2 NMR Av, Major Prion Protein, Mar 1997 106 1HMP Hypoxanthine Guanine Phosphoribosyltransferase, 1994 (HGPRT may be popular because it is mutated in myelomas to make hybridomas for monoclonal antibodies) 106 1HCQ Estrogen receptor bound to DNA, 1993 105 1BRR Bacteriorhodopsin Trimerlipid Complex (XRD), July 1998 104 1AO6 Serum Albumin, July 1997 103 1A56 Ferricytochrome C (NMR Av), Feb 1998 100 1ACJ Acetylcholinesterase Complexed With Tacrine, 1993 During this same 3-month period at the end of 1998, for the BNL server alone (not counting mirrors), there were on average 1,100 searches per day (26% thru PDB Lite and the remainder thru 3DB browser), 273 entries were viewed in Chime per day, and RasMol was spawned to view entries 345 times/day. The access log showed that 47,000 files of all types (html pages, images, etc.) were viewed per day, a total of 4.6 million for the 3-month period. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - UMass Chime Resources: www.umass.edu/microbio/chime Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: "Robert M. Horton" Subject: PowerPoint vs. RasMol/Chime Date: Mon, 05 Apr 1999 09:58:26 -0800 To: rasmol@dhcp-srv2.oit.umass.edu Well, it ain't exactly PowerPoint, but I have written a Javascript program to generate HTML presentations; it automatically embeds .PDB files for viewing with Chime. http://www.attotron.com/pub/presmaker.html -- Robert M. Horton, Ph.D. 0 []~ ~ ~ ~ http://www.attotron.com ~ ~ ~ ~[] 0 |-/_| rmhorton@attotron.com |_\-| -\_|| He travels swiftest who telecommutes. ||_/- ++++------+------+------+------+------+------+------+------+------+------+ From: "Robert M. Horton" Subject: Scripting Wizards - new version Date: Mon, 05 Apr 1999 10:35:09 -0800 To: rasmol list Dear Chime/Rasmol users; The latest version of my Chime/Rasmol Scripting Wizards is now on line at http://www.attotron.com/pub/cs/ These are a set of menu-driven authoring tools for creating Rasmol/Chime scripts. New features: - works with Nav4.5 on Win98 and Mac. - makes semi-automatic altscripts in either of two ways (take your pick): * by guessing that everything you turn "on" in a script you want to turn "off" in the altscript, and vice-versa. * by using "reset". The semi-automatic altscript serves as a first draft; you can edit it easily. - cross-references the RasMol Manual or the Chime Embed tags page when run on the net, or will use local copies if they are in the same directory when run from a local drive. You have to copy these reference files off the net yourself; see the read.me file for details. - can be downloaded as a zip file. After unzipping, open "ChScript.htm". - runs much better at 450MHz than at 200 MHz, in case you needed an excuse to get a new computer. ;^) Requires in Netscape 4 or higher, not IE. Note that these Wizards are subwindows that return results to the calling window. They can thus be called by other Javascript programs; this approach might be a useful and integratable complement to graphical authoring tools. -- Robert M. Horton, Ph.D. 0 []~ ~ ~ ~ http://www.attotron.com ~ ~ ~ ~[] 0 |-/_| rmhorton@attotron.com |_\-| -\_|| He travels swiftest who telecommutes. ||_/- X-Confirm-reading-to: pacsch@ritvax.isc.rit.edu X-PMrqc: 1 ++++------+------+------+------+------+------+------+------+------+------+ From: "Paul A. Craig" Subject: Installing Chime in Internet Explorer 5.0 Date: Mon, 05 Apr 1999 16:32:39 -0400 To: rasmol@dhcp-srv2.oit.umass.edu I just installed Internet Explorer 5.0. I tried to install the Chime 2.0 plug-in, but the Chime installer did not recognize the executable either in the Windows Registry, or by searching the hard drive, or if I pointed to the folder that contains the executable (Iexplore.exe). Furthermore, when I look up the file, Iexplore.exe, on Windows Explorer, it is only 77 kb. Thanks for your help. Paul Paul A. Craig Phone: 716-475-6145 Rochester Institute of Technology FAX: 716-475-5766 Dept. of Chemistry Lab: 716-475-2495 1 Lomb Memorial Dr. e-mail: pacsch@rit.edu Rochester, NY 14623 WWW: http://www.rit.edu/~pac8612 charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3155.0 X-SLUIDL: 6A760BCC-EB4D11D2-A2FD0010-5AE22C37 ++++------+------+------+------+------+------+------+------+------+------+ From: "Dr.Fisher" Subject: RE: Installing Chime in Internet Explorer 5.0 Date: Mon, 5 Apr 1999 17:59:08 -0400 To: Associated with this problem, I am able to run Chime on my Web page using IE4.0 but not with Netscape 4.5. Looking at MDL's web page and the problem seems to be fixable if the server administrator enters code on the configuration and/or registry files (see http://www.mdli.com/support/chime/faq_install.html, "How do I make my server understand the various chemical mime types"). However, before I approach the server staff (already overworked), will this code fix this problem? Thanks, Gregg Fisher New Milford High School 25 Sunny Valley Road New Milford, CT 06776 tel: 203/263-6283; http:/www.wtco.net/homepage/gfisher; gfisher@wtco.net > -----Original Message----- > From: owner-rasmol@lists.umass.edu > [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Paul A. Craig > Sent: Monday, April 05, 1999 4:33 PM > To: rasmol@dhcp-srv2.oit.umass.edu > Subject: Installing Chime in Internet Explorer 5.0 > > > I just installed Internet Explorer 5.0. I tried to install the Chime 2.0 > plug-in, but the Chime installer did not recognize the executable > either in the Windows Registry, or by searching the hard drive, or if > I pointed to the folder that contains the executable (Iexplore.exe). > Furthermore, when I look up the file, Iexplore.exe, on Windows > Explorer, it is only 77 kb. Thanks for your help. > > Paul > Paul A. Craig Phone: 716-475-6145 > Rochester Institute of Technology FAX: 716-475-5766 > Dept. of Chemistry Lab: 716-475-2495 > 1 Lomb Memorial Dr. e-mail: pacsch@rit.edu > Rochester, NY 14623 WWW: http://www.rit.edu/~pac8612 > ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Installing Chime in Internet Explorer 5.0 Date: Mon, 05 Apr 1999 21:35:35 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Instructions for installing Chime 2 under IE5 are at http://www.mdli.com/support/chime/chimefree.htm where it says Using the Chime installer will not automatically place the Chime files in the required location to allow you to render structures with Microsoft Internet Explorer 5.0. You must have either Internet Explorer 4.n or Netscape Communicator 4.n already installed on the operating system. Copy the Chime files from the Netscape Plug-ins or Internet Explorer 4.n plug-ins directory into your Microsoft Internet Explorer 5.n directory. We will fix this in the next release of Chime. At 4/5/99, you wrote: >I just installed Internet Explorer 5.0. I tried to install the Chime 2.0 >plug-in, but the Chime installer did not recognize the executable >either in the Windows Registry, or by searching the hard drive, or if >I pointed to the folder that contains the executable (Iexplore.exe). >Furthermore, when I look up the file, Iexplore.exe, on Windows >Explorer, it is only 77 kb. Thanks for your help. > >Paul >Paul A. Craig Phone: 716-475-6145 >Rochester Institute of Technology FAX: 716-475-5766 >Dept. of Chemistry Lab: 716-475-2495 >1 Lomb Memorial Dr. e-mail: pacsch@rit.edu >Rochester, NY 14623 WWW: http://www.rit.edu/~pac8612 > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Kell Doll Subject: about none-heme center Date: Mon, 5 Apr 1999 21:06:16 -0700 (PDT) To: rasmol@dhcp-srv2.oit.umass.edu Hello, friends I'm a new Rasmol user and want to know how to make a good expression for the none-heme diiron cluster(MMO and RNR). Within what radius? Thanks. Kendoll Dept.of Chemistry Uconn _________________________________________________________ Do You Yahoo!? Get your free @yahoo.com address at http://mail.yahoo.com X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id EAA04806 ++++------+------+------+------+------+------+------+------+------+------+ From: Gerard Pujadas Subject: Animated gifs Date: Tue, 6 Apr 1999 10:44:21 +0100 To: rasmol@dhcp-srv2.oit.umass.edu Dear Rasmol/Chime users: I would like to build an animated gif from a serie of rasmol gifs. I wonder if any one known any free software (for mac or UNIX if possible) to do that. With many thanks in advances !!! Yours. Gerard. =========================================================================== DR. GERARD PUJADAS BIOTECNOLOGIA COMPUTACIONAL DEPT. BIOQUIMICA I BIOTECNOLOGIA E-MAIL: pujadas@quimica.urv.es UNIV. ROVIRA I VIRGILI PHONE: 34-977 559565 PLAÇA IMPERIAL TARRACO 1 FAX: 34-977 559597 43005 TARRAGONA (CATALONIA) STATE: SPAIN (EUROPEAN UNION) =========================================================================== X-Operating-System: Debian GNU/Linux 2.0 X-Editor: Vim 5.0 - Vi Improved ++++------+------+------+------+------+------+------+------+------+------+ From: "K. Arun" Subject: Re: Animated gifs Date: Tue, 6 Apr 1999 15:59:44 +0530 To: rasmol@dhcp-srv2.oit.umass.edu On Tue, Apr 06, 1999 at 10:44:21AM +0100, Gerard Pujadas said: => I would like to build an animated gif from a serie of rasmol gifs. => I wonder if any one known any free software (for mac or UNIX if possible) => to do that. Try the Unix command line program, whirlgif, from: http://www.msg.net/utility/whirlgif - K. Arun ++++------+------+------+------+------+------+------+------+------+------+ From: yip@ibme.utoronto.ca (Christopher Yip) Subject: Re: Animated gifs Date: Tue, 6 Apr 1999 07:52:32 -0400 To: rasmol@dhcp-srv2.oit.umass.edu >On Tue, Apr 06, 1999 at 10:44:21AM +0100, Gerard Pujadas said: > > => I would like to build an animated gif from a serie of rasmol gifs. > => I wonder if any one known any free software (for mac or UNIX if possible) > => to do that. > > Try the Unix command line program, whirlgif, from: > > http://www.msg.net/utility/whirlgif > > - K. Arun Another option is GifBuilder for the Mac. Works really well... Here's the link... http://iawww.epfl.ch/Staff/Yves.Piguet/clip2gif-home/GifBuilder.html Chris. Christopher M. Yip, Ph.D., P.Eng. Assistant Professor Department of Chemical Engineering and Applied Chemistry Institute of Biomaterials and Biomedical Engineering Department of Biochemistry University of Toronto 407 Rosebrugh Building, 4 Taddle Creek Rd. Toronto, Ontario CANADA M5S 3G9 Office:(416) 978-7853; Lab:(416) 946-5022; Fax: (416) 978-4317; e-mail: yip@ibme.utoronto.ca WWW: http://goldie.ibme.utoronto.ca X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id JAA05476 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Animated gifs Date: Tue, 06 Apr 1999 09:29:13 -0400 To: rasmol@dhcp-srv2.oit.umass.edu At 4/6/99, you wrote: > > Dear Rasmol/Chime users: > > I would like to build an animated gif from a serie of rasmol gifs. >I wonder if any one known any free software (for mac or UNIX if possible) >to do that. > > With many thanks in advances !!! > > Yours. Gerard. > >=========================================================================== >DR. GERARD PUJADAS >BIOTECNOLOGIA COMPUTACIONAL >DEPT. BIOQUIMICA I BIOTECNOLOGIA E-MAIL: pujadas@quimica.urv.es >UNIV. ROVIRA I VIRGILI PHONE: 34-977 559565 >PLAÇA IMPERIAL TARRACO 1 FAX: 34-977 559597 >43005 TARRAGONA (CATALONIA) >STATE: SPAIN (EUROPEAN UNION) >=========================================================================== > Instructions for generating the frames from a RasMol script, and for Windows shareware, are available by clicking on 'animated picture' under the animated gif at the rasmol home page, namely at http://www.umass.edu/microbio/rasmol/rotating.htm /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: <19990406040616.1764.rocketmail@web205.mail.yahoo.com> ++++------+------+------+------+------+------+------+------+------+------+ From: Adrian Lee Subject: Re: about none-heme center Date: Tue, 06 Apr 1999 11:58:11 -0400 To: rasmol@dhcp-srv2.oit.umass.edu select hetero spacefill select hoh wireframe this should show you all the metal sites in methane monooxygenase and no water molecules. Kell Doll wrote: > Hello, friends > > I'm a new Rasmol user and want to know how to make a good expression > for the none-heme diiron cluster(MMO and RNR). Within what radius? > Thanks. > > Kendoll > Dept.of Chemistry > Uconn > > _________________________________________________________ > Do You Yahoo!? > Get your free @yahoo.com address at http://mail.yahoo.com References: <199904061326.JAA14865@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: AGC Subject: Re: Animated gifs Date: Fri, 02 Apr 1999 10:16:28 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Puede usar el gif construcction set, o si quiere ser mas elegante use el director, ese viene para Mac. PS una pregunta aparte: hay alguna escuela de verano en biocomputacion en espana? acepta ud estudientes por el verano? que postgrados en espan hay en biocomputacion? graicas. Eric Martz wrote: > At 4/6/99, you wrote: > > > > Dear Rasmol/Chime users: > > > > I would like to build an animated gif from a serie of rasmol > gifs. > >I wonder if any one known any free software (for mac or UNIX if > possible) > >to do that. > > > > With many thanks in advances !!! > > > > Yours. Gerard. > > > > > ========================================================================== > > >DR. GERARD PUJADAS > >BIOTECNOLOGIA COMPUTACIONAL > >DEPT. BIOQUIMICA I BIOTECNOLOGIA E-MAIL: > pujadas@quimica.urv.es > >UNIV. ROVIRA I VIRGILI PHONE: 34-977 559565 > >PLAÇA IMPERIAL TARRACO 1 FAX: 34-977 559597 > >43005 TARRAGONA (CATALONIA) > >STATE: SPAIN (EUROPEAN UNION) > >============================= > ============================================= > > > > Instructions for generating the frames from a RasMol script, and for > Windows shareware, are available by clicking on 'animated picture' > under > the animated gif at the rasmol home page, namely at > > http://www.umass.edu/microbio/rasmol/rotating.htm > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Eric Martz, Professor (Immunology), Dept Microbiology > Morrill IVN 203, U Mass, Amherst MA US 01003-5720 > 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu > > Molecular visualization in bioscience education at the > RasMol Home Page > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Brian Beck Subject: Re: about none-heme center Date: Tue, 6 Apr 1999 11:40:59 -0500 (CDT) To: rasmol@dhcp-srv2.oit.umass.edu Kell Doll wrote: > > > Hello, friends > > I'm a new Rasmol user and want to know how to make a good expression > for the none-heme diiron cluster(MMO and RNR). Within what radius? > Thanks. > > Kendoll > Dept.of Chemistry > Uconn > > Kendoll: I've found that the Rasmol default covalent radii and atom names/types are insufficient to represent most metalloproteins (which have weird names and long bond lengths). I was forced to add some new atom types with larger covalent radii to molecule.* and abstree.* -Brian -- ============================================================== | Brian W. Beck |E-mail Address: beck@uh.edu | | Inst. Molec. Design| | | Univ. of Houston |URL: | | 220 Fleming |http://www.chem.uh.edu/pettitt/beck | | Houston, TX, USA |VOICE (713) 743-3264 | | 77204-5641 |FAX (713) 743-2709 | ============================================================== edmolvis@dhcp-srv2.oit.umass.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: 12 carbohydrates Date: Tue, 06 Apr 1999 23:22:15 -0400 To: pdb-l@rcsb.org, rasmol@dhcp-srv2.oit.umass.edu, For years, the "12 carbohydrates" announced on the PDB home page at BNL had me frustrated, because I could find no way to locate them with 3DB Browser or NCBI Entrez. Today I noticed that the BNL PDB CDROMs include a file ENTRYTYP.TXT with each entry receiving one of four designations: prot, nuc, prot-nuc, or carb. Sure enough, grepping for 'carb' extracted exactly 12 entries, namely: 1aga Agarose 2 chains, 6 residues each -- 1978 1c4s Chondroitin-4-Sulfate, 6 residues and 6 Na -- 1978 1cap E coli capsular polysaccharide, 12 residues -- 1978 1car Iota Carrageenan, 2 chains, 6 residues each -- 1978 1hpn Heparin, 2 NMR structures (reflecting the 2 known conformations of one moiety, O2-sulfo-glucuronic acid/IDS) 12 residues -- 1995 1hua Hyaluronan 2 NMR models, 3 residues -- 1994 1hya Hyaluronic Acid (trigonal form), 6 residues, 3 Na -- 1977 1kes Keratan Sulfate, 4 residues -- 1978 2c4s Chondroitin-4-Sulfate, 4 residues, 2 Ca -- 1978 2hya Hyaluronic Acid (tetragonal form), 8 residues, 4 Na -- 1977 3hya Hyaluronic Acid (sodium salt, orthorhombic), 8 residues, 4 Na -- 1977 4hya Hyaluronic Acid (high humidity Ca salt, trigonal), 6 residues, 3 Ca -- 1977 S. Arnott is an author on 10 of these, often with W. T. Winter. 1hua and 1hpn are by separate groups. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime 2 with IE5 Date: Wed, 07 Apr 1999 08:52:10 -0400 To: rasmol@dhcp-srv2.oit.umass.edu [I am forwarding this from Jean Holt at MDL in case any of you are trying to use Chime 2 with IE5. Be sure to see the installation instructions at www.mdli.com/support/chime for IE5. Jean also confirms that there is no way known at MDL for an html page to detect whether Chime is installed in the client's browser, e.g. with javascript. -Eric Martz] We have confirmed that a setting in IE 5.0 crashes Chime and Chime Pro. The setting (described below) is on by default and should to be turned off. The problem occurs in the initialization of the Chime plug-in's LiveConnect code. We are working on a fix to resolve this. The temporary solution is as follows: Start IE 5.0 Select the Internet Options menu item on the Tools menu Select the Advanced tab Uncheck Launch browser windows in a separate process Click Apply, then OK. Exit IE 5.0. Restart IE 5.0. The setting 'Launch browser windows in a separate process' is on by default (used to be off in earlier versions of IE). Turning this off allows Chime to work properly. Hope this helps, Jean Holt MDL Information Systems, Inc. San Leandro, CA, USA edmolvis@dhcp-srv2.oit.umass.edu PDB X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id MAA15864 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Whales and shrews -- the largest & smallest molecules in the Date: Thu, 08 Apr 1999 12:32:24 -0400 To: pdb-l@rcsb.org, rasmol@dhcp-srv2.oit.umass.edu, I was curious what are the extremes of size in PDB files. I know of no way to search by number of atoms, residues, or file size at the PDB or elsewhere (if there is a place to do this please enlighten me!). I have scanned the January 1998 CD-ROM set from BNL with the following observations. (*** Note that my CD-ROM set is more than a year old. ***) BIGGEST MOLECULES DETERMINED BY XRD I found the non-NMR structures with the largest _file sizes_. These are not necessarily the largest molecules because some file sizes are inflated by the inclusion of modeled hydrogen atoms. Some smaller files without hydrogens may actually contain larger molecules (more atoms with positions assigned crystallographically). I excluded files containing the word "NMR". Since some crystallographically determined structure files mention NMR, I may have inadvertantly overlooked the largest XRD file. Perhaps the new PDB search engine will eventually allow searches by method and number of non-hydrogen atoms and number of non-hydrogen atoms/model (for NMR files)? The largest XRD structure in the PDB may be 1bgl+1bgm, deposited in 1994. This 132,670-atom structure had to be deposited as two PDB files because it exceeds the 99,999 atom limit of the PDB format. It is beta-galactosidase.  The asymmetric unit contained 4 tetramers, so 16 chains, each of 1023 residues. Each file is 5.5 megabytes, 66K atoms. These files contain no hydrogens; with hydrogens*, the files would have 132K atoms each, total 264K atoms. Perhaps the second largest structure is 1aon, chaperonin with 58K atoms (file 5 megabytes). This file contains no hydrogens; with them, it would have 116K atoms. Third could be the similarly sized chaperonon 1der (evidently a true wonder) with 56K non-hydrogen atoms (6 megabyte file). This file contains about 26% of the hydrogens (15K hydrogen atoms), making a total of 70K atoms; it may therefore be the largest XRD file, but not the largest molecule determined by XRD. With all hydrogens it would have 112K atoms. (Note that the file size is larger than that for 1aon, which contains a larger molecule but no hydrogens.) Fourth may be the proteasome 1ryp with 53K atoms (no hydrogens, file 4.4 megabytes). It would have 106K atoms with hydrogens. Fifth may be the proteasome pma, with 46K non-hydrogen atoms (file 4.6 megabytes). This file contains about 23% of the hydrogens, making 56K atoms; with all hydrogens, it would have 92K atoms. BIGGEST NMR FILE It was my understanding that NMR does not allow assignment of all hydrogen atom positions, notably those which exchange rapidly. Yet the few NMR files I have looked at appear to have all or over 90% of the hydrogens present (unless the authors elected to omit all hydrogens, e.g. 1bha). Perhaps those not empirically determined were added by modeling. I would appreciate some enlightenment here from an NMR expert. The largest NMR file appears to be 10LH, 7.9 megabytes, with 97,859 atoms. It contains the oligomerization domain of p53. There are 35 models of four identical chains of 42 residues each. It appears that all hydrogens are assigned positions, as there are (exactly) 49,000 hydrogens. Thus there are 48,720 non-hydrogen atoms, or 1,160 non-hydrogen atoms/model. Finding the largest _molecule_ determined by NMR would require knowing the chain lengths, or non-hydrogen atom-counts/model. I have not done such an analysis. The ENTRYTYP.TXT file contains chain lengths but does not indicate method. Perhaps someone can tell us what is the largest molecule determined by NMR? LONGEST CHAINS The PDB CD-ROM file ENTRYTYP.TXT contains one record for each chain. Each record contains a length field with the residue count. I extracted these fields and sorted for the largest, which was the 1023-residue chain in 1bgl/1bgm mentioned above. Tied for second place are two structures for the 967-residue chain of adenovirus 2 hexon coat protein, 0ad2 and 1dhx.  The first was deposited in 1986 and the second in 1995, both at 2.9A resolution.  Honorable mention goes to 1alo, aldehyde oxidoreductase, at 907 residues. LARGEST NUMBER OF CHAINS Perhaps the winner of this category is the bacteriophage GA protein capsid, 1gav, with 45 chains identified A-Z, 0-9, and !, #, _, -, =, :, <, >, |. It has 43K atoms arranged in a beautiful bowl-shape. The proteasome and chaperonin structures 1pma, 1del, 1aon have 28-29 chains. SMALLEST MOLECULES DETERMINED BY XRD File size is less indicative at the small end since the header is larger than the coordinate section of the file. Probably the smallest number of atoms is 1tn1, which contains only three Pb atoms, deposited in a 1986 study of tRNA. There are many small files containing only protein alpha carbons which I am not listing here. A small non-protein structure is the trisaccharide nam-nag-nam in 1lyz, 53 atoms (which interestingly is categorized as 'prot' rather than 'carb' in ENTRYTYP.TXT). 1dn8 contains 4 DNA bases and cobalt hexamine, 91 atoms. 1al1 contains a 12-amino acid peptide with a bound sulfate, 100 atoms. SMALLEST MOLECULES DETERMINED BY NMR Again, without access to atoms/model for the PDB collections, this is difficult to determine. The smallest NMR PDB I found is 3rec, containing two DNA nucleotides, AT, linked with a single phosphorus (no backbone trace here!), 63 atoms, a single model. 2soc contains 2 models of an 8-residue structure (5 standard amino acids and 3 unusual ones), 274 atoms total. 1ANP contains 11 models of a 28 amino acid chain, alpha carbons only, 308 atoms. 1tos contains 3 models of a 10 amino acid peptide, 423 atoms. 1hpn contains 2 models of heparin, 602 atoms. ---- * Thomas E. Creighton's book "Proteins: Structures and molecular properties" (2nd ed, Freeman, 1993) contains a table on page 5 with amino acid residue masses and frequencies in 1,021 unrelated proteins of known sequence, from which he calculates the weighted average residue mass as 119.40. (Incidentally, our calculation from the data in this table gives 111.21.) From these frequencies I calculated the weighted average number of atoms/residue as 15.6, or, without hydrogens, 7.76. Thus the weighted average number of hydrogens/non-hydrogen atom is 2.01. So the number of hydrogens in a protein can be roughly estimated by multiplying the number of non-hydrogen atoms by two. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ PDB References: ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: Re: Whales and shrews -- the largest & smallest molecules in the Date: Thu, 08 Apr 1999 19:48:23 +0200 To: rasmol@dhcp-srv2.oit.umass.edu, PDB Listserver > I was curious what are the extremes of size in PDB files. I know of no way to > search by number of atoms, residues, or file size at the PDB or elsewhere (if > there is a place to do this please enlighten me!). With the 3DB browser it is possible to search by chain size (the penultimate category). Searching with >1050 gives one hit: 1JDB which, amongst others, contains four chains each of 1073 residues. I think this is based on the SEQRES part od the file, and so does not exactly reflect the number of resolved atoms. Kurt -- --------------------------------------------------------------- Dr. Kurt Giles kurt@inn-prot.weizmann.ac.il Israeli National Node Biological Computing Unit Tel: +-972-8-9342614 Weizmann Institute of Science Fax: +-972-8-9466269 Rehovot 76100, Israel http://inn-prot.weizmann.ac.il/ --------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: Brian Beck Subject: Re: Whales and shrews Date: Thu, 8 Apr 1999 16:28:18 -0500 (CDT) To: rasmol@dhcp-srv2.oit.umass.edu Eric Martz wrote: > > I was curious what are the extremes of size in PDB files. I know of no way to > search by number of atoms, residues, or file size at the PDB or elsewhere (if > there is a place to do this please enlighten me!). I have scanned the January > 1998 CD-ROM set from BNL with the following observations. (*** Note that my > CD-ROM set is more than a year old. ***) > > BIGGEST MOLECULES DETERMINED BY XRD > The various viruses that have been xtallized generally only list the atoms of one of the sixty identical protomers of the viral capsid, but list the symmetry angles necessary to replicate the entire capsid. Thus the size of the entire macrolmolecular assembly is 1-2 orders of magnitude larger than the what's listed. This is similarly true for other symmetrical macromolecular assemblies. Do these count in your search for the largest xtallized molecules. -Brian -- ============================================================== | Brian W. Beck |E-mail Address: beck@uh.edu | | Inst. Molec. Design| | | Univ. of Houston |URL: | | 220 Fleming |http://www.chem.uh.edu/pettitt/beck | | Houston, TX, USA |VOICE (713) 743-3264 | | 77204-5641 |FAX (713) 743-2709 | ============================================================== References: X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: David Fahrney Subject: Re: Whales and shrews -- the largest & smallest molecules in thePDB Date: Thu, 08 Apr 1999 19:09:37 -0600 To: rasmol@dhcp-srv2.oit.umass.edu There are a number of pdb files for viruses. For example, tomato bushy stunt virus (2tbv.mmol) has an icosahedral protein shell comprised of 180 identical subunits (roughly 384,000 nonhydrogen atoms). The coordinate set is truly a whale (29,138,966 bytes) but RasMol has no trouble with it. The wireframe model loads in about six seconds on my computer (a 400 MHz PC). Of course, the complete protein shell is derived by symmetry transformation of the original pdb file (5 protomers), so this may not be what Eric had in mind. Dave Fahrney Professor of Biochemistry Colorado State University dfahrney@lamar.colostate.edu Eric Martz wrote: > > I was curious what are the extremes of size in PDB files. I know of no way to > search by number of atoms, residues, or file size at the PDB or elsewhere (if > there is a place to do this please enlighten me!). I have scanned the January > 1998 CD-ROM set from BNL with the following observations. (*** Note that my > CD-ROM set is more than a year old. ***) > > BIGGEST MOLECULES DETERMINED BY XRD > > I found the non-NMR structures with the largest _file sizes_. These are not > necessarily the largest molecules because some file sizes are inflated by the > inclusion of modeled hydrogen atoms. Some smaller files without hydrogens may > actually contain larger molecules (more atoms with positions assigned > crystallographically). > > I excluded files containing the word "NMR". Since some crystallographically > determined structure files mention NMR, I may have inadvertantly overlooked > the > largest XRD file. Perhaps the new PDB search engine will eventually allow > searches by method and number of non-hydrogen atoms and number of non-hydrogen > atoms/model (for NMR files)? > > The largest XRD structure in the PDB may be 1bgl+1bgm, deposited in 1994. This > 132,670-atom structure had to be deposited as two PDB files because it exceeds > the 99,999 atom limit of the PDB format. It is beta-galactosidase. The > asymmetric unit contained 4 tetramers, so 16 chains, each of 1023 residues. > Each file is 5.5 megabytes, 66K atoms. These files contain no hydrogens; with > hydrogens*, the files would have 132K atoms each, total 264K atoms. > > Perhaps the second largest structure is 1aon, chaperonin with 58K atoms > (file 5 > megabytes). This file contains no hydrogens; with them, it would have 116K > atoms. > > Third could be the similarly sized chaperonon 1der (evidently a true wonder) > with 56K non-hydrogen atoms (6 megabyte file). This file contains about > 26% of > the hydrogens (15K hydrogen atoms), making a total of 70K atoms; it may > therefore be the largest XRD file, but not the largest molecule determined by > XRD. With all hydrogens it would have 112K atoms. (Note that the file size is > larger than that for 1aon, which contains a larger molecule but no hydrogens.) > > Fourth may be the proteasome 1ryp with 53K atoms (no hydrogens, file 4.4 > megabytes). It would have 106K atoms with hydrogens. > > Fifth may be the proteasome pma, with 46K non-hydrogen atoms (file 4.6 > megabytes). This file contains about 23% of the hydrogens, making 56K atoms; > with all hydrogens, it would have 92K atoms. > > BIGGEST NMR FILE > > It was my understanding that NMR does not allow assignment of all hydrogen > atom > positions, notably those which exchange rapidly. Yet the few NMR files I have > looked at appear to have all or over 90% of the hydrogens present (unless the > authors elected to omit all hydrogens, e.g. 1bha). Perhaps those not > empirically determined were added by modeling. I would appreciate some > enlightenment here from an NMR expert. > > The largest NMR file appears to be 10LH, 7.9 megabytes, with 97,859 atoms. It > contains the oligomerization domain of p53. There are 35 models of four > identical chains of 42 residues each. It appears that all hydrogens are > assigned positions, as there are (exactly) 49,000 hydrogens. Thus there are > 48,720 non-hydrogen atoms, or 1,160 non-hydrogen atoms/model. > > Finding the largest _molecule_ determined by NMR would require knowing the > chain lengths, or non-hydrogen atom-counts/model. I have not done such an > analysis. The ENTRYTYP.TXT file contains chain lengths but does not indicate > method. Perhaps someone can tell us what is the largest molecule determined by > NMR? > > LONGEST CHAINS > > The PDB CD-ROM file ENTRYTYP.TXT contains one record for each chain. Each > record contains a length field with the residue count. I extracted these > fields > and sorted for the largest, which was the 1023-residue chain in 1bgl/1bgm > mentioned above. Tied for second place are two structures for the 967-residue > chain of adenovirus 2 hexon coat protein, 0ad2 and 1dhx. The first was > deposited in 1986 and the second in 1995, both at 2.9A resolution. Honorable > mention goes to 1alo, aldehyde oxidoreductase, at 907 residues. > > LARGEST NUMBER OF CHAINS > > Perhaps the winner of this category is the bacteriophage GA protein capsid, > 1gav, with 45 chains identified A-Z, 0-9, and !, #, _, -, =, :, <, >, |. It > has > 43K atoms arranged in a beautiful bowl-shape. The proteasome and chaperonin > structures 1pma, 1del, 1aon have 28-29 chains. > > SMALLEST MOLECULES DETERMINED BY XRD > > File size is less indicative at the small end since the header is larger than > the coordinate section of the file. Probably the smallest number of atoms is > 1tn1, which contains only three Pb atoms, deposited in a 1986 study of tRNA. > There are many small files containing only protein alpha carbons which I am > not > listing here. A small non-protein structure is the trisaccharide > nam-nag-nam in > 1lyz, 53 atoms (which interestingly is categorized as 'prot' rather than > 'carb' > in ENTRYTYP.TXT). 1dn8 contains 4 DNA bases and cobalt hexamine, 91 atoms. > 1al1 > contains a 12-amino acid peptide with a bound sulfate, 100 atoms. > > SMALLEST MOLECULES DETERMINED BY NMR > > Again, without access to atoms/model for the PDB collections, this is > difficult > to determine. The smallest NMR PDB I found is 3rec, containing two DNA > nucleotides, AT, linked with a single phosphorus (no backbone trace here!), 63 > atoms, a single model. 2soc contains 2 models of an 8-residue structure (5 > standard amino acids and 3 unusual ones), 274 atoms total. 1ANP contains 11 > models of a 28 amino acid chain, alpha carbons only, 308 atoms. 1tos > contains 3 > models of a 10 amino acid peptide, 423 atoms. 1hpn contains 2 models of > heparin, 602 atoms. > > ---- > > * Thomas E. Creighton's book "Proteins: Structures and molecular properties" > (2nd ed, Freeman, 1993) contains a table on page 5 with amino acid residue > masses and frequencies in 1,021 unrelated proteins of known sequence, from > which > he calculates the weighted average residue mass as 119.40. (Incidentally, our > calculation from the data in this table gives 111.21.) From these > frequencies I > calculated the weighted average number of atoms/residue as 15.6, or, without > hydrogens, 7.76. Thus the weighted average number of hydrogens/non-hydrogen > atom is 2.01. So the number of hydrogens in a protein can be roughly estimated > by multiplying the number of non-hydrogen atoms by two. > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Eric Martz, Professor (Immunology), Dept Microbiology > Morrill IVN 203, U Mass, Amherst MA US 01003-5720 > 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu > > Molecular visualization in bioscience education at the > RasMol Home Page > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: New Location of Graphics Tutorials Date: Sun, 11 Apr 1999 15:06:50 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Dear RasMolluscs and Chimeleons, My RasMol and SwissPdbViewer tutorials are moving. Find links to them at my new home page address: http://www.usm.maine.edu/~rhodes/GRHomePage.html In addition, I just made a new frames version of the RasMol tutorial, which I hope is easier to navigate than the old one-large-page version (still available, but it will not be further updated). Some of you may not be aware that I provide these tutorials for graphics beginners at my website. Include there are self-guiding introductions to RasMol, SwissPdbViewer, and MAGE (the last one somewhat dated). The tutorials are aimed specifically at students in introductory biochemistry courses (they teach both the programs and the basics of protein structure), but my e-mail tells me that graphics beginners at all levels of teaching and research have found them helpful. The goal of my tutorials is is to equip users to study and analyse macromolecular structure on their own (without prepared animations), as well as to use the Protein Data Bank. If you or your colleagues teach biochemistry or molecular biology, and are thinking about making modelers out of your students, these tutorials may save you a lot of work. They have been thoroughly tested by students. They include assignments for independent work to hand in on disk or as files attached to e-mail. At my home page you can find links to these tutorials, a comparison of RasMol and SwissPdbViewer, other resources for students and teachers of biochemistry and general chemistry, and miscellaneous goodies. ATTENTION: POSSIBLE HELP FROM SWISSPDBVIEWER IN SCRIPT CREATION RasMolluscs and Chimeleons alike might want to get to know SwissPdbViewer for its file creating and modifying tools, which may help you in creating files of desired content for RasMol or Chime scripts. File handling features of SPV include combining contents of multiple PDB files (such as from manual docking or for side-by-side structural comparison), renaming chains or parts of chains, renaming hetero groups or atoms within them (coming very soon), building symmetrically related subunits, adding hydrogens (soon), adding or "mutating" residues, adding OXT or NH3 to termini (soon), breaking or ligating chains (soon), building peptides from scratch (starting with a text file of sequence in one-letter code), and others. Although you can better do structural comparisons within SPV, you should be able to do primitive comparisons of homologous structures in RasMol by superimposing them in SPV, combining them into one file as separate chains, and them treating them like multiple models in an NMR coordinates file. Another nice feature is that when you do the SPV equivalent of "select within" (Select: Neighbors of Selection), you get whole residues, or whole side chains, not just the atoms within the specified distance. This allows you easily to create files containing only the ligands of heteros or metal ions, for example. (Might help with the recent request about a di-iron center.) Just thought you might like to know. Cheers! ***************************** Gale Rhodes mailto:rhodes@usm.maine.edu http://www.usm.maine.edu/~rhodes/GRHomePage.html Professor of Chemistry Chemistry Department University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 Phone: (207)780-4734 Fax: (207)780-5607 References: <199904071248.IAA07847@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: " Dr. Frank Eblinger" Subject: RasMol Script Date: Thu, 15 Apr 1999 16:46:36 +0200 To: rasmol@dhcp-srv2.oit.umass.edu Hi all, Got a problem with RasMol scripts: Why doesn't RasMol load any structure when I call a script from file manager or from another apllication? The script works from Rasmol - no problem- by script file.spt like load pdb file.pdb select all wireframe 50 .... If I open a pdb file the same way it works! Any suggestions? Thanks Frank References: <199904071248.IAA07847@marlin.bio.umass.edu> <3715FBCC.C594D7E9@rz.uni-sb.de> ++++------+------+------+------+------+------+------+------+------+------+ From: jr Subject: Re: RasMol Script Date: Thu, 15 Apr 1999 17:11:33 +0200 To: rasmol@dhcp-srv2.oit.umass.edu may be, because of the environment variable $RASMOLPDBPATH pointing the PDB files Regards, Jan References: <199904071248.IAA07847@marlin.bio.umass.edu> <3715FBCC.C594D7E9@rz.uni-sb.de> boundary="------------AE1AA93C407D92C13ADFC44C" X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: "Jeffrey J. Ayres" Subject: Re: RasMol Script Date: Thu, 15 Apr 1999 08:17:17 -0700 To: rasmol@dhcp-srv2.oit.umass.edu This is a multi-part message in MIME format. --------------AE1AA93C407D92C13ADFC44C Frank, You must list the directory the file is in as well. For example C:/Chemistryfiles/my_molecule.pdb Jeff Ayres " Dr. Frank Eblinger" wrote: > Hi all, > > Got a problem with RasMol scripts: Why doesn't RasMol load any structure when I > call > a script from file manager or from another apllication? The script works from > Rasmol - no problem- by script file.spt > like > load pdb file.pdb > select all > wireframe 50 > .... > > If I open a pdb file the same way it works! > Any suggestions? > > Thanks > Frank --------------AE1AA93C407D92C13ADFC44C name="jayres.vcf" Content-Description: Card for Jeffrey J. Ayres Content-Disposition: attachment; filename="jayres.vcf" begin:vcard n:Ayres;Jeffrey x-mozilla-html:FALSE url:http://www.mc.maricopa.edu/users/jayres/org_molecules http://www.geocities.com/yosemite/trails/5681 org:Yavapai Community College;Math Sciences/ Learning Center adr:;;;Prescott;AZ;; version:2.1 email;internet:jayres@ycpo.yavapai.cc.az.us jeffayres@hotmail.com title:Adjunct Faculty Chemistry, Tutor Math/Chemistry note:Views taken are not necessarily those of Yavapai College. x-mozilla-cpt:;0 fn:Jeffrey Ayres end:vcard --------------AE1AA93C407D92C13ADFC44C-- X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id OAA22005 ++++------+------+------+------+------+------+------+------+------+------+ From: Rick Lee Subject: Chime 2.0a & Mac & Netscape 4.51 Date: Thu, 15 Apr 1999 11:16:28 -0700 To: rasmol@dhcp-srv2.oit.umass.edu I'm not sure if this is a known problem already discussed on this list. If so, I'm sorry to repeat. I can't view Chime molecules with Netscape 4.51 on Macs (7.6.1 or 8.5.1) from a local disk only. Viewing from a server (any server) is fine. I get an error: "This page contains information of type application/x-unknown-content-type that can only be viewed with the appropriate plug-in." And I get a broken plug symbol. This does not happen on the PC at all or with Netscape 4.0x on the Mac. I'm delivering a CD-based Chime product. What can be done? Thanks, Rick ******************************************** *  Richard H. Lee, PhD *  Editor/Lead Scientist, Biochemistry *  rick@sciencemedia.com * *  ScienceMedia, Inc. *  6540 Lusk Blvd., Suite C148 *  San Diego, CA 92121-2767 * *  TEL: 619/625-9261, Ext. 7 *  FAX: 619/625-9262 * *  http://www.sciencemedia.com ********************************************* ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Re: Chime 2.0a & Mac & Netscape 4.51 Date: Thu, 15 Apr 1999 14:32:51 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Let me share with you the helpful quick fix for Chime/Mac problems that John Wiley and Sons provides with their CD to accompany the new biochemistry text by Voet, Voet, and Pratt. In the instructions for installation on Macintoshes, you find this sentence: "Chime 2.0 will often crash on some of these pages." Sure makes me want to use it. Cheers! >I'm not sure if this is a known problem already discussed on this list. If >so, I'm sorry to repeat. > >I can't view Chime molecules with Netscape 4.51 on Macs (7.6.1 or 8.5.1) >>from a local disk only. Viewing from a server (any server) is fine. I get >an error: > "This page contains information of type application/x-unknown-content-type > that can only be viewed with the appropriate plug-in." >And I get a broken plug symbol. > >This does not happen on the PC at all or with Netscape 4.0x on the Mac. > >I'm delivering a CD-based Chime product. What can be done? > >Thanks, >Rick > >******************************************** >* Richard H. Lee, PhD >* Editor/Lead Scientist, Biochemistry >* rick@sciencemedia.com >* >* ScienceMedia, Inc. >* 6540 Lusk Blvd., Suite C148 >* San Diego, CA 92121-2767 >* >* TEL: 619/625-9261, Ext. 7 >* FAX: 619/625-9262 >* >* http://www.sciencemedia.com >********************************************* ***************************** Gale Rhodes mailto:rhodes@usm.maine.edu http://www.usm.maine.edu/~rhodes/GRHomePage.html Professor of Chemistry Chemistry Department University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 Phone: (207)780-4734 Fax: (207)780-5607 References: <3.0.5.32.19990415111628.0083fcf0@pop3.sciencemedia.com> X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id PAA22757 ++++------+------+------+------+------+------+------+------+------+------+ From: Rick Lee Subject: Re: Chime 2.0a & Mac & Netscape 4.51 Date: Thu, 15 Apr 1999 12:23:02 -0700 To: rasmol@dhcp-srv2.oit.umass.edu At 02:32 PM 4/15/99 -0400, you wrote: >Let me share with you the helpful quick fix for Chime/Mac problems that >John Wiley and Sons provides with their CD to accompany the new >biochemistry text by Voet, Voet, and Pratt. In the instructions for >installation on Macintoshes, you find this sentence: "Chime 2.0 will often >crash on some of these pages." Yes, I wrote those instructions! I found the problem that caused the crashing mentioned in those instructions, so the final edition of the CD will use Chime 2.0, Netscape 4.51 and Shockwave 7 exclusively. This was a new problem. Someone at MDL sent me this URL, and that fixed this new problem: http://www.mdli.com/support/chime/pres.htm#9 The problem only occurs if you have an old copy of Chime already installed. Thanks, Rick PS. The song "It's a Small World" swells to a crescendo in the background...Fade out. ******************************************** *  Richard H. Lee, PhD *  Editor/Lead Scientist, Biochemistry *  rick@sciencemedia.com * *  ScienceMedia, Inc. *  6540 Lusk Blvd., Suite C148 *  San Diego, CA 92121-2767 * *  TEL: 619/625-9261, Ext. 7 *  FAX: 619/625-9262 * *  http://www.sciencemedia.com ********************************************* ++++------+------+------+------+------+------+------+------+------+------+ From: baucom@gorby.UCSC.EDU (Albion Baucom) Subject: New resources for viewing Chime models Date: Thu, 15 Apr 1999 22:14:57 -0700 To: rasmol@dhcp-srv2.oit.umass.edu Chime Users, C4, Computers and Chemistry at Cabrillo College, is excited to introduce a BETA version of the MacroViewer. It can be found on our home page at http://c4.cabrillo.cc.ca.us Please read the "System Requirements and Release Notes" page on the main MacroViewer page carefully before using it. What is the MacroViewer? The MacroViewer is an interface for the presentation of macromolecules integrated with on-screen controls. The MacroViewer includes a pull-down menu of molecular models which allow one to place a selected model into a designated screen space. Next to the visualized model is a selected set of Chime Tools (Java applets) which control its display attributes. The Chime tools include sliders, pull-down menus for scripts and models, a label maker, a scripting interface, and a simple motion controller. The MacroViewer is also an introduction to the Chime Toolbox, a collection of Java applets that control Chime using "LiveConnect" in Netscape. These applets are easily added to any web page and provide the user control over complex sequences of Chime scripting commands. The MacroViewer is just one of many possible uses of these tools in chemical education. A separate downloadable packages containing the MacroViewer, as well as the Chime Toolbox, will be available at the C4 home page soon. Please send any suggestions or comments about the overall functionality to baucom@gorby.ucsc.edu If you would like to know more about how you can use this particular piece of software at your institution please contact haungar@cabrillo.cc.ca.us Enjoy! Albion E. Baucom baucom@gorby.ucsc.edu http://tito.ucsc.edu/baucom http://c4.cabrillo.cc.ca.us '71 R75/5 '74 R90/6 '79 R65 charset="iso-8859-1" X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id DAA26727 ++++------+------+------+------+------+------+------+------+------+------+ From: =?iso-8859-1?Q?PE=D1UELAS_SANCHEZ=2C_Iv=E1n?= Subject: Where's Chime's command line window? Date: Fri, 16 Apr 1999 08:20:38 +0200 To: rasmol@dhcp-srv2.oit.umass.edu Hi all, I've been working with Rasmol in my classes using the "command line window". In this way all my students make the same changes in the molecule at the same time; I'm quite new with Chime, and I'd like to modify the molecules I load in the same way, instead of using the mouse and the emergent menus of Chime. Nonetheless, I cannot find the command line! Can anybody help this Chime rookie? Thanks. Iván Peñuelas References: <199904071248.IAA07847@marlin.bio.umass.edu> <3715FBCC.C594D7E9@rz.uni-sb.de> <371602FC.CA105448@ycpo.yavapai.cc.az.us> ++++------+------+------+------+------+------+------+------+------+------+ From: " Dr. Frank Eblinger" Subject: Re: RasMol Script Date: Fri, 16 Apr 1999 10:10:28 +0200 To: rasmol@dhcp-srv2.oit.umass.edu --------------7018A7FDD7E00010B18FA3A1 Dear Jeffrey, That's not the problem, I tried with and without the full path! RasMol opens, but no file is loaded. Maybe RasMol does not understand open file.spt! But I want to invoke RasMol (with a loaded structure e.g. with ribbons etc.) from another application! Frank Jeffrey J. Ayres wrote: > Frank, > You must list the directory the file is in as well. For example > C:/Chemistryfiles/my_molecule.pdb > > Jeff Ayres > --------------7018A7FDD7E00010B18FA3A1 Dear Jeffrey,

That's not the problem, I tried with and without the full path!
RasMol opens, but no file is loaded. Maybe RasMol does not understand open file.spt!
But I want to invoke RasMol (with a loaded structure e.g.  with ribbons etc.) from another application!

Frank

Jeffrey J. Ayres wrote:

Frank,
    You must list the directory the file is in as well. For example
C:/Chemistryfiles/my_molecule.pdb

Jeff Ayres
 

--------------7018A7FDD7E00010B18FA3A1-- X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id HAA28051 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Where's Chime's command line window? Date: Fri, 16 Apr 1999 07:14:55 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Perhaps the best thing for you to use is the Protein Explorer, a RasMol-like interface in Chime. It can be used off the web, or you can download it and install it in your computer lab. I am presently completing the tutorial with the goal that people who have not used RasMol will be able to use the Explorer. The Explorer will be publically linked to my site when the tutorial is completed. Already, however, all the functionality works just fine, as has been announced on this list recently. It is at www.umass.edu/microbio/chime/explorer The answer to your question 'Where's the command line' is that you must provide it in the html of a page. It is not built into Chime. In the case of the Protein Explorer, the command line and other enhancements required several thousand lines of javascript. However, a simple command line can be done much more easily, and examples of how to do this have been available from the URL below since Chime has been available. -Eric At 4/16/99, you wrote: >Hi all, >I've been working with Rasmol in my classes using the "command line >window". In this way all my students make the same changes in the >molecule at the same time; I'm quite new with Chime, and I'd like to >modify the molecules I load in the same way, instead of using the mouse >and the emergent menus of Chime. Nonetheless, I cannot find the command >line! >Can anybody help this Chime rookie? >Thanks. > > Iván Peñuelas > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: <199904071248.IAA07847@marlin.bio.umass.edu> <3715FBCC.C594D7E9@rz.uni-sb.de> <371602FC.CA105448@ycpo.yavapai.cc.az.us> <3716F074.901B2F0B@rz.uni-sb.de> boundary="------------D70A4845287FA5506FC71A65" X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: "Jeffrey J. Ayres" Subject: Re: RasMol Script Date: Fri, 16 Apr 1999 09:00:24 -0700 To: rasmol@dhcp-srv2.oit.umass.edu This is a multi-part message in MIME format. --------------D70A4845287FA5506FC71A65 boundary="------------E1B894D0F45060AB8C00982D" --------------E1B894D0F45060AB8C00982D Frank, Chime is the easiest to open from other applications, just use the embed tag. The help pages show how to use the embed tag. I was successful in opening it into Adobe Pagemill as well as Netscape. Jeff Ayres " Dr. Frank Eblinger" wrote: > Dear Jeffrey, > > That's not the problem, I tried with and without the full path! > RasMol opens, but no file is loaded. Maybe RasMol does not understand > open file.spt! > But I want to invoke RasMol (with a loaded structure e.g. with > ribbons etc.) from another application! > > Frank > > Jeffrey J. Ayres wrote: > >> Frank, >> You must list the directory the file is in as well. For example >> C:/Chemistryfiles/my_molecule.pdb >> >> Jeff Ayres >> > --------------E1B894D0F45060AB8C00982D Frank,
        Chime is the easiest to open from other applications, just use the embed tag.  The help pages show how to use the embed tag.  I was successful in opening it into Adobe Pagemill as well as Netscape.

Jeff Ayres

" Dr. Frank Eblinger" wrote:

Dear Jeffrey,

That's not the problem, I tried with and without the full path!
RasMol opens, but no file is loaded. Maybe RasMol does not understand open file.spt!
But I want to invoke RasMol (with a loaded structure e.g.  with ribbons etc.) from another application!

Frank

Jeffrey J. Ayres wrote:

Frank,
    You must list the directory the file is in as well. For example
C:/Chemistryfiles/my_molecule.pdb

Jeff Ayres
 

--------------E1B894D0F45060AB8C00982D-- --------------D70A4845287FA5506FC71A65 name="jayres.vcf" Content-Description: Card for Jeffrey J. Ayres Content-Disposition: attachment; filename="jayres.vcf" begin:vcard n:Ayres;Jeffrey x-mozilla-html:FALSE url:http://www.mc.maricopa.edu/users/jayres/org_molecules http://www.geocities.com/yosemite/trails/5681 org:Yavapai Community College;Math Sciences/ Learning Center adr:;;;Prescott;AZ;; version:2.1 email;internet:jayres@ycpo.yavapai.cc.az.us jeffayres@hotmail.com title:Adjunct Faculty Chemistry, Tutor Math/Chemistry note:Views taken are not necessarily those of Yavapai College. x-mozilla-cpt:;0 fn:Jeffrey Ayres end:vcard --------------D70A4845287FA5506FC71A65-- Content-Disposition: inline X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id AAA17444 ++++------+------+------+------+------+------+------+------+------+------+ From: "Brendan O'Malley" Subject: Hi All, Date: Tue, 20 Apr 1999 14:03:27 +1000 To: Hi All, I'm attemting to put together a chime web page with embedded pdb files and have a problem with the server. It appears to tag pdb files as mime type text/plain no matter what I put in the mailcap and .mime.types The server is an O2 SGI running irix 6.5. Chime works on the sgi with both local and downloaded files, but if i look at the web page from another computer I get the chime plugin starting but no image. A check of the page source info shows the pdb file has been given a mime type text/plain. This doesnt happen if I download someone elses chime web page. I'm stumped. Has anyone else had this sort of problem. Cheers Brendan O'Malley Brendan O'Malley (brendan.omalley@rmit.edu.au) Applied Physics RMIT ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Rasmol and color in PDB files Date: Tue, 20 Apr 1999 13:36:18 -0400 To: Douglas du Boulay Cc: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu Making carbon black instead of gray is much more easily and portably accomplished with a 2-line script file, named e.g. cblack.spt, containing select carbon color black (you might prefer dark gray, e.g. 'color [80,80,80]') This script can be called for any molecule loaded with 'script cblack.spt' (provided the script is in the same folder as RasMol, else use an absolute path). In contrast, adding user colors to the PDB file works for only that one file. For a more complex custom color scheme script, see http://www.umass.edu/microbio/rasmol/makescrp.htm#allmol -Eric At 4/20/99, you wrote: >Hi Eric, > Please excuse this intrusion, but ... > >I was wanting to change the default colors to "user" colors in >RasMol2.6. From the online help it says this can be achieved with >COLO lines in the PDB file. > >I am wondering what the format for these lines are as I can't find them >in the PDB file format, nor yet on your Rasmol WWW pages. >(my problem is that carbon is grey, when everyone else knows its black :-) > >Any pointers you could give would be much appreciated. >Thanks >Doug > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id JAA01150 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: distributing RasMol Date: Thu, 22 Apr 1999 09:04:19 -0400 To: " Dr. Frank Eblinger" Cc: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu Both Chime and RasMol can be distributed freely on your CD. For RasMol, see http://www.umass.edu/microbio/rasmol/faq_ras.htm#pubdom to confirm this. For confirmation with Chime, please consult MDL via http://www.mdli.com/support/chime At 4/22/99, you wrote: >Dear Prof. Martz, > >we're preparing an interactive textbook (CD) on some aspects of >biochemistry. We would like to use RasMol or Chime as helper programs >to show some nice structures. Are we allowed to distruíbute one of the >programs on cd-rom? Perhaps you have some experience with this or maybe >know the people responsible for the copyright permissions. > >Thanks for your help in advance > > Frank > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - UMass Chime Resources: www.umass.edu/microbio/chime Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: "Patrick Flash" Subject: Use studies Date: Thu, 22 Apr 1999 13:44:06 EST To: rasmol@dhcp-srv2.oit.umass.edu Dear Rasmolers and Chimers, I would like to organize a session on Rasmol/Chime at the16th Biennial Chem Ed conference at the University of Michigan in summer 2000. I'm particularly interested in people willing to present documentation on the successful (or unsuccessful) use of these programs. While a presentation on "what I've done" is useful, results from student feedback and scholarly studies on the effectiveness! of the programs would be particularly appreciated. Reply to me at flash@ashtabula.kent.edu. Patrick Flash Kent-Ashtabula Campus Ashtabula, OH 44004 mmciflist@ndbdev.rutgers.edu ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: RasMol Version 2.7.0.1 Date: Thu, 22 Apr 1999 18:12:06 -0400 To: pdb-l@rcsb.org, rasmol@dhcp-srv2.oit.umass.edu, We are pleased to say that http://www.bernstein-plus-sons.com/software/rasmol/ has been updated to RasMol_2.7.0.1, which combines Roger Sayle's version 2.6.4 with Herbert Bernstein's CIF modified version 2.6_CIF(Rev 2) and with Arne Mueller's version 2.6x1. This combined version allows selection by alternate conformers as well as by models, production of Ramachandran printer plots (as in F. Bernstein's fisipl), and access to A. Mueller's POVray output as POVray3 in addition to the existing POVray version 2 output. (POVray3 should not be used in the PC or Mac version, yet). RasMol version 2.6x1 was an upgrade to RasMol by Arne Mueller to add code to allow listing of information about the chains, groups or atoms in a selection, listing of phi-psi, allow selection by cis angle cutoff, and to provide a POV-Ray version 3 output. RasMol version 2.6.4 was a major code cleanup and reorganization by Roger Sayle, dropping obsolete non-ANSI C options and providing speed improvements. RasMol version 2.6_CIF added several new features to RasMol: Support for reading IUCr CIF and mmCIF format; Coloring for alternate conformers and multiple NMR models; Display of all NMR models in a data set. This version is available for the Apple Macintosh and PowerMac in addition to UNIX, VMS and Microsoft Windows versions. However, because of limitations in the memory management under MacOS, very large multiple NMR model datasets are not supported on the Mac or PowerMac at this time. IMPORTANT Please read the file NOTICE: http://www.bernstein-plus-sons.com/software/rasmol/doc/NOTICE.html for important notices which apply to this package. If you are not going to make changes to RasMol, you are not only permitted to freely make copies and distribute them, you are encouraged to do so, provided you do the following: * 1. Either include the complete documentation, especially the file NOTICE, with what you distribute or provide a clear indication where people can get a copy of the documentation; and * 2. Please give credit where credit is due citing the version and original authors properly; and * 3. Please do not give anyone the impression that the original authors are providing a warranty of any kind. If you would like to use major pieces of RasMol in some other program, make modifications to RasMol, or in some other way make what a lawyer would call a "derived work", you are not only permitted to do so, you are encouraged to do so. In addition to the things we discussed above, please do the following: * 4. Please explain in your documentation how what you did differs from this version of RasMol; and * 5. Please make your modified source code available. This version of RasMol is not in the public domain, but it is given freely to the community in the hopes of advancing science. If you make changes, please make them in a responsible manner, and please offer us the opportunity to include those changes in future versions of RasMol. ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-516-286-1339 FAX: 1-516-286-1999 ===================================================== Content-Disposition: inline X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id VAA04097 ++++------+------+------+------+------+------+------+------+------+------+ From: "Brendan O'Malley" Subject: MSI/ Cerius Molecule File Format Date: Fri, 23 Apr 1999 11:52:13 +1000 To: Is their a program that can convert *.msi files to a set of atomic coordinates and/or a file format that can be read by Rasmol or Chime? Thanks to everyone for help with my previous question. Brendan O'Malley Brendan O'Malley (brendan.omalley@rmit.edu.au) Applied Physics RMIT X-Operating-System: Debian GNU/Linux ++++------+------+------+------+------+------+------+------+------+------+ From: "K. Arun" Subject: Re: RasMol Version 2.7.0.1 Date: Fri, 23 Apr 1999 08:22:59 +0530 To: rasmol@dhcp-srv2.oit.umass.edu On Thu, Apr 22, 1999 at 06:12:06PM -0400, Herbert J. Bernstein said: => This version of RasMol is not in the public domain, but it is given freely => to the community in the hopes of advancing science. If you make changes, => please make them in a responsible manner, and please offer us the => opportunity to include those changes in future versions of RasMol. This is rather tangential to the topic, but why isn't RasMol simply placed under the GNU General Public License ? - arun charset="koi8-r" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3612.1700 ++++------+------+------+------+------+------+------+------+------+------+ From: "Sergey Vasil'ev" Subject: RE: RasMol Version 2.7.0.1 Date: Fri, 23 Apr 1999 13:23:28 +0400 To: > Arne Mueller's version 2.6x1. This combined version allows selection by > alternate conformers as well as by models, production of Ramachandran > printer plots (as in F. Bernstein's fisipl), and access to A. Mueller's > POVray output as POVray3 in addition to the existing POVray version 2 > output. (POVray3 should not be used in the PC or Mac version, yet). Sorry, but I can't find how to show information about how many NMR models has this PDB file. Sergey Vasil'ev /*------------------------------------------------ DNA-Protein Interaction DataBase project team. Belozersky Institute of Physico-Chemical Biology, Moscow State University & Inst. of Agricultural BioTechnology RAAS. 42 Timiryazevskaya St., Moscow 127550, RUSSIA email vasil@iab.ac.ru vasil@biocom.genebee.msu.su fax +7-095-9770947 ------------------------------------------------*/ References: X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Marc Saric Subject: Re: MSI/ Cerius Molecule File Format Date: Sat, 24 Apr 1999 14:07:28 +0200 To: rasmol@dhcp-srv2.oit.umass.edu Brendan O'Malley wrote: > > Is their a program that can convert *.msi files to a set of atomic coordinates and/or a file format that can be read by Rasmol or Chime? Thanks to everyone for help with my previous question. Just a quick guess: Babel??? It can read/write many common molecule-file-formats, maybe also msi??? On the other hand: MSI-apps should be able to save pdb-format, so... -- Bye, Marc Saric Visit my homepage http://homepage.ruhr-uni-bochum.de/Marc.Saric/ Visit the FS98 3D-accelerators FAQ at http://www.simflight.com/marc -----BEGIN PGP SIGNATURE----- Version: PGP for Personal Privacy 5.0 Charset: noconv iQA/AwUBNVixqiPrGHYouWn/EQLa7ACgr2TjKYnCykN5wcBA12HKdJQHCo0AoJYQ OcHnuzgguAy+EvWhe/fwG+3m =JQ9Y -----END PGP SIGNATURE----- ++++------+------+------+------+------+------+------+------+------+------+ From: Franklin Adler (by way of Eric Martz ) Subject: New release of Chime supports IE 5.0 on Windows Date: Sat, 24 Apr 1999 10:38:51 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Dear Chime User, Thank you for choosing Chime(TM) for your Intranet and Internet applications. Chime 2.0.2 is available for Windows 95 and Windows NT 4.0. This release has the following enhancements for the Windows platform: * Support for Internet Explorer 5.0 * Support for the Mouse Control Help Page in Internet Explorer 4.01 and 5.0 * Improved support for hot-linking to Interactive Simulations' Sculpt visualization application If you use Internet Explorer 5.0 on Windows 95 or NT, you should download this version of Chime. Chime software and documentation are delivered via the MDL Information Systems, Inc. (MDL) web site. To access the product, installation instructions, and technical materials, please use your web browser to connect to one of the following URLs: http://www.mdli.com/support/chime http://www-uk.mdli.com/support/chime Read the instructions on the web pages to download and install your software. Please check the MDL web site regularly since release notes, documentation and future updates of Chime will be delivered from that location. Thank you again for choosing Chime as your Intranet and Internet visualization tool. Sincerely, The Chime Team MDL Information Systems, Inc. chime-feedback@mdli.com ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: GNU and RasMol Date: Sun, 25 Apr 1999 13:47:56 -0400 To: rasmol@dhcp-srv2.oit.umass.edu [I am posting this message from Roger Sayle to circumvent technical difficulties. -Eric] Hi Arun, > This is rather tangential to the topic, but why isn't RasMol > simply placed under the GNU General Public License ? Richard Stallman was keen for RasMol to be included in the GNU suite under the GPL, but under the restriction that the GIF generation and Apple Macintosh specific code be removed. I believed that these features were major assets for the RasMol user community and risked commercial exploitation rather than strive for 100% political correctness. I also thought that the GPL was too restrictive not allowing many of the useful algorithms and novel implementations in RasMol to be used in commercial or other software. Unfortunately its impossible to allow students or other software developers to make use of integer square root, fake specular, lookup sphere rendering etc... without openning the door for someone to sell the same program under a different name. Roger -- Roger Sayle, E-mail: roger@metaphorics.com Bioinformatics Group, Metaphorics, WWW: http://www.metaphorics.com/ 419 East Palace Avenue, Tel: (+1) 505-984-0613 Santa Fe, New Mexico, 87501. Fax: (+1) 505-989-1200 ++++------+------+------+------+------+------+------+------+------+------+ Beginning May 1, 1999: ++++------+------+------+------+------+------+------+------+------+------+ From: Judy Voet Subject: H-bonds in tRNA Date: Tue, 4 May 1999 08:31:23 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Does anyone know why RasMol/Chime does not seem to find any H-bonds in tRNA? When I type hbond it replys "Number of H-bonds...0". How can I remedy this situation? I'm using the file 1tna.pdb. Thanks. Judy Judith G. Voet, J. H. Hammons Professor Swarthmore College jvoet1@swarthmore.edu Department of Chemistry 610-328-8520 500 College Avenue FAX 610-328-7355 Swarthmore, PA 19081 ++++------+------+------+------+------+------+------+------+------+------+ From: Robert Bateman Subject: new kinemage site Date: Tue, 04 May 1999 13:40:11 -0400 To: rasmol@dhcp-srv2.oit.umass.edu For those of you that are not aware of it yet, the Kinemage web site was rebuilt this spring at http://kinemage.biochem.duke.edu/website/kinhome.htm and contains the latest versions of MAGE and PREKIN as well as the recently released supplement to Branden and Tooze. We are trying to gather information on kinemage use, so if you have used kinemages before, please fill out the kinemage survey form at http://www.duke.edu/~dcr/surveyform.htm Thanks. Bob Bateman Professor of Biochemistry on sabbatical in the Richardson lab ++++------+------+------+------+------+------+------+------+------+------+ From: Duane Sears Subject: Re: Use studies Date: Tue, 04 May 1999 14:12:38 -0700 To: rasmol@dhcp-srv2.oit.umass.edu Cc: sears@lifesci.lscf.ucsb.edu Dear Patrick, I have been developing and using RasMol/Chime-based interactive web pages in a Biochemistry Computer Laboratory I've been teaching for a few years. My main focus has been to emphasize critical thinking and inquiry-based learning through the exploration of biological structures and their functions. You can view some of the contents of the interactive multimedia approach to my course at the following web site (although many of the links may not work because I just began putting a new "front end" on the site in order to make navigation to different topics easier.) http://mentor.lscf.ucsb.edu/mcdb108a/ I am also in the early stages of deveolping a reliable assessment of the pedagogical value of various activities. I would be interested in participating in your workshop if invited depending on the exact time of the meeting. Duane EST, you wrote: >Dear Rasmolers and Chimers, > I would like to organize a session on Rasmol/Chime at the16th >Biennial Chem Ed conference at the University of Michigan in summer >2000. I'm particularly interested in people willing to present >documentation on the successful (or unsuccessful) use of these >programs. While a presentation on "what I've done" is useful, >results from student feedback and scholarly studies on the >effectiveness! of the programs would be particularly appreciated. >Reply to me at flash@ashtabula.kent.edu. > >Patrick Flash >Kent-Ashtabula Campus >Ashtabula, OH 44004 > > __________________________________________________________ Professor Duane W Sears Department of Molecular, Cellular and Developmental Biology University of California Santa Barbara, CA 93106 Phones: 805-893-3499 (Office) 805-893-4272(Lab) 805-893-4724(FAX) E-mail: sears@lifesci.ucsb.edu Instructional web sites @ Immunology -- http://mentor.lscf.ucsb.edu/mcdb133/ Biochemistry -- http://mentor.lscf.ucsb.edu/mcdb108a/ ++++------+------+------+------+------+------+------+------+------+------+ From: Brian Salter-Duke Subject: pdb and xyz files in Chime and Rasmol over the web. Date: Wed, 5 May 1999 11:24:06 +1100 To: rasmol@dhcp-srv2.oit.umass.edu When I just used rasmol as helper application over the web, I configured the system so *.pdb files brought up rasmol while *.xyz files brought up either xmol or review depending on the system. Now I have chime and want to continue to use it for *.pdb files, but I want to continue to use xmol or review for *.xyx files. Unfortunately the installation of chime gets chime brought up for both *.pdb and *.xyz files. Is there any way I can change this? Cheers, Brian. -- Associate Professor Brian Salter-Duke (Brian Duke) School of Mathematical and Physical Sciences, Northern Territory University, Darwin, NT 0909, Australia. Phone 08-89466702. Fax 08-89466847 e-mail: b_duke@lacebark.ntu.edu.au WWW http://lacebark.ntu.edu.au/chemistry References: <19990505112406.A18971@lacebark.ntu.edu.au> x-mac-creator="4D4F5353" ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: pdb and xyz files in Chime and Rasmol over the web. Date: Wed, 05 May 1999 07:23:40 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Brian, What are your platform, browser, and version? Tim Driscoll Brian Salter-Duke wrote: > When I just used rasmol as helper application over the web, I > configured the system so *.pdb files brought up rasmol while > *.xyz files brought up either xmol or review depending on the > system. Now I have chime and want to continue to use it for > *.pdb files, but I want to continue to use xmol or review > for *.xyx files. Unfortunately the installation of chime > gets chime brought up for both *.pdb and *.xyz files. > > Is there any way I can change this? > > Cheers, Brian. > -- > Associate Professor Brian Salter-Duke (Brian Duke) > School of Mathematical and Physical Sciences, Northern Territory University, > Darwin, NT 0909, Australia. Phone 08-89466702. Fax 08-89466847 > e-mail: b_duke@lacebark.ntu.edu.au WWW http://lacebark.ntu.edu.au/chemistry -- ******************** Timothy Driscoll UMass Amherst Molecular and Cellular Biology Chemistry-Biology Interface Program * Department of Chemistry Amherst College Amherst, MA 01002 413 542 2738 * http://merckx.chem.amherst.edu/tdriscoll/ ******************** ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: pdb and xyz files in Chime and Rasmol over the web. Date: Wed, 05 May 1999 09:51:18 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Hi, I presume you are using a UNIX system? Anyway, go to Netscape -> Preferences and select Applications under Navigator. In the list of applications, select chemical/x-xyz You will note that the Chime plug in is selected. Select Application instead and type in the path for review or xmol (or use the Choose...) Click OK. Should work. Shoba ==============================*** UPDATED ***========================== Shoba Ranganathan, Ph D Tel:+61-2-9351-1870 ANGIS, Bay 16, Suite 104 Toll free:1-800-728-028 Australian Technology Park Fax:+61-2-9351-1878 Eveleigh NSW 1430 Australia Personal URL: http://seal.angis.org.au/~shoba ================MolMod Home Page: http://molmod.angis.org.au=========== References: <209E72F2E67@ksuac.ashtabula.kent.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Patrick Flash" Subject: Re: Use studies Date: Wed, 5 May 1999 09:55:09 EST To: rasmol@dhcp-srv2.oit.umass.edu Cc: sears@lifesci.lscf.ucsb.edu Duane, The meeting is scheduled for July 30-Aug 3 2000 at the U of Michigan. This is my first attempt at organizing a session for a BCCE so I'm unssure how things will work. If we get enough participants, the organizers will schedule a session. The length of the session could run from a morning to multiple days, depending on the participation level. Each person gets about 20 minutes and usually computer projection equipment is available. So far I've heard from about a half dozen people and as the time gets closer and the advertizing for papers gets broader coverage, I hope we'll get lots more. Even if a dedicated session doesn't materialize, I would still encourage you to present in a general session. Hope you can come. Check out the conference web site at http://www.umich.edu/~bcce Patrick Flash Kent State-Ashtabula Campus X-Envelope-to: rasmol@lists.umass.edu X-VMS-To: IN%"rasmol@lists.umass.edu" X-VMS-Cc: WCOLEMAN ++++------+------+------+------+------+------+------+------+------+------+ From: FLICK COLEMAN Subject: Re: Use studies Date: Wed, 05 May 1999 11:08:06 -0500 (EST) To: rasmol@dhcp-srv2.oit.umass.edu Pat, I would like to participate in the session. In particular I would like to talk about using Chime/RasMol/WebLabView in Introductory and Inorganic Chemistry, with a focus on metal complexes, organometallics, comparison of isomers and teaching crystal latties. I have some data from the past five years and could present it also (but am a little sceptical of its value). Flick Coleman William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 email: wcoleman@wellesley.edu phone: 781-283-3129 fax: 781-283-3642 web: http://www.wellesley.edu/Chemistry/colemanw.html References: ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: H-bonds in tRNA Date: Wed, 05 May 1999 19:11:32 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Cc: jvoet1@swarthmore.edu Judy, are you aware that Rasmol/Chime only show hbonds based on simple rules for protein backbone and DNA double helix? They don't actually look at distances, and they never show e.g. nonbackbone hbonds with the hbonds command. In 1d66, there is one GC pair out of alignment and one 'hbond' is drawn across several intervening atoms! Evidently, they have no rules for RNA, tho even recognizing RNA is problematic since AGC are always recognized as DNA regardless of whether ribose or deoxyribose. It should be possible to use another program to generate real hbond information, and then display that information in Chime (in RasMol one could do it only as monitor lines). But I haven't worked out the details. Swiss PDB Viewer shows the hbonds. P.S. I assume you meant 1tra.pdb instead of 1tna. -Eric At 5/4/99, you wrote: >Does anyone know why RasMol/Chime does not seem to find any H-bonds in >tRNA? When I type hbond it replys "Number of H-bonds...0". How can I >remedy this situation? I'm using the file 1tna.pdb. > >Thanks. > >Judy > > >Judith G. Voet, J. H. Hammons Professor Swarthmore College >jvoet1@swarthmore.edu Department of Chemistry >610-328-8520 500 College Avenue >FAX 610-328-7355 Swarthmore, PA 19081 > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Robert Bateman Subject: assessment instrument Date: Sat, 08 May 1999 12:14:25 -0400 To: rasmol@dhcp-srv2.oit.umass.edu I am very interested in hearing about how others have evaluated the effectiveness of using computer modeling of biomolecules (no matter what the program) in the biochemistry classroom. How do we know the models are more effective than illustrations in the text? If anyone has an assessment instrument that addresses this issue I would sure like to see it. Bob Bateman _______________________ Robert C. Bateman, Jr. Associate Professor Department of Chemistry and Biochemistry University of Southern Mississippi 39406-5043 robert.bateman@usm.edu http://ocean.otr.usm.edu/~rbateman ++++------+------+------+------+------+------+------+------+------+------+ From: "Julian A. Peterson" Subject: RE: assessment instrument Date: Sun, 9 May 1999 09:00:46 -0500 To: "'rasmol@lists.umass.edu'" No real assessment other than student comments like: WOW is that what they really look like. I would never have realized that from a two-dimensional picture! -----Original Message----- Sent: Saturday, May 08, 1999 11:14 AM From: Robert Bateman [SMTP:robert.bateman@usm.edu] Subject: assessment instrument To: rasmol@dhcp-srv2.oit.umass.edu I am very interested in hearing about how others have evaluated the effectiveness of using computer modeling of biomolecules (no matter what the program) in the biochemistry classroom. How do we know the models are more effective than illustrations in the text? If anyone has an assessment instrument that addresses this issue I would sure like to see it. Bob Bateman _______________________ Robert C. Bateman, Jr. Associate Professor Department of Chemistry and Biochemistry University of Southern Mississippi 39406-5043 robert.bateman@usm.edu http://ocean.otr.usm.edu/~rbateman ++++------+------+------+------+------+------+------+------+------+------+ From: "Brian White" Subject: evaluation Date: Mon, 10 May 1999 10:45:00 -0400 To: "rasmol@lists.umass.edu" This is a multi-part message in MIME format. --------------59D7610050B22C9806B212E8 Here is my crude, preliminary attempt at evaluation. I handed out the attached survey in my class (about 200 students) before I talked about proteins at all. I then gave 1/2 the class the same survey after I'd lectured using chime. The other 1/2 got it after I had lectured & they'd used chime in lab. We're still compiling the results. Let me know what you think. Brian -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://omega.cc.umb.edu/~bwhite/ --------------59D7610050B22C9806B212E8 Content-Description: Microsoft Word Document Content-Disposition: inline; filename="protein structure 1" 0M8R4KGxGuEAAAAAAAAAAAAAAAAAAAAAOwADAP7/CQAGAAAAAAAAAAAAAAABAAAAAQAAAAAA AAAAEAAAAgAAAAEAAAD+////AAAAAAAAAAD///////////////////////////////////// //////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////// 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++++------+------+------+------+------+------+------+------+------+------+ From: Robert Bateman Subject: Re: evaluation Date: Mon, 10 May 1999 15:42:10 -0400 To: rasmol@dhcp-srv2.oit.umass.edu I like your approach of a specific problem that requires 3-D insight rather than the more general "how did you feel about the class" approach. I would like to see this listserv do some brainstorming and come up with a generally acceptable framework for evaluating the use of computerized molecular models in undergraduate education. Bob At 10:45 AM 5/10/99 -0400, you wrote: >Here is my crude, preliminary attempt at evaluation. >I handed out the attached survey in my class (about 200 students) before >I talked about proteins at all. >I then gave 1/2 the class the same survey after I'd lectured using >chime. >The other 1/2 got it after I had lectured & they'd used chime in lab. >We're still compiling the results. > >Let me know what you think. > >Brian >-- >Prof. Brian White >Biology Department >University of Massachusetts, Boston >100 Morrissey Blvd >Boston MA 02125 >(617) 287-6630 >fax:(617) 287-6650 >brian.white@umb.edu >http://omega.cc.umb.edu/~bwhite/ > >Attachment Converted: "c:\my documents\eudora\attach\protein structure 1.doc" > >Attachment Converted: "c:\my documents\eudora\attach\protein structure 2.doc" > _______________________ Robert C. Bateman, Jr. Associate Professor Department of Chemistry and Biochemistry University of Southern Mississippi 39406-5043 robert.bateman@usm.edu http://ocean.otr.usm.edu/~rbateman References: <3.0.5.32.19990508121425.0099ee08@kinemage.biochem.duke.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Jeffrey A. Cohlberg" Subject: Re: assessment instrument Date: Mon, 10 May 1999 11:48:39 -0700 To: rasmol@dhcp-srv2.oit.umass.edu This is a multi-part message in MIME format. --------------E4979011C6D Robert Bateman wrote: > > I am very interested in hearing about how others have evaluated the > effectiveness of using computer modeling of biomolecules (no matter what > the program) in the biochemistry classroom. How do we know the models are > more effective than illustrations in the text? If anyone has an assessment > instrument that addresses this issue I would sure like to see it. > Bob Bateman I developed a self-guided exercise in the use of Cn3D. The students had to look at a number of protein structures illustrating helices, beta sheets, myoglobin, and hemoglobin and answer questions about them. This was about a third of the way through the semester. At the end of the semester I administered the attached questionnaire. I can't locate the results at the moment, but I remember that the students overwhelmingly thought the exercise was useful and taught them a lot. Most of them wanted more use of molecular modeling in lecture, and a substantial although lesser number thought there should have been more assignments using molecular modeling. Only a very few had voluntarily used the program on their own beyond the assignment. And not a single student admitted to copying his friend's responses rather than actually doing the assignment. (Haha! -- I'm a bit skeptical of this last answer, since while the students were filling out the questionnaires in class, one student actually copied her neighbor's answers to the questionnaiare!) Anyway, for what it's worth, here's the questionnaire. Jeff Cohlberg -- Jeffrey A. Cohlberg, Professor Department of Chemistry and Biochemistry California State University, Long Beach 1250 Bellflower Blvd. Long Beach, CA 90840 phone (562) 985-4944 fax (209) 821-4471 --------------E4979011C6D Content-Disposition: inline; filename="class survey" /jcAIwAAAAAAAAQAABkAAAAAAAAAAAEAAAAHcgAADZkAAAAAAAAGcgAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAADAAAGgAADAAAGgAADBoAAAAADBoAAAAADBoADgAADCgAEgAADDoAAAAA DDoAAAAADDoAAAAADDoACgAADEQACgAADE4AAAAADE4AYgAADLAAeAAADDoAAAAADSgAIAAA DUgAGAAADW8AKgAADZkAAAAADBoAAAABAAEAAA1vAAAAAA1gAA8AAA1vAAAAAA1vAAAAAA2Z AAAAAA1vAAAAAA1vAAAAAA1vAAAAAA1vAAAAAA1vAAAAAA1vAAAAAENoZW0gNDQxQSAtLSBF dmFsdWF0aW9uIG9mIENvbXB1dGVyIE1vZGVsaW5nIEFzc2lnbm1lbnQNMS4gSG93IGRpZCB5 b3UgZG8gdGhlIGFzc2lnbm1lbnQ/DQkJSSBkaWQgdGhlIGFzc2lnbm1lbnQgYnkgbXlzZWxm Lg0JCUkgd29ya2VkIG9uIHRoZSBhc3NpZ25tZW50IGJ5IG15c2VsZiwgd2l0aCBoZWxwIGZy b20gc29tZW9uZSBlbHNlLg0JIAlJIHdvcmtlZCBvbiB0aGUgYXNzaWdubWVudCB0b2dldGhl ciB3aXRoIGFub3RoZXIgc3R1ZGVudCBpbiB0aGUgY2xhc3MuDQkJSSBkaWQgbm90IHdvcmsg 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AAAAAAAAAAIAAAAABAIEBQAAAAA94C/QA/AFEAPwBRAAAALQQgAAAQABAAFCAAAAAAAASAAY Dy06RFcgNjAwIFNlcmllcwAKAAAAAAABAAAAEAhQYWxhdGlub4ABAQAAAAG9AAABvQAGgACA AAAAAb0AAAAAACgAAgHVAi4AKAACAPoCLgAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAA= --------------E4979011C6D-- References: <3.0.5.32.19990508121425.0099ee08@kinemage.biochem.duke.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Just wondering... Date: Tue, 11 May 1999 08:23:53 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Does this conversation about testing and assessment belong on the RasMol list? I don't need statistics to tell me that better illustrations are helpful. I just want to know more about how to do it. Cheers! ***************************** Gale Rhodes mailto:rhodes@usm.maine.edu http://www.usm.maine.edu/~rhodes/GRHomePage.html Professor of Chemistry Chemistry Department University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 Phone: (207)780-4734 Fax: (207)780-5607 References: <37372A07.726F@csulb.edu> <3.0.5.32.19990508121425.0099ee08@kinemage.biochem.duke.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: Re: Just wondering... Date: Tue, 11 May 1999 09:05:51 -0400 To: rasmol@dhcp-srv2.oit.umass.edu >Does this conversation about testing and assessment belong on the RasMol list? > >I don't need statistics to tell me that better illustrations are helpful. I >just want to know more about how to do it. > >Cheers! > I have been following this conversation with great interest. I think that many of us are enthusiastic about molecular visualization and teaching, and it is both useful and natural, as scientists, that many of us would want to quantify the results of these teaching methods. This quantification is often necessary to persuade funding sources to support new approaches. So I, for one, feel that it has a place on this list. Perhaps those commenting on this could make sure to use the "evaluation" subject line entry to make it easier for those not interested to just hit "delete". Of course, if this is not a topic of interest to the majority or a significant minority of the list, then it should continue privately between interested parties. Count me in! Frieda _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ Frieda Reichsman, Ph.D. _/_/_/_/_/ Biochemistry and Molecular Biology _/_/_/_/_/ University of Massachusetts _/_/_/_/_/ Amherst, MA 01003 _/_/_/_/_/ Phone: (413) 545-4029 _/_/_/_/_/ Fax: (413) 545-3291 _/_/_/_/_/ http://www.bio.umass.edu/biochem/reichsman _/_/_/_/_/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ "Time flies like an arrow, but fruit flies like a banana." -Groucho Marx References: <37372A07.726F@csulb.edu> <3.0.5.32.19990508121425.0099ee08@kinemage.biochem.duke.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Just wondering... Date: Tue, 11 May 1999 09:34:45 -0400 To: rasmol@dhcp-srv2.oit.umass.edu At 5/11/99, Gale Rhodes wrote: >Does this conversation about testing and assessment belong on the RasMol list? > >I don't need statistics to tell me that better illustrations are helpful. I >just want to know more about how to do it. > >Cheers! I, for one, am intensely interested in this discussion of assessment of the impact of molecular visualization in teaching. Those of us who request funding from the US NSF *must* deal with assessment! If, in the future, this discussion continues and results in frequent messages, we could always create a separate list. But for now, I think this list is exactly where this discussion belongs. My 2 cents (facing the 6/7/99 NSF CCLI deadline ...), -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 To unsubscribe from the RasMol Email List, change your address, etc., see References: <3.0.5.32.19990510154210.009adca8@kinemage.biochem.duke.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Brian White" Subject: Re: evaluation Date: Tue, 11 May 1999 10:41:41 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Robert - Thanks - I was hoping to get at what was going on inside their heads. As for a "generally acceptable format" - I'm not so sure - we may have different goals for using chime. It would be interesting to see what our goals are, first. Brian Robert Bateman wrote: > I like your approach of a specific problem that requires 3-D insight rather > than the more general "how did you feel about the class" approach. I would > like to see this listserv do some brainstorming and come up with a > generally acceptable framework for evaluating the use of computerized > molecular models in undergraduate education. Bob > _______________________ > Robert C. Bateman, Jr. > Associate Professor > Department of Chemistry and Biochemistry > University of Southern Mississippi 39406-5043 > robert.bateman@usm.edu > http://ocean.otr.usm.edu/~rbateman -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://omega.cc.umb.edu/~bwhite/ References: <3.0.5.32.19990508121425.0099ee08@kinemage.biochem.duke.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Brian White" Subject: Re: Just wondering... Date: Tue, 11 May 1999 10:55:16 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Perhaps not, but... Gale Rhodes wrote: > Does this conversation about testing and assessment belong on the RasMol list? > > I don't need statistics to tell me that better illustrations are helpful. before Galileo, people didn't need statistics to tell them that the sun went around the earth. Sometimes you'd be surprised..... > I > just want to know more about how to do it. > > Cheers! > > ***************************** > > Gale Rhodes mailto:rhodes@usm.maine.edu > http://www.usm.maine.edu/~rhodes/GRHomePage.html > Professor of Chemistry > Chemistry Department > University of Southern Maine > PO Box 9300 > Portland, Maine 04104-9300 > Phone: (207)780-4734 > Fax: (207)780-5607 Brian -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://omega.cc.umb.edu/~bwhite/ ++++------+------+------+------+------+------+------+------+------+------+ From: stone@fairvax.ucdavis.edu Subject: Re: Just wondering... Date: Tue, 11 May 1999 10:47:52 EDT To: rasmol@dhcp-srv2.oit.umass.edu At 5/11/99, Gale Rhodes wrote: }>Does this conversation about testing and assessment belong on the RasMol }>list? }>I don't need statistics to tell me that better illustrations are helpful. I }>just want to know more about how to do it. }I, for one, am intensely interested in this discussion of assessment of the }impact of molecular visualization in teaching. I think it's plenty interesting, and appropriate to the list, but these binary .doc attachments I find intensely annoying. They haven't yet released M$Word for VMS (or *nix, for that matter), wich makes it basically impossible for me to decode them. If you're going to include documents like that, is there any chance you could do them as text, or make a web page of them and reference the URL? -- Remington JS Stone Dept. of Biophysics UCDavis, CA, 95616 References: <37372A07.726F@csulb.edu> <3.0.5.32.19990508121425.0099ee08@kinemage.biochem.duke.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eugene Leitl Subject: Re: Just wondering... Date: Tue, 11 May 1999 11:55:29 -0700 (PDT) To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu Eric Martz writes: > I, for one, am intensely interested in this discussion of assessment of the > impact of molecular visualization in teaching. Those of us who request I think visualization alone is only the one side of the coin, an interactive chemistry simulator would also illustrate structural dynamics and reactivity. There is for instance OpenChem http://openchem.org and MMTK http://starship.python.net/crew/hinsen/mmtk.html which both use RasMol for visualization (OpenChem uses just the rendering engine). > funding from the US NSF *must* deal with assessment! If, in the future, > this discussion continues and results in frequent messages, we could always > create a separate list. But for now, I think this list is exactly where > this discussion belongs. Very true. Regards, Eugene Leitl References: <199905111335.JAA14307@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Patrick Flash" Subject: Re: Just wondering... Date: Tue, 11 May 1999 15:12:56 EST To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu Eugene, Can you give another reference for OpenChem. The one in your message doesn't match a URL Pat Flash Kent-Ashtabula References: <199905111335.JAA14307@marlin.bio.umass.edu> <14136.31747.511374.749307@lrz.de> ++++------+------+------+------+------+------+------+------+------+------+ From: Eugene Leitl Subject: Re: Just wondering... Date: Tue, 11 May 1999 13:14:39 -0700 (PDT) To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu Patrick Flash writes: > Eugene, > Can you give another reference for OpenChem. The one in your > message doesn't match a URL Sorry, probably just a typo on my part: http://www.openchem.org/ It is a derivate of Konrad Hinsen's MMTK, and is yet in an early stage. (Hint: developers welcome). Eugene > Pat Flash > Kent-Ashtabula References: <199905111335.JAA14307@marlin.bio.umass.edu> <14136.31747.511374.749307@lrz.de> ++++------+------+------+------+------+------+------+------+------+------+ From: "Peter C. McCluskey" Subject: Re: Just wondering... Date: Tue, 11 May 1999 13:46:06 -0700 To: rasmol@dhcp-srv2.oit.umass.edu eugene.leitl@lrz.uni-muenchen.de (Eugene Leitl) writes: >Patrick Flash writes: > > Eugene, > > Can you give another reference for OpenChem. The one in your > > message doesn't match a URL > >Sorry, probably just a typo on my part: http://www.openchem.org/ >It is a derivate of Konrad Hinsen's MMTK, and is yet in an early >stage. (Hint: developers welcome). It hasn't reached the stage where more developers are likely to be usefull. Maybe in another month it will reach that stage. And end-users should definitely wait at least a month before expecting anything valuable. It uses a Python interface to RasMol that I originally wrote for use with MMTK, and it will probably make substantial use of MMTK, but it is unlikely to be primarily an MMTK derivative - it's more of an attempt at making a better Hyperchem. ------------------------------------------------------------------------ Peter McCluskey | Critmail (http://crit.org/critmail.html): http://www.rahul.net/pcm | Accept nothing less to archive your mailing list ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Electrostatic potential: SPDBV vs. Chime? Date: Tue, 11 May 1999 19:13:33 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Swiss PDB Viewer version 3.5beta1 is now available, and has new abilities to do molecular surfaces with molecular electrostatic potential (MEP) coloring (or electrostatic potential maps), as well as GROMOS 43B1 force field energy minimization. Congratulations to Nicolas and Manuel, since the documentation, although scanty, is already better than that for Chime in the areas of surfaces and MEP! Has anyone familiar with MEP (which I'm not) created the MEP-colored surfaces for the same molecule in SPDBV and Chime to compare them? If so, please share the results and perhaps some snapshots. (Don't attach snapshot GIF's to any message to the list! Many of us are using slow modem connections, including me half of the time. Make them available on the web.) Speaking of which, is there a good illustrated explanation of MEP and MLP on the web somewhere? The URL for SPDBV 3.5b1 is http://expasy.hcuge.ch/spdbv/mainpage.html (the BNL mirror in the US has not been updated since version 3.1). -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: "Dr. Don Harden" Subject: 3D graphics Date: Fri, 14 May 1999 15:50:34 -0400 (EDT) To: rasmol@dhcp-srv2.oit.umass.edu Hello, Does anyone know of a way to convert the images that RasMol displays so well into 3D graphics files? That is one of the following file formats or other 3D format. 2DMF/3DMF - QuickDraw 3D Metafile 3DS - Autodesk 3D Studio ART - Another Ray Tracer AVS - Application Visualization System BRL-CAD - Ballistic Research Laboratory CAD BYU - BYU Movie CAD-3D COB - Calgari trueSpace2 File Format DKB - DKB-Trace DXF - Autodesk Drawing eXchange Format IFF - Imagine Object File Format [TDDD (3D Data Description)] MSDL - Manchester Scene Description Language OBJ - Wavefront Object OFF - Object File Format PLY - ZipPack POL - InnovMetric Software Polygon Models Format POV - Persistence of Vision Raytracing RAD - Radience RAY - Rayshade Thanks, Don ---------------------------------------------------- Dr. Don Harden don-harden@Gsu.EDU Department of Chemistry Georgia State University ph: (404) 651-3580 Atlanta, Ga. 30302 fax: (404) 651-1416 http://chemistry.Gsu.EDU/glactone ++++------+------+------+------+------+------+------+------+------+------+ From: AGC Subject: inquiry Date: Fri, 16 Apr 1999 00:29:11 -0500 To: "rasmol@lists.umass.edu" from a seq of aminoacids how can I generate a pdb file? ++++------+------+------+------+------+------+------+------+------+------+ From: Me Subject: rasmol & linux Date: Sun, 16 May 1999 23:15:59 -0700 To: rasmol@dhcp-srv2.oit.umass.edu Hi...I'm getting linux configured & so far, so good - however I downloaded the tar gz file and decompressed it, and the binary won't run ("cannot run binary file" error message). Is thete a trick to starting rasmol in linux, or mayhaps did I get the wrong version? I'm running redhat 5.x. Looking forward to trying some unix native mol. modeling software...... Thank you kindly. ++++------+------+------+------+------+------+------+------+------+------+ From: slaton Subject: Re: rasmol & linux Date: Sun, 16 May 1999 23:45:39 -0700 To: "Rasmol Email List" On 5/16/99 11:15 PM Me wrote: >Hi...I'm getting linux configured & so far, so good - however I downloaded >the tar gz file and decompressed it, and the binary won't run ("cannot run >binary file" error message). Is thete a trick to starting rasmol in linux, >or mayhaps did I get the wrong version? I'm running redhat 5.x. >Looking forward to trying some unix native mol. modeling software...... Which version of Rasmol are you attempting to run? Did you download a Linux binary from somewhere or compile from source (again, which version)? I recently referred a colleague to the Rasmol 2.7.0.1 source that Herbert Bernstein announced a few weeks ago. He downloaded the source tarfile at http://www.bernstein-plus-sons.com/software/rasmol/RasMol.tar.gz and reported that it compiled without trouble under Linux/ppc (release 3 or 4, not sure). I haven't tried compiling this version under Linux/x86 but will give it a shot on a Redhat 5.2 box when I get a chance. good luck, Slaton Lipscomb C4: Computers in Chemistry at Cabrillo College http://c4.cabrillo.cc.ca.us X-Accept-Language: de ++++------+------+------+------+------+------+------+------+------+------+ From: " Dr. Frank Eblinger" Subject: 3D graphics Date: Mon, 17 May 1999 09:47:03 +0200 To: "rasmol@lists.umass.edu" Don: With the new RasMol vs. 2.7.0.1 (http://www.bernstein-plus-sons.com/software/rasmol/) it is possible to convert almost all rasmol displays (except ribbons or strands) into povray files: write povray3 filename Frank ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Re: inquiry Date: Mon, 17 May 1999 07:33:56 -0400 To: acad@accefyn.org.co, rasmol@dhcp-srv2.oit.umass.edu >from a seq of aminoacids how can I generate a pdb file? You can do it with SwissPdbViewer. Write a text file with the sequence in one-letter abbreviations, like this: SQ MQQPMNYPCP QIFWVDSSAT SSWAPPGSVF PCPSCGPRGP DQRRPPPPPP // Start SPV, cancel the open dialog, and pick SwissModel: Load Raw Sequence to Model. SPV builds the sequence as a single alpha helix. Then using Build tools, you can reset conformational angles to suit yourself. For instruction about how to use SPV, see http://www.usm.maine.edu/~rhodes/SPVTut/index.html For a comparison of RasMol and SPV, see http://www.usm.maine.edu/~rhodes/0Help/Which%3F.html Even if you primarily use RasMol, SPV has many useful features for handling, merging, creating files that are hard or impossible to create in RasMol. Cheers! Cheers! ***************************** Gale Rhodes mailto:rhodes@usm.maine.edu http://www.usm.maine.edu/~rhodes/GRHomePage.html Professor of Chemistry Chemistry Department University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 Phone: (207)780-4734 Fax: (207)780-5607 References: <3.0.6.32.19990516231559.0079c6c0@asis.com> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: rasmol & linux Date: Mon, 17 May 1999 14:35:24 +0100 To: rasmol@dhcp-srv2.oit.umass.edu Me wrote: > > Hi...I'm getting linux configured & so far, so good - however I downloaded > the tar gz file and decompressed it, and the binary won't run ("cannot run > binary file" error message). Is thete a trick to starting rasmol in linux, > or mayhaps did I get the wrong version? I'm running redhat 5.x. > Looking forward to trying some unix native mol. modeling software...... > Thank you kindly. Hi, Yes, sounds like you got the wrong binary. Maybe a silly question, but are you sure you got the linux binary and not e.g. a Silicon Graphics one? I've never heared about souch a problem but maybe it's a libc/glibc problem, anybody here who got experience with that? By the way, if you've configured a linux system on your PC, It'll be a good idea to test your configuration by compiling rasmol your self. Have look in the 'INSTALL' file about how to compile rasmol for a unix/linux system. If you can't get along with it, let me know about it. greetings, Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)171 2693405 | Fax : +44-(0)171 269 3258 email : a.mueller@icrf.icnet.uk | http://www.icnet.uk/bmm/ References: <3.0.6.32.19990516231559.0079c6c0@asis.com> <37401B1C.87D6B6C9@icrf.icnet.uk> X-Accept-Language: German/Germany, de-DE, en ++++------+------+------+------+------+------+------+------+------+------+ From: Karl Sarnow Subject: Re: rasmol & linux Date: Mon, 17 May 1999 16:27:02 +0200 To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu Arne Mueller wrote: > > Me wrote: > > > > Hi...I'm getting linux configured & so far, so good - however I downloaded > > the tar gz file and decompressed it, and the binary won't run ("cannot run > > binary file" error message). Is thete a trick to starting rasmol in linux, > > or mayhaps did I get the wrong version? I'm running redhat 5.x. > > Looking forward to trying some unix native mol. modeling software...... > > Thank you kindly. > > Hi, > > Yes, sounds like you got the wrong binary. Maybe a silly question, but > are you sure you got the linux binary and not e.g. a Silicon Graphics > one? I've never heared about souch a problem but maybe it's a libc/glibc > problem, anybody here who got experience with that? > > By the way, if you've configured a linux system on your PC, It'll be a > good idea to test your configuration by compiling rasmol your self. Have > look in the 'INSTALL' file about how to compile rasmol for a unix/linux > system. If you can't get along with it, let me know about it. > Another potential problem could be the resolution. In the original binaries, you will find a version of rasmol running only in an 8-Bit color environment. You need to recomplie the source with other color settings, when you want to use your 24Bit-color card. If this was your problem, you may also download the 32bit binaries from my homepage: http://www.h.shuttle.de/h/dadoka/rasmol/ CU karl -- Dr. Karl Sarnow Teacher at Gymnasium Isernhagen German national co-ordinator of the European Schools Project e-Mail: karl@dadoka.h.ni.schule.de Attention: New URL: http://www.shuttle.schule.de/h/dadoka References: <3716CAA6.EDF29623@accefyn.org.co> ++++------+------+------+------+------+------+------+------+------+------+ From: Eugene Leitl Subject: inquiry Date: Mon, 17 May 1999 11:13:21 -0700 (PDT) To: acad@accefyn.org.co Cc: "rasmol@lists.umass.edu" AGC writes: > from a seq of aminoacids how can I generate a pdb file? Try X-PLOR or TINKER. References: <199904251749.NAA18015@marlin.bio.umass.edu> <3.0.6.32.19990516231559.0079c6c0@asis.com> ++++------+------+------+------+------+------+------+------+------+------+ From: Eugene Leitl Subject: rasmol & linux Date: Mon, 17 May 1999 11:18:28 -0700 (PDT) To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu Me writes: > Hi...I'm getting linux configured & so far, so good - however I downloaded > the tar gz file and decompressed it, and the binary won't run ("cannot run > binary file" error message). Is thete a trick to starting rasmol in linux, Try chmod +x rasmol, but it is most probably due to local directory not being in the search path. Try typing ./rasmol in the directory containing the extracted tarball. > or mayhaps did I get the wrong version? I'm running redhat 5.x. > Looking forward to trying some unix native mol. modeling software...... Try http://sal.kachinatech.com for an extensive list. > Thank you kindly. Eugene References: <3716CAA6.EDF29623@accefyn.org.co> <14144.23596.299319.75473@lrz.de> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Christopher Hogue Subject: Re: inquiry Date: Mon, 17 May 1999 14:31:38 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Hi All, AGC writes: > from a seq of aminoacids how can I generate a pdb file? Our conformer generator software makes probabilistic all-atom proteins from sequence. For one-offs, try: http://bioinfo.mshri.on.ca/trades/conform.html up to 250 residues This is easy, just paste in the sequence... For larger tries download "foldtraj" the command-line version, which is unlimited in the number of residues: ftp://bioinfo.mshri.on.ca/pub/TraDES/ Cheers, Chris --------------------------------------- Christopher W.V. Hogue, Ph.D. Samuel Lunenfeld Research Institute Mt. Sinai Hospital 600 University Ave. Toronto Ontario Canada M5G 1X5 (416) 586-4800 xt2866 fax (416) 586-8857 hogue@mshri.on.ca http://bioinfo.mshri.on.ca mmciflist@ndbdev.rutgers.edu X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id WAA00291 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: RasMol 2.7.0.1 mirrors Date: Mon, 17 May 1999 21:51:48 -0400 To: pdb-l@rcsb.org, rasmol@dhcp-srv2.oit.umass.edu, We are pleased to say that, thanks to Brian McMahon at the IUCr office in Chester, the RasMol 2.7.0.1 web pages are being now being mirrored at: England: IUCr, Chester, England http://www.iucr.org/iucr-top/cif/software/rasmol/ France: Université P. et M. Curie, Paris, France http://www.se.iucr.org/iucr-top/cif/software/rasmol/ Israel: Weizmann Institute of Science, Rehovot, Israel http://www.il.iucr.org/iucr-top/cif/software/rasmol/ South Africa: University of the Witwatersrand, South Africa http://www.za.iucr.org/iucr-top/cifsoftware/rasmol/ Sweden: University of Stockholm, Stockholm, Sweden http://www.fr.iucr.org/iucr-top/cif/software/rasmol/ Switzerland: University of Geneva, Geneva, Switzerland http://www.ch.iucr.org/iucr-top/cif/software/rasmol/ USA: SDSC, San Diego, California, USA http://www.us.iucr.org/iucr-top/cif/software/rasmol/ In addition the current and development versions are at: http://www.bernstein-plus-sons.com/software/rasmol/ ftp://ftp.bernstein-plus-sons.com/software/rasmol/ Note that the RasMol site at U. Mass Amherst does NOT point to RasMol 2.7.0.1 at this time. ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-516-286-1339 FAX: 1-516-286-1999 ===================================================== ++++------+------+------+------+------+------+------+------+------+------+ From: "Robert M. Horton" Subject: Grant opportunity for teaching chemistry Date: Tue, 18 May 1999 22:48:24 -0700 To: rasmol list Dear Rasmoleans; I ran across this announcement (http://www.usalert.com/public/newsletter.asp) and thought it might be of interest: > Chemistry Grant: Camille & Henry Dreyfus Foundation > > The Camille and Henry Dreyfus Special Grant Program in the Chemical > Sciences offers support to eligible institutions for innovative > projects. The Special Grant program is intended to advance the > science of chemistry, with the expectation that grant recipients > will find continuing funding from other sources. > > Past areas of support include development of curricular and > instructional materials, including new media; institutional enhancement > of education and research; public understanding of the role of > chemistry in society, and encouragement of high school students > and teachers. > > The deadline is June 15, 1999. Eligible insitutions include schools, > colleges and universities, as well as other not-for-profit > organizations with a related focus, such as museums and libraries. > The Foundation encourages innovative and creative approaches to the > advancement of the chemical sciences. Projects not already embraced > by substantial support from government agencies or other foundations > are preferable. > > For more information, go to > http://www.usalert.com/htdoc/usoa/fnd/any/any/proc/any/cami04029804a.htm -- Robert M. Horton, Ph.D. 0 []~ ~ ~ ~ http://www.attotron.com ~ ~ ~ ~[] 0 |-/_| rmhorton@attotron.com |_\-| -\_|| He travels swiftest who telecommutes. ||_/- ++++------+------+------+------+------+------+------+------+------+------+ From: "Joachim Greipel" Subject: Hardware Stereo on PC? Date: Thu, 3 Jun 1999 08:02:24 +0100 To: rasmol@dhcp-srv2.oit.umass.edu Hi, there Does anyone have a suggestion for using hardware-stereo (shutter- glasses) on an Intel-based PC with Rasmol, PDB-View or any other comparable molecular graphics software? Thank You kindly! _________________________________ Dr. Joachim Greipel Medizinische Hochschule Hannover Biochem. Biophys. Verfahren OE 8830 Postfach 30623 Hannover Tel: +49-511-532-3718 Fax: +49-511-532-5966 e-mail: greipel@bpc.mh-hannover.de References: <168F4855AB9@bpc.mh-hannover.de> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: Hardware Stereo on PC? Date: Thu, 03 Jun 1999 14:26:34 +0100 To: rasmol@dhcp-srv2.oit.umass.edu Joachim Greipel wrote: > > Hi, there > > Does anyone have a suggestion for using hardware-stereo (shutter- > glasses) on an Intel-based PC with Rasmol, PDB-View or any other > comparable molecular graphics software? > > Thank You kindly! Hi All, I'm afraid the software itself has to support it and there's no souch support in rasmol at the moment :-( . Maybe you can try MolMol, which uses OpenGL. I know the 'Real 3D' support works on Silicon Graphics machines but I've no idead about the curretn state on WINtel platforms. Anybody here who knows the URL ? I've lost the appropiate bookmark :-( Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)171 2693405 | Fax : +44-(0)171 269 3258 email : a.mueller@icrf.icnet.uk | http://www.icnet.uk/bmm/ ++++------+------+------+------+------+------+------+------+------+------+ From: Judy Voet Subject: chime 2 menu explanation Date: Fri, 4 Jun 1999 13:43:18 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Does anyone know where to find a good explanation of the functions in the chime 2 menu that students can be referred to? All the references I've been able to find to the chime menu are for early versions of chime. Judy Judith G. Voet, J. H. Hammons Professor Swarthmore College jvoet1@swarthmore.edu Department of Chemistry 610-328-8520 500 College Avenue FAX 610-328-7355 Swarthmore, PA 19081 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: mime-type for rasmol visualization Date: Fri, 04 Jun 1999 18:56:35 -0400 To: rasmol@dhcp-srv2.oit.umass.edu, pdb-l@rcsb.org I thought this message about RasMol/Chime/PDB MIME types, in response to a question by Elisabeth Gasteiger, would be of interest so I forward it with Henry Rzepa's permission. -Eric Martz >Date: Fri, 4 Jun 1999 >To: Eric Martz >From: "Rzepa, Henry" >Subject: Re: mime-type for rasmol visualization >Cc: Elisabeth.Gasteiger@isb-sib.ch > >> >> Hello, >>>> >>>> I am just adapting the ExPASy scripts (e.g. >>>> http://www.expasy.ch/cgi-bin/get-pdb.pl?1hhh) >>>> with respects to PDB links. >>>> Looking at the RCSB pages, I have the following question: >>>> Is there one standard mime-type for the visualisation of >>>> a pdb entry using rasmol? >>>> We used to (and still do) use 'chemical/x-pdb' (see also >>>> http://www.umass.edu/microbio/rasmol/cfgnsras.htm), >>>> you are using 'chemical/x-ras' (e.g. in >>>> http://www.rcsb.org/pdb/cgi/explore.cgi?job=graphicspdbId=1HHHpage=&pid=), >>>> and the PDB has 'application/x-rasmol'. >>>> (e.g. http://www.pdb.bnl.gov/cgi-bin/send-ras?filename=2hladefault=1). >>>> >>>> I think it would be nice if there were one standard mime type >>>> which would avoid the hassle of reconfiguring their browsers >>>> back and forth depending on the server they are accessing >> >> PDB from. Can you help me in this matter? > >Dear Elizabeth, > >I started to try and achieve what you hope for in January 1994. Some organisations >responded, and chemical/x-pdb became adopted. Perhaps a year later I >noticed that EBI etc had adopted application/x-rasmol. This went rather against >the spirit of "media types", which were supposed to reflect the content of the >file (for which a good definition was presumed to exist somewhere) > rather than the specific program capable of parsing it (few proprietary programs have >well specified open descriptions). At the time, I sent >a number of emails to the organisations using it, but received no response. >They had rationalised on that file type, and presumably it would have been >inconvenient for them to change. MDI, with the Chime plug in initially adopted >chemical/x-pdb, and subsequently application/x-rasmol, but not as far as I >am aware chemical/x-ras. The latter by the way has never been sent to me to include >in the list of chemical types (the official page for which is www.ch.ic.ac.uk/chemime/ ), >and because its in the chemical namespace, it has to be deprecated and regarded as >unofficial. > >An article describing chemical MIME was published in JCICS last year[see reference >added below], and I >still need to write the official IUPAC article, which I have been asked to do. > >So I suspect that we have ended up with three different MIME types for essentially >the same content. Unsatisfactory, but unless we can persuade two of them to drop out >in favour of one, its difficult to see what else can be done. Anyway, the "official" one >as endorsed by IUPAC is chemical/x-pdb. > >Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; >mailto:rzepa@ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. >URL: http://www.ch.ic.ac.uk/rzepa/ > The Application of Chemical Multipurpose Internet Mail Extensions (Chemical MIME) Internet Standards to Electronic Mail and World-Wide Web information exchange, H. S. Rzepa, P. Murray-Rust and B. J. Whitaker, J. Chem. Inf. Comp. Sci., 1998, 38, 976-982. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ mmciflist@ndbdev.rutgers.edu, pdb-l@rcsb.org ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: mime-type for rasmol visualization Date: Sat, 5 Jun 1999 07:48:12 -0400 (EDT) To: Andrew Dalke Cc: Eric Martz , rasmol@dhcp-srv2.oit.umass.edu, Andrews Dalke has suggested: >> My final option is to fix RasMol in some way so that it can read >> PDB files without the addition of the two "load/exit" lines. >> As I mentioned, this is an assumption of mine, but I cannot imagine >> any other reason for having those two lines or having the >> distinction for the "trivial" x-rasmol scripts currently sent >> by RCSB or the PDB. Since I am working on the RasMol 2.7.1 release right now, this is a very timely suggestion, but it would be a mistake to simply make such a change without a community consensus and consideration of the implications, so let me propose a specific straw man: If RasMol 2.7.1 were to recieve a line which begins with the token "header" (case insensitive) on its command line input, it would process the rest of that line and the following lines just as if it had received a "load pdb inline" and an "exit" before that. I think this has sensible implications for most people, and since "header" is not a valid rasmol command right now, it should not disable anything. It would, of course, cause very strange results for people who accepted such file and tried to process it with an older version of RasMol or with a program expecting a RasMol script instead of a "straight" pdb-file. It would also be my intention to add a few similar "magic number" style commands for other file types that RasMol accepts. Suggestions appreciated for each of the file types. For example, is there something we can use to quickly auto-recognize Acta style CIF and RCSB style mmCIF files? -- Herbert J. Bernstein ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-516-286-1339 FAX: 1-516-286-1999 ===================================================== ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: mime-type for rasmol visualization Date: Sat, 05 Jun 1999 12:24:57 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Cc: h.rzepa@ic.ac.uk [I am reposting this message from Andrew Dalke to circumvent technical difficulties. It is the antecedent to Herbert Bernstein's message of the same subject. -Eric Martz] Eric Martz forwarded some email from Henry Rzepa regarding the use of rasmol specific file formats. Here are some of my thoughts on the subject. http://www.expasy.ch/cgi-bin/get-pdb-entry-rasmol?1hhh returns > Content-Type: chemical/x-pdb and it is a PDB file. http://www.rcsb.org/pdb/cgi/render.cgi/1hhh?pdbId=1hhhformat=rasmol_default returns > Content-Type: chemical/x-ras which starts off > load pdb inline > exit so it not a PDB file, although every PDB viewer I know of will read it. The RCSB option "Save full entry to disk", as in: http://www.rcsb.org/pdb/cgi/export.cgi/1HHH.pdb?job=downloadpdbId=1HHH&page =&pid=15931928557473format=PDB&pre=1&compression=None returns > Content-Type: application/octet-stream but this is a PDB file. Though truthfully it is to "save to disk" and not "use appropriate viewer". RCSB does not have an option to view as chemical/x-pdb The old PDB lets you view the entry, as in http://www.pdb.bnl.gov/pdb-bin/send-pdb?id=1hhh which returns > Content-Type: text/html because it really is HTML and not a PDB file. The RasMol option http://www.pdb.bnl.gov/pdb-bin/send-ras?id=1hhh returns > Content-Type: application/x-rasmol but that also returns a non-PDB file, because the first two lines are > load pdb inline > exit As far as I know of, neither the PDB nor RCSB have options to serve out raw PDB files. The closest they gave are files which are HTML converted or ones which start with a RasMol specific preamble. So while chemical/x-rasmol (or x-ras) files may look like PDB files, they are not, so must not labeled chemical/x-pdb. I worked on VMD, a visualization program which isn't RasMol, so have some concern about the program specific nature of this addition. I sent mail to both sites (several years ago to PDB and a couple months ago to RCSB) asking for some option to view PDB files with a Content-Type of chemical/x-pdb. It has yet to happen. Since the > load pdb inline > exit is there to make it easier for RasMol/Chime users to view molecules, (this is an assumption!) and since most people use those viewers, I doubt they will get rid of it, so the question is how to make it be more agnostic. I believe that anything with that type can contain any Rasmol script, such as a rotation, scaling, atom selection, etc. I see from the PDB "rasmolscript" options that this is true, since http://www.pdb.bnl.gov/pdb-bin/rasgen?pd=1hhhpr=a:1-181 returns > Content-Type: application/x-rasmol which contains some RasMol specific code which affects the final viewpoint. This Content-Type is, alas, the same type as used to get just the PDB file with the little preamble for easy RasMol viewing. This is problematical because it is hard to write a general purpose converter from RasMol scripts to the VMD scripting language -- I tried :), but there are semantic differences between the two programs which are hard to overcome. I think there is a solution, though not one I am overly fond of, by having three different data types: chemical/x-pdb -- the one we know and love chemical/x-rasmol -- the same data as x-pdb except that the two header lines "load pdb inline" and "exit" are added to the top. This makes it easy to support RasMol but because the format is strictly defined, it allows other programs to be used as a viewer. application/x-rasmol -- contains general RasMol scripts which are usable only to RasMol. This allows for things like the rasmolscript files for specialized functionality. My proposal is for one additional MIME type, chemical/x-rasmol, which contains the RasMol specific preamble which can safely be ignored by other viewers. Then RCSB and others can return their PDB files in that form and still be viewer agnostic. The only big downsides are that it calls for end-users to add that new MIME type to their list, and it's a new type needed only as a real-world workaround; meaning its ugly but it works. Oh, and it requires that people who serve files for RasMol files know when to choose one over the other. Another option is to define that any file of the Content-Type application/x-rasmol cannot contain any characters in columns 1 through 6 which can be interpreted as a PDB card identifier. (This works since RasMol is case insensitive.) The downside of this is that something like the PDB's assymetric unit rasmolscript files will not be viewable in anything other than RasMol, so you lose the distinction between the two. (specifically, in the first proposal I could have VMD set up to view chemical/x-pdb and chemical/x-rasmol files, and Rasmol for application/x-rasmol. I cannot with this second proposal.) My final option is to fix RasMol in some way so that it can read PDB files without the addition of the two "load/exit" lines. As I mentioned, this is an assumption of mine, but I cannot imagine any other reason for having those two lines or having the distinction for the "trivial" x-rasmol scripts currently sent by RCSB or the PDB. Andrew Dalke dalke@bioreason.com ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: Re: mime-type for rasmol visualization (2) Date: Mon, 7 Jun 1999 14:56:24 +0300 (IDT) To: rasmol@dhcp-srv2.oit.umass.edu, pdb-l@rcsb.org I've been meaning to raise the MIME type disussion for some time now, so I'm happy it's being discussed. >I worked on VMD, a visualization program which isn't RasMol, so >have some concern about the program specific nature of this addition. >I sent mail to both sites (several years ago to PDB and a couple >months ago to RCSB) asking for some option to view PDB files with >a Content-Type of chemical/x-pdb. It has yet to happen. >From the old PDB, in the atlas pages the links to visualisation with Chime are chemical/x-pdb MIME >There is no need to do any changes to RasMol. RasMol is currently able >to read pure PDB files (no command line option or option '-pdb') as >well as special RasMol scripts (command line option '-script'). I believe there is a need. When you serve PDB files to be used by RasMol as a helper application, if the 'load inline pdb/exit' lines are missing, they cannot be read correctly to RasMol on Macintosh (and possibly also others) since each line of the file is read as a command. The modification suggested by Herbert Bernstein should overcome this. Another thing that was mentioned was a MIME type of chemical/x-rasmol, to the best of my knowledge no-one uses this. RCSB uses chemical/x-ras. Personally I find it useful to be able to serve files in different ways e.g. serving structures in pages for use with the Chime plugin requires a different MIME type from those with RasMol scripts. As for the application/x-rasmol vs. chemical/x-ras, I think application/x-rasmol is used by a larger number of servers (old PDB, SCOP, CATH, FSSP etc.) but I don't think it will be easy to get RCSB (or others using chemical/x-ras) to change their minds. chemical/x-pdb should be the plain PDB file to be used with whatever you want application/x-rasmol or chemical/x-ras should be RasMol specific to allow users to take advantage of the powerful script features of RasMol to take advantage of the powerful script features of RasMol (for example the very nice 'Fold Deviation Score' from RCSB) In a related problem - does anyone know how to modify the MIME types used by Chime on PC (I don't want it to accept application/x-rasmol) it does not seem possible to edit the MIME types, as it is in Mac. Kurt --------------------------------------------------------------- Dr. Kurt Giles kurt@inn-prot.weizmann.ac.il Israeli National Node Biological Computing Unit Tel: +972-8-9342614 Weizmann Institute of Science Fax: +972-8-9466269 Rehovot 76100, Israel http://inn-prot.weizmann.ac.il/ --------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: mime-type for rasmol visualization Date: Mon, 07 Jun 1999 09:54:11 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Anyone interested in the discussion on this rasmol MIME subject should either subscribe to the pdb list (http://www.rcsb.org/pdb/forum.html) (traffic is considerably less than on the rasmol list!) and/or read the June archives at http://www.rcsb.org/pdb/lists/pdb-l/#browse Today there have already been three very informative new messages which were sent to the pdb list, only one of which was also sent to the rasmol list. -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE OR UNSUBSCRIBE, GO TO THE ABOVE ADDRESS. ++++------+------+------+------+------+------+------+------+------+------+ From: Helge Weissig Subject: Re: mime-type for rasmol visualization Date: Mon, 7 Jun 1999 10:26:06 -0700 To: rasmol@dhcp-srv2.oit.umass.edu, pdb-l@rcsb.org Dear Andrew (and others), thank you for bringing this issue up for discussion. At RCSB we have long been looking for guidance on this subject as there are no true standards as everyone is now certainly aware of. I am again cross-posting this message to both the pdb-l discussion list and the rasmol list maintained by Eric. Sorry for any duplicate copies you might receive! Andrew has done some thorough looking at the different mime-types in use and came up with three suggestions that generally seem very acceptable. Also, please note that we will be VERY flexible as to which mime-type to use with which option, as long as we are not forcing a majority to change their settings :)) One of the issues that was not clearly touched upon and is the actual underlying reason for us to use the "dummy script" approach are the two different command line options (or file types on Macs) for rasmol: plain pdb file and rasmol scripts. As was pointed out by someone else, the Mac implementation also seems to have some problems with the script missing but I have not confirmed this myself. Essentially, it seems that we would at least need chemical/x-pdb and application/x-ras(mol) to serve plain pdb and rasmol scripts respectively. (I am not sure why I used the abbreviated x-ras. It was carried over from a script written for http://pdbobs.sdsc.edu/ and I am very certain that it was based on a rasmol manual somewhere else. However, I am now unable to track down that reference!) To complicate the picture even further, due to the great work of Herbert Bernstein, mmCIF "compliant" versions of rasmol are available now as well. Should these receive their own mime-types? At least chemical/x-mmcif seems appropriate!? As Herbert pointed out, the decision process should include the appropriate amount of community input and I am again grateful that this subject was brought up. with best regards, Helge Weissig +--------------------------------------------+ | Helge Weissig, PhD | | Project Manager, Structural Bioinformatics | | San Diego Supercomputer Center +-----------------------------------+ | voice: +1 619 534 8399 | mail: PO Box 85608 | | fax: +1 619 822 0873 | San Diego, CA 92186-5608 | +---------------------------------| direct: 10100 John J. Hopkins Dr. | | La Jolla, CA 92093-0537 | +-----------------------------------+ On Fri, 4 Jun 1999, Andrew Dalke wrote: [snip] > chemical/x-pdb -- the one we know and love > > chemical/x-rasmol -- the same data as x-pdb except that the two > header lines "load pdb inline" and "exit" are added to the top. > This makes it easy to support RasMol but because the format is > strictly defined, it allows other programs to be used as a viewer. > > application/x-rasmol -- contains general RasMol scripts which > are usable only to RasMol. This allows for things like the > rasmolscript files for specialized functionality. > > My proposal is for one additional MIME type, chemical/x-rasmol, > which contains the RasMol specific preamble which can safely be > ignored by other viewers. Then RCSB and others can return their > PDB files in that form and still be viewer agnostic. The only > big downsides are that it calls for end-users to add that new > MIME type to their list, and it's a new type needed only as a > real-world workaround; meaning its ugly but it works. Oh, and > it requires that people who serve files for RasMol files know > when to choose one over the other. > > Another option is to define that any file of the Content-Type > application/x-rasmol cannot contain any characters in columns > 1 through 6 which can be interpreted as a PDB card identifier. > (This works since RasMol is case insensitive.) The downside of > this is that something like the PDB's assymetric unit rasmolscript > files will not be viewable in anything other than RasMol, so > you lose the distinction between the two. (specifically, in the > first proposal I could have VMD set up to view chemical/x-pdb > and chemical/x-rasmol files, and Rasmol for application/x-rasmol. > I cannot with this second proposal.) > > My final option is to fix RasMol in some way so that it can read > PDB files without the addition of the two "load/exit" lines. > As I mentioned, this is an assumption of mine, but I cannot imagine > any other reason for having those two lines or having the > distinction for the "trivial" x-rasmol scripts currently sent > by RCSB or the PDB. > > Andrew Dalke > dalke@bioreason.com ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: mime-type for rasmol visualization (2) Date: Mon, 7 Jun 1999 12:13:37 -0600 (MDT) To: rasmol@dhcp-srv2.oit.umass.edu > I believe there is a need. When you serve PDB files to be used by RasMol > as a helper application, if the 'load inline pdb/exit' lines are > missing, they cannot be read correctly to RasMol on Macintosh (and > possibly also others) since each line of the file is read as a command. > The modification suggested by Herbert Bernstein should overcome this. I suspect (and forgive me if I'm wrong) that the problem here is in configuring the client MIME types on the Macintosh. Alas the Macintosh does't have command line options and therefore file types are handled by a dialog box when configuring a helper application. Use the Apple filetype 'TEXT' for PDB files, 'RSML' for RasMol script files and 'mMOL' for MDL Mol files (chemical/mdl-molfile). Unfortunately, detecting "HEADER" at the beginning of a PDB file isn't a foolproof solution and doesn't work for files containing only ATOM records generated by packages such as XPLOR, SPARTAN, Corina, RasMol etc... Indeed, I've come across many files beginning with REMARK or COMPND. I completely agree with the earlier posting that PDB files without 3D rendering information be transmitted across the WWW as plain PDB files. The RasMol script file format is used as a way of providing a graphic representation, such as VRML or Kinemage, whilst still preserving the semantics of the object being viewed. Although this was never a design consideration of the scripting language, it has proved to be an area for which it is particularly well suited and widely used. Finally, The availability of the RasMol source code makes the scripting language as "open" and "standard" as the MOPAC or GAUSSIAN file formats. Hence it should be just as eligible for a chemical MIME type. Perhaps more so than some of the unpublished proprietary binary file formats currently under consideration. Perhaps a better solution is to use CSML or TGF (and add support to read and write them from within RasMol), file formats designed for describing molecular representations. Roger -- Roger Sayle, E-mail: roger@metaphorics.com Bioinformatics Group, Metaphorics, WWW: http://www.metaphorics.com/ 419 East Palace Avenue, Tel: (+1) 505-984-0613 Santa Fe, New Mexico, 87501. Fax: (+1) 505-989-1200 ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: Re: mime-type for rasmol visualization (2) Date: Tue, 8 Jun 1999 11:55:13 +0300 (IDT) To: rasmol@dhcp-srv2.oit.umass.edu, pdb-l@rcsb.org > > I believe there is a need. When you serve PDB files to be used by RasMol > > as a helper application, if the 'load inline pdb/exit' lines are > > missing, they cannot be read correctly to RasMol on Macintosh (and > > possibly also others) since each lineof the file is read as a command. > > The modification suggested by Herbert Bernstein should overcome this. > > I suspect (and forgive me if I'm wrong) that the problem here is in > configuring the client MIME types on the Macintosh. Alas the Macintosh > does't have command line options and therefore file types are handled by a > dialog box when configuring a helper application. Use the Apple filetype > 'TEXT' for PDB files, 'RSML' for RasMol script files and 'mMOL' for MDL > Mol files (chemical/mdl-molfile). Yes, I just want to confirm that Roger Sayle correctly identified the problem on the Macintosh. chemical/x-pdb should be set with File type TEXT to correctly read plain PDB files, application/x-rasmol (or chemical/x-ras) should be set with File type RSML to correctly read RasMol scripts. If you try and read a plain PDB file with the RSML File type selected you get the problem of every line of the file being read in and giving an error, hence the need for the 'dummy' script of 'load pdb inline/exit'. BTW in an earlier post I commented that chemical/x-pdb files could be found in the old PDB, this is not the case (the files are embeded in a page, and can only be viewed with Chime). chemical/x-pdb encoded files can be obtained via PDBsum (which is linked from the atlas pages of the old PDB). Kurt --------------------------------------------------------------- Dr. Kurt Giles kurt@inn-prot.weizmann.ac.il Israeli National Node Biological Computing Unit Tel: +972-8-9342614 Weizmann Institute of Science Fax: +972-8-9466269 Rehovot 76100, Israel http://inn-prot.weizmann.ac.il/ --------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: "Dr. Don Harden" Subject: compile THIRTYTWOBIT Date: Tue, 8 Jun 1999 14:05:28 -0400 (EDT) To: rasmol@dhcp-srv2.oit.umass.edu Hello All, I am trying to compile RasMol 2.7.0.1 to use 32 bit color depth on an SGI O2 running IRIX 6.5.3m using the IRIX c compiler. I've changed rasmol.h to define THIRTYTWOBIT: #if !defined(EIGHTBIT) && !defined(THIRTYTWOBIT) && !defined(SIXTEENBIT) #define THIRTYTWOBIT /* #define SIXTEENBIT */ /* #define EIGHTBIT */ #endif However; when I run make I get the following warning: ld32: WARNING 84: /usr/lib32/libXi.so is not used for resolving any symbol And rasmol runs at the default 8 bit color depth. I get the same results when I compile RasMol26b2. I would apperciate any advice on compiling 32 bit color depth version of RasMol. Thanks Don ---------------------------------------------------- Dr. Don Harden don-harden@Gsu.EDU Department of Chemistry Georgia State University ph: (404) 651-3580 Atlanta, Ga. 30302 fax: (404) 651-1416 http://chemistry.Gsu.EDU/glactone References: X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: compile THIRTYTWOBIT Date: Tue, 08 Jun 1999 19:17:43 +0100 To: rasmol@dhcp-srv2.oit.umass.edu "Dr. Don Harden" wrote: > > Hello All, > > I am trying to compile RasMol 2.7.0.1 to use 32 bit color > depth on an SGI O2 running IRIX 6.5.3m using the IRIX c compiler. I've > changed rasmol.h to define THIRTYTWOBIT: > > #if !defined(EIGHTBIT) && !defined(THIRTYTWOBIT) && !defined(SIXTEENBIT) > #define THIRTYTWOBIT > /* #define SIXTEENBIT */ > /* #define EIGHTBIT */ > #endif > > However; when I run make I get the following warning: > > ld32: WARNING 84: /usr/lib32/libXi.so is not used for resolving any > symbol > > And rasmol runs at the default 8 bit color depth. > > I get the same results when I compile RasMol26b2. > > I would apperciate any advice on compiling 32 bit color depth version of > RasMol. > > Thanks Don Hm, check yout makefile you mey find the string -DEIGHTBIT in there. In my Makefile I find: # DEPTHDEF = -DTHIRTYTWOBIT # DEPTHDEF = -DSIXTEENBIT DEPTHDEF = -DEIGHTBIT Simply comment the EIGHTBIT line and and uncomment -DTHIRTYTWOBIT, or comment all the lines, in that case the definitions in rasmol.h are used. Your linker warning has nothing to do with the colour depth, if your terminal window (rasmol commandline) behaves properly and you can type in commands even if your mouse pointer is in the rasmol graphics window then everything is ok. Greetings, Arne ++++------+------+------+------+------+------+------+------+------+------+ From: "Dr. Don Harden" Subject: Re: compile THIRTYTWOBIT Date: Tue, 8 Jun 1999 14:35:02 -0400 (EDT) To: rasmol@dhcp-srv2.oit.umass.edu Dear Arne, Thanks you for replying so quickly. I did edit the Makefile as you suggested an recompiled, but I got the same warning. I am also rather sure that I am getting an 8 bit version because xwininfo reports my complied versions have RasMol windows with a depth of 8 while the pre-compiled 32 bit RasMol has a window with a depth of 24. Don On Tue, 8 Jun 1999, Arne Mueller wrote: > Date: Tue, 08 Jun 1999 19:17:43 +0100 > From: Arne Mueller > Reply-To: rasmol@lists.umass.edu > To: rasmol@dhcp-srv2.oit.umass.edu > Subject: Re: compile THIRTYTWOBIT > > "Dr. Don Harden" wrote: > > > > Hello All, > > > > I am trying to compile RasMol 2.7.0.1 to use 32 bit color > > depth on an SGI O2 running IRIX 6.5.3m using the IRIX c compiler. I've > > changed rasmol.h to define THIRTYTWOBIT: > > > > #if !defined(EIGHTBIT) && !defined(THIRTYTWOBIT) && !defined(SIXTEENBIT) > > #define THIRTYTWOBIT > > /* #define SIXTEENBIT */ > > /* #define EIGHTBIT */ > > #endif > > > > However; when I run make I get the following warning: > > > > ld32: WARNING 84: /usr/lib32/libXi.so is not used for resolving any > > symbol > > > > And rasmol runs at the default 8 bit color depth. > > > > I get the same results when I compile RasMol26b2. > > > > I would apperciate any advice on compiling 32 bit color depth version of > > RasMol. > > > > Thanks Don > > Hm, check yout makefile you mey find the string -DEIGHTBIT in there. In > my Makefile I find: > > # DEPTHDEF = -DTHIRTYTWOBIT > # DEPTHDEF = -DSIXTEENBIT > DEPTHDEF = -DEIGHTBIT > > Simply comment the EIGHTBIT line and and uncomment -DTHIRTYTWOBIT, or > comment all the lines, in that case the definitions in rasmol.h are > used. > > Your linker warning has nothing to do with the colour depth, if your > terminal window (rasmol commandline) behaves properly and you can type > in commands even if your mouse pointer is in the rasmol graphics window > then everything is ok. > > Greetings, > > Arne > ---------------------------------------------------- Dr. Don Harden don-harden@Gsu.EDU Department of Chemistry Georgia State University ph: (404) 651-3580 Atlanta, Ga. 30302 fax: (404) 651-1416 http://chemistry.Gsu.EDU/glactone ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: BIOpolymer Markup Language (XML) Date: Thu, 10 Jun 1999 13:07:44 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Steve Shaw at NCBI/NCI pointed out to me the BIOpolymer Markup Language at http://proteometrics.com/BIOML/index.html Excerpts from their site: BEGIN QUOTE This page is devoted to a new XML language, designed to be used for the annotation of biopolymer sequence information. BIOML allows the full specification of all experimental information known about molecular entities composed of biopolymers, for example, proteins and genes. There is currently no general method of annotating biopolymer sequences, in their biological context. The goal of BIOML is to provide an extensible framework for this annotation and to provide a common vehicle for exchanging this information between scientists using the World Wide Web. ... a BIOML document will describe a physical object, e.g., a particular protein, in such a way that all known experimental information about that object can be associated with the object in a logical and meaningful way. The advantage of using a Markup Language for this task is that the information is necessarily nested at different levels of complexity and it fits in very well with the tree-leaf structure inherent in XML. Additionally, although the primary purpose of BIOML is the transfer of information between machines, the additional style information available when using an XML-based approach will simplify the task of displaying that information on various types of browsing and display software. END QUOTE They provide a specialized browser for BioML files (.bml). Downloading, installing, and running it takes only a few minutes. The resulting example of hierarchical information on insulin is quite interesting as a demonstration of where they want to go. I didn't see any evidence of 3D visualization. -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE OR UNSUBSCRIBE, GO TO THE ABOVE ADDRESS. References: <199904071248.IAA07847@marlin.bio.umass.edu> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: David Fahrney Subject: 3D structures in Bioml-Biobrowser Date: Sat, 12 Jun 1999 08:21:56 -0600 To: rasmol@dhcp-srv2.oit.umass.edu Eric, Thanks for passing on the link to Proteometrics' "Bioml-Biobrowser." They do mention access to 3D structures in their sample .bml file for thrombin: "3D Structure There are several structures for thrombin known. The three sequences represented here represent normal thrombin, thrombin complexed with the inhibitor hirudin (the clot inhibitor used by leeches) and a low resolution structure of gamma-thrombin. The 3D structure viewer was written by the Abagyan group at NYU Medical Center." However, I have no knowledge of the above 3D structure viewer and nothing happens when you select one of the structures (presumbably because this is just a mock example to illustrate the syntax). Dave Fahrney Professor of Biochemistry Colorado State University ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Fixing the label font in RasMol/Chime Date: Tue, 15 Jun 1999 16:01:42 -0400 To: rasmol@dhcp-srv2.oit.umass.edu The font used for labels in RasMol, inherited by Chime, could be improved. The lower case letter i is too far to the left in the cell, and it would be nice if characters could be made 2 pixels thick. At least for fixing the i, I'm wondering if it would be possible to patch the executable, for the case of Chime where source is not available and no such fixes are planned. The label font source code for Chime is hopefully identical to that in RasMol. Would one of our subscribers who has worked on the RasMol source code be kind enough to take a look for the label font source and see whether it could be patched in the binary executable? If so, please tell us how to find the letter "i" in particular. -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 To unsubscribe from the RasMol Email List, change your address, etc., see ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: Fixing the label font in RasMol/Chime Date: Tue, 15 Jun 1999 20:16:33 -0600 (MDT) To: rasmol@dhcp-srv2.oit.umass.edu > The font used for labels in RasMol, inherited by Chime, could be > improved. The lower case letter i is too far to the left in the cell, > and it would be nice if characters could be made 2 pixels thick. The internal font used by RasMol is encoded in the file "font.h". Each glyph (or character) is cleverly encoded as a text string. The representation works much like a plotter, with "move to coordinates" and "line to coordinates" commands. Each coordinate is represented by a pair of characters, the first represents the x ordinate and the second the y ordinate. 'a' represents 0, 'b' represents 1, etc... If the x ordinate is upper case is the "pen" moves to that position, and if lower case the plotter draws a line to that position from the previous position. All coordinates lie in a 16x24 box. The underscore character "_" is represented as "Bglg", which is translated as "move to (1,6) and line to (11,6)". The caret "^" is represented as "Cqgwkq" which means "move to (2,16), line to (6,22), line to (10,16)". Hence "i" is represented as the string "AgegCgcpbpCrcsbsbrcr", and when shifted over by 4, becomes "EgigGggpfpGrgsfsfrgr". This should correct the problem with it not be centered correctly. Roger -- Roger Sayle, E-mail: roger@metaphorics.com Bioinformatics Group, Metaphorics, WWW: http://www.metaphorics.com/ 419 East Palace Avenue, Tel: (+1) 505-984-0613 Santa Fe, New Mexico, 87501. Fax: (+1) 505-989-1200 ++++------+------+------+------+------+------+------+------+------+------+ From: Julia Yu Subject: MDL's New Web Site at http://www.mdli.com Date: Wed, 16 Jun 1999 13:43:36 -0700 To: "'rasmol@dhcp-srv2.oit.umass.edu'" MDL Information Systems, Inc. recently redesigned and updated its Web site at http://www.mdli.com. Here are some items that you may find useful and interesting: * MDL File Formats * Free Software & Support * Metabolite 99.1 Contains NDA Data * RiboGene Licenses SMART for Inventory Management MDL FILE FORMATS This 100 page technical document in Adobe PDF is located in our new Download Center. Go to http://www.mdli.com. and select Download Center > Free Products and Information > MDL File Formats, or go directly to the following URL: http://www.mdli.com/cgi/dynamic/downloadsect.html?uid=$uid&key=$key&id=1 and select MDL File Formats. --------------------------------------------------- FREE SOFTWARE & SUPPORT You will also find free versions of Chime and ISIS/Draw in the free products section of the Download Center. Go to http://www.mdli.com and select Download Center > Free Products and Information, or go directly to the following URL: http://www.mdli.com/cgi/dynamic/downloadsect.html?uid=$uid&key=$key&id=1 and select the product. There is an entire area dedicated to free Chime support. Go to http://www.mdli.com and select Support > Click here for Chime Support, or go directly to the following URL: http://www.mdli.com/support/chime/default.html --------------------------------------------------- METABOLITE 99.1 CONTAINS NDA DATA MDL today introduced version 99.1 of its Metabolite database, which now includes non-proprietary new drug application (NDA) information. Metabolite's NDA data, combined with its comprehensive metabolism information from published sources, enhance pharmaceutical and agrochemical companies' ability to make cost-effective candidate promotion decisions in early stage R&D. For more information, go to http://www.mdli.com and select About MDL > Press Releases > Metabolite 99.1 Contains NDA Data, or go directly to the following URL: http://www.mdli.com/cgi/dynamic/pressrelease.html?uid=&key=&id=54 --------------------------------------------------- RIBOGENE LICENSES SMART FOR INVENTORY MANAGEMENT MDL today announced that RiboGene, Inc. of Hayward, CA, has licensed MDL's Sample Management and Reagent Tracking (SMART) system to manage its chemical and biological inventories from receipt and storage to disposal. For more information, go to http://www.mdli.com and select About MDL > Press Releases > RiboGene of Hayward, CA Licenses SMART, or go directly to the following URL: http://www.mdli.com/cgi/dynamic/pressrelease.html?uid=&key=&id=53 Dori Luzbetak Web Communications Manager MDL Information Systems, Inc. 14600 Catalina Street San Leandro, CA 94577 Email: dori@mdli.com Jean Jean C Holt Marketing Scientist Core Technologies MDL Information Systems, Inc San Leandro, CA USA http://www.mdli.com > ++++------+------+------+------+------+------+------+------+------+------+ From: Hoo Doo the Doo Doo Subject: Re: MDL's New Web Site at http://www.mdli.com Date: Wed, 16 Jun 1999 14:27:07 -0700 To: rasmol@dhcp-srv2.oit.umass.edu Thanks for the heads up on the filetype data.....great stuff! If you have trouble opening it with acroread, try GS view which (with ghostscript) can view pdf as well as postscript & other filetypes.... ---- - - - - - - - - - - - - - - - - - - - - _ _ _ _ _ _ _ _ _ _ _ _ _ "I believe in the doctrine of non-violence as a weapon of the weak. I believe in the doctrine of non-violence as a weapon of the strongest. I believe that a man is the strongest soldier for daring to die unarmed" Mohandes Gandhi ++++------+------+------+------+------+------+------+------+------+------+ From: Julia Yu Subject: Broken Links on the Chime Support Site Date: Wed, 16 Jun 1999 16:29:07 -0700 To: "'rasmol@dhcp-srv2.oit.umass.edu'" Dear Chime Users MDL has just released a new web site at http://www.mdli.com. We have found that the upgrade of content and servers has led to the breaking of certain customer's Chime links. We sincerely apologize for this inconvenience. We have spent a considerable amount of time working through some of your web sites and creating redirection pages where the links have broken. Please email chime-feedback@mdli.com if you find that a link from your web site fails. Kind regards Jean C Holt Product Manager Chemscape,Chime Marketing Scientist Core Technologies MDL Information Systems, Inc San Leandro, CA USA http://www.mdli.com ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer now works on the Mac, has surfaces Date: Thu, 17 Jun 1999 19:55:47 -0400 To: rasmol@dhcp-srv2.oit.umass.edu, pdb-l@rcsb.org I have upgraded my Protein Explorer (PE, see URL below) freeware to version 0.99. Although the Chime-2-based PE is similar in concept to RasMol, there are already 17 features which make it easier or more powerful than RasMol (see the link to "What's New" on the main page). New in 0.99: Thanks to a loan from MDLI, I have a Macintosh for testing; with that and hours of help from Tim Driscoll, PE now appears to work on Macs. Also in this version I have added new control panels to make generation of surfaces or contact surfaces as easy as the push of a button. Ligand contact surfaces colored by distance between ligand and receptor are particularly informative -- an example is included to demonstrate this on the 'Contact Surfaces' page. Features in 0.99 and earlier versions: PE can load PDB files from your disk or via Internet from the Protein Data Bank. The last 10 molecules loaded are remembered on a pull-down select list. The initial view of a molecule is maximally informative. Atom identifications obtained by clicking on the molecule are interpreted into a more verbose explanation than RasMol's terse 'one-liner'. A full command-line interface is always available (a la RasMol). Common command words are aliased to easy-to-type (and user customizable) abbreviations -- "s p" means "select protein". A Comparator mode has two Chime windows, making side by side comparisons easy. User-preferences are remembered between sessions. When a multiple-model NMR file is loaded, all models are shown initially, and an NMR model selection panel makes selection, animation, and viewing of models easy. You can specify project folders on your disk, from which you can run scripts saved from Chime or developed and edited manually (or saved from RasMol). PE can be downloaded freely for local installation. I'll be working on the PE a lot this summer so feedback in the next few weeks will be especially useful. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ protein. ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: how to define the interface between the secondary strut. of Date: Fri, 18 Jun 1999 12:21:53 -0400 To: He Dayong , pdb-l@rcsb.org Cc: rasmol@dhcp-srv2.oit.umass.edu At 6/17/99, He Dayong wrote: >Would you please point me to some references on how to define the >interface between the secondary structures on one protein ? such as the >interface between a-helix and alpha-helix, alpha-helix and beta-sheet, >beta-sheet and beta-sheet. My Protein Explorer (URL below) allows you to specify an alpha helix, and then show the contact surface for an adjacent helix, colored by distance. This makes it really easy to see the bonding pattern -- the hbonds between beta strands stand out nicely, for example. Here's a concrete example. Take the N-terminal helix of hemoglobin, from Thr 4 through Val 18 in chain B in 1HHO. Take 1hho.pdb and, using RasMol, select chain B and the associated heme and water (select :b or within(5., (:b and not protein))), then save it to a smaller PDB file (save pdb 1hho_b.pdb). Now load this in the Protein Explorer, and type the following commands: r p bb co bb black (You can click on Show Aliases, below the message box, to find out the full commands these represent.) Go to the Contact Surfaces panel, and fill in the two slots as follows Generate the surface on: not 4-18 which is contacted by: 4-18 and not water Now press the [Show Contact Surface] button, and voila! Click here to see the resulting image, http://www.umass.edu/microbio/chime/explorer/explor1.gif (How to view this in Stereo? http://www.usm.maine.edu/~rhodes/0Help/StereoView.html#div This is divergent stereo.) When you're using the Protein Explorer, you can rotate and zoom this image at will, and click on any residue to identify it. For more detail, my Noncovalent Bond Finder (URL below) allows you to select, for example, one alpha helix, and display the closest atoms of neighboring structures clearly. You just push the [Find] button and it steps out in 0.1 Angstrom increments, showing what is there in each shell. To simplify the analysis, you can specify, for example, that only nitrogen atoms, or only carbon atoms in hydrophobic sidechains, be displayed. Thus you can display contacts at increasing distances in several runs, each concentrating on a different category of bonds. Load your 1hho_b.pdb in the Noncovalent Bond Finder, and select the helix (select 4-18:b). Click on the [Find] button and you'll find the closest hbond, namely Tyr130 hbonding to the backbone oxygen of Val11. Click here to see such an image http://www.umass.edu/microbio/chime/find-ncb/ncbf1.gif Continue to click [Find] and you'll find the closest hydrophobic interaction, http://www.umass.edu/microbio/chime/find-ncb/ncbf2.gif (which looks really nice in stereo, http://www.umass.edu/microbio/chime/find-ncb/ncbf2s.gif). -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - UMass Chime Resources: www.umass.edu/microbio/chime Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Jens Grabenstein Subject: Re: Protein Explorer now works on the Mac, has surfaces Date: Fri, 18 Jun 1999 22:07:44 +0200 To: Hi Eric, I just downloaded the protein explorer. I wanted to test it on my Mac, however I wasn't able to load any molecules. I always got a javascript error message that protein explorer is unable to work with urls longer than 75 characters. All my molecules are on deeper levels on my hard disk, so I couldn't load one. Why exists this limitation in the program? Thanks, Jens The optimist believes we live in the best of all worlds; the pessimist fears this is so. ----------------------------------------------------------- Visit my website: http://home.surf24.de/~grabenst/ ----------------------------------------------------------- E-mail: Jens.Grabenstein@surf24.de Jens.Grabenstein@uni-konstanz.de ----------------------------------------------------------- Made with an Apple Macintosh, the only computer brand ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Protein Explorer now works on the Mac, has surfaces Date: Fri, 18 Jun 1999 16:42:25 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Cc: Jens.Grabenstein@surf24.de This is a bug in Chime which I myself just discovered. I have reported it to MDLI but I'm sure they won't fix it for a long time if ever. So the best thing to do is put the molecules at shorter paths on your tree. Actually, I have only tested this bug on Windows -- it is possible that it doesn't exist in the Mac. You can test this yourself and please let us know. In the file shared:s2c2.js, search for the word "maximum". Comment out or delete the following lines and this will enable you to try longer url's. Delete these lines: if (tss.length > 70) { alert("ERROR: Chime cannot accept a URL as long as this one:\n" + tss + "\nThe maximum length for the URL is 70 characters including quotes." + "\nSo the maximum length for a load command is 75 characters." + "\nIf accepted, Netscape 4.6 crashes. Commands other than 'load' can be longer."); top.force_ready(); return; } At 6/18/99, you wrote: >Hi Eric, > >I just downloaded the protein explorer. I wanted to test it on my Mac, >however I wasn't able to load any molecules. I always got a javascript >error message that protein explorer is unable to work with urls longer >than 75 characters. All my molecules are on deeper levels on my hard >disk, so I couldn't load one. Why exists this limitation in the program? > >Thanks, > >Jens > >The optimist believes we live in the best of all worlds; >the pessimist fears this is so. >----------------------------------------------------------- >Visit my website: http://home.surf24.de/~grabenst/ >----------------------------------------------------------- >E-mail: Jens.Grabenstein@surf24.de > Jens.Grabenstein@uni-konstanz.de >----------------------------------------------------------- >Made with an Apple Macintosh, the only computer brand > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Jens Grabenstein Subject: Re: Protein Explorer now works on the Mac, has surfaces Date: Sat, 19 Jun 1999 18:37:09 +0200 To: "Eric Martz" , >This is a bug in Chime which I myself just discovered. I have reported it >to MDLI but I'm sure they won't fix it for a long time if ever. So the best >thing to do is put the molecules at shorter paths on your tree. > >Actually, I have only tested this bug on Windows -- it is possible that it >doesn't exist in the Mac. You can test this yourself and please let us >know. In the file shared:s2c2.js, search for the word "maximum". Comment >out or delete the following lines and this will enable you to try longer >url's. Delete these lines: > >if (tss.length > 70) >{ > alert("ERROR: Chime cannot accept a URL as long as this one:\n" + > tss + > "\nThe maximum length for the URL is 70 characters including quotes." + > "\nSo the maximum length for a load command is 75 characters." + > "\nIf accepted, Netscape 4.6 crashes. Commands other than 'load' can be >longer."); > top.force_ready(); > return; >} Hi there, I followed Eric's instructions (see above), and it worked without problems. I was able to load pdb-files with urls that exceeded the maximum path length of 75 characters. So it seems that this problem only occurs with Chime installed on Windows-PCs, but not on Macs. Jens The optimist believes we live in the best of all worlds; the pessimist fears this is so. ----------------------------------------------------------- Visit my website: http://home.surf24.de/~grabenst/ ----------------------------------------------------------- E-mail: Jens.Grabenstein@surf24.de Jens.Grabenstein@uni-konstanz.de ----------------------------------------------------------- Made with an Apple Macintosh, the only computer brand X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id NAA05754 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: help Date: Mon, 21 Jun 1999 13:24:33 -0400 To: Luis Miguel =?iso-8859-1?Q?Gon=E7alves?= Lopes Cc: rasmol@dhcp-srv2.oit.umass.edu At 6/21/99, Luis Lopes wrote: > My problem is this: I have my own partial charges values for each atom >calculated with the group electronegativity method and I want to display >these molecules (in PDB format) with colours assigned to each atom >according with my partial charges values...I've been reading the manual but >i can´t understand how to do it, or if it's possibly to do that...probably >my english knowledge it's not enough... > What I have are PDB files with 5 fields: > > (Atom Type) x y z Charge > > The Atom type, the coordinates, and the charge value that ranges form 1 to >-1. > I would like to assign a red colour to -1, a blue colour to 1 and white >colour to 0, and I'de like to have some distribution like the one for the >electostatic potentials. > If this is possible can you help me? If the Charge is in the correct columns in your PDB files, you should be able to use 'color temperature' command or from the menu. However, I don't think you can restrict those colors to red white and blue. In a separate message I will attach an example of cytochrome C which has mutation frequencies in the last column -- color temperature works with this file. I have never seen an example of a PDB file with COLO records suitable for 'color user'. I don't know the format of COLO records. Perhaps the best solution is to write a script like this select atomno=### color [255, 180, 180] repeating this for each atom. This will give you exactly what you want. There may be better solutions, so I am copying this to the rasmol email list to hear other people's ideas. - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE OR UNSUBSCRIBE, GO TO THE ABOVE ADDRESS. ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer: Longer URL's allowed on Macs Date: Mon, 21 Jun 1999 21:24:08 -0400 To: rasmol@dhcp-srv2.oit.umass.edu, pdb-l@rcsb.org I have released version 0.991 of my Protein Explorer (URL below). This version allows Macintoshes to use URL's up to 98 characters long when loading PDB files. If you weren't able to load some of your PDB files because the path to them was long, this may solve the problem. (If not, you'll have to move these PDB files to shorter paths on your hard disk.) The previous version 0.99 placed a 70-character limit, which still applies to Windows, but it turned out that the limit on the Macintosh is longer. These limits are due to a bug in Chime 2 which has been reported to MDLI. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Joseph R Fioretti 00 Subject: Databanks Date: Wed, 23 Jun 1999 13:26:53 -0400 (EDT) To: rasmol@dhcp-srv2.oit.umass.edu My name is Joseph Fioretti, and I'm currently working for a Middlebury College professor on some 3-D animated visualizations of molecules. I have been experimenting with the RasMol and Chime languages, but I am writing in hopes that one of you might be able to direct me to a website (or other resource) at which I can obtain royalty-free, non-copyrighted pdb files of lipids, proteins, and other structures associated with membrane fluidity. I truly appreciate any help any of you can provide, and if you'd like to email me directly instead of posting to the listserver, you can send me email at: fioretti@panther.middlebury.edu. Thank you very much! -Joe Fioretti References: ++++------+------+------+------+------+------+------+------+------+------+ From: Eugene Leitl Subject: Databanks Date: Wed, 23 Jun 1999 12:51:24 -0700 (PDT) To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu Joseph R Fioretti 00 writes: > (or other resource) at which I can obtain royalty-free, non-copyrighted > pdb files of lipids, proteins, and other structures associated with > membrane fluidity. I truly appreciate any help any of you can provide, Have a look at Helmut Heller's membrane pages: http://www.lrz-muenchen.de/~heller/membrane/membrane.html You can contact him for X-PLOR scripts he used to build the structures. Also, you can simply paint the structure with the CACTVS program http://www2.ccc.uni-erlangen.de/software/cactvs/index.html and let the structures being crunched remotely on the CORINA server http://www2.ccc.uni-erlangen.de/software/corina/free_struct.html Another large depository of 3d structures is the free NCI database http://dtp.nci.nih.gov/docs/3d_database/structural_information/structural_data.html You can also use MMTK to build structures, using a powerful script language http://starship.python.net/crew/hinsen/mmtk.html A braindead way to make movies is to dump Povray files from each trajectory frame using VMD (does this now work with RasMol?), and then fuse them into an animation (I've never done mpg, only animated gif). HTH, Eugene References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Brian White" Subject: Re: Databanks Date: Thu, 24 Jun 1999 11:01:52 -0400 To: rasmol@dhcp-srv2.oit.umass.edu try Eric Martz's site: www.umass.edu/microbio/rasmol Joseph R Fioretti 00 wrote: > My name is Joseph Fioretti, and I'm currently working for a Middlebury > College professor on some 3-D animated visualizations of molecules. I > have been experimenting with the RasMol and Chime languages, but I am > writing in hopes that one of you might be able to direct me to a website > (or other resource) at which I can obtain royalty-free, non-copyrighted > pdb files of lipids, proteins, and other structures associated with > membrane fluidity. I truly appreciate any help any of you can provide, > and if you'd like to email me directly instead of posting to the > listserver, you can send me email at: fioretti@panther.middlebury.edu. > > Thank you very much! > > -Joe Fioretti -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://omega.cc.umb.edu/~bwhite/ ++++------+------+------+------+------+------+------+------+------+------+ From: "Brian White" Subject: rasmol for sparc linux Date: Thu, 24 Jun 1999 11:05:09 -0400 To: "rasmol@lists.umass.edu" Does anyone have a version of rasmol compiled for red hat linux on a sparc classic workstation? -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://omega.cc.umb.edu/~bwhite/ boundary="----=_NextPart_000_000E_01BEBE9B.4ED14B20" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 ++++------+------+------+------+------+------+------+------+------+------+ From: "VAN DE WIELE" Subject: selecting helix by color after displaying "group"? Date: Thu, 24 Jun 1999 23:43:06 -0000 To: "Rasmol list" This is a multi-part message in MIME format. ------=_NextPart_000_000E_01BEBE9B.4ED14B20 charset="x-user-defined" To Rasmol Users =20 After displaying "helix"and "sheet" by "group", with "cartoon", would it = be possible to select for example, helix red and how to do that ? Some = others commands as the same style shoud be well-timed. =20 Thanks to all. =20 Annie Van de Wiele. =20 I'am a beginner with Rasmol, preparing a thesis on a mushroom toxin. Annie Van de Wiele, Pharmacie de la Lys 12 Rue L=E9on Six, Bousbecque 59166 France tel:03 20 23 52 67 Fax: from abroad (00 33)320 236 234=20 avandewiele@nordnet.fr=20 ------=_NextPart_000_000E_01BEBE9B.4ED14B20 charset="x-user-defined"
To  Rasmol Users
 
After = displaying=20 "helix"and "sheet" by "group", with=20 "cartoon", would it be possible to select for example, helix = red and=20 how to do that ? Some others commands as the same style shoud be=20 well-timed. 
Thanks to all.
 
Annie Van de Wiele.
 
I'am a beginner with Rasmol, = preparing a=20 thesis on a mushroom toxin.
Annie Van de Wiele, Pharmacie de la = Lys
12=20 Rue Léon Six, Bousbecque 59166 France
tel:03 20 23 52 67 Fax: = from=20 abroad (00 33)320 236 234
avandewiele@nordnet.fr=20
------=_NextPart_000_000E_01BEBE9B.4ED14B20-- References: <001301bebe9b$85643da0$a2e492c3@w3> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: selecting helix by color after displaying "group"? Date: Fri, 25 Jun 1999 12:12:49 +0100 To: rasmol@dhcp-srv2.oit.umass.edu > VAN DE WIELE wrote: > > To Rasmol Users > > After displaying "helix"and "sheet" by "group", with "cartoon", would > it be possible to select for example, helix red and how to do that ? > Some others commands as the same style shoud be well-timed. > Thanks to all. > > Annie Van de Wiele. > > I'am a beginner with Rasmol, preparing a thesis on a mushroom toxin. > Annie Van de Wiele, Pharmacie de la Lys > 12 Rue Léon Six, Bousbecque 59166 France > tel:03 20 23 52 67 Fax: from abroad (00 33)320 236 234 > avandewiele@nordnet.fr Hi, if I understodd you in the right way you sould type e.g.: select helix color red select strand color green if your pdb-fiel doens't contain any secondary structure information you first have to calculate str sec structure with: select protein structure strand, helix, turn can be included in any rasmol expression, look at http://www.umass.edu and exspecially at http://www.umass.edu/microbio/rasmol/rastut.htm and http://www.umass.edu/microbio/rasmol/distrib/rasman.htm good luck, Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)171 2693405 | Fax : +44-(0)171 269 3258 email : a.mueller@icrf.icnet.uk | http://www.icnet.uk/bmm/ ++++------+------+------+------+------+------+------+------+------+------+ From: "Patrick Flash" Subject: Printing circles for atoms Date: Fri, 25 Jun 1999 11:21:19 EST To: rasmol@dhcp-srv2.oit.umass.edu I would like to print small molecules from Rasmol where the atoms are printed as circles with white interiors and the bonds are printed as parallel lines or angled lines indicating a receeding bond. So far I've been unable to find a way to do this from the Rasmol help file and I've not seen the answer on the listserve over the last couple of years. Is either option possible and, if so, how could I do it? Thanks in advance for any help. Patrick Flash Kent-Ashtabula Campus ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: Printing circles for atoms Date: Fri, 25 Jun 1999 13:55:34 -0600 (MDT) To: rasmol@dhcp-srv2.oit.umass.edu > I would like to print small molecules from Rasmol where the atoms > are printed as circles with white interiors and the bonds are printed > as parallel lines or angled lines indicating a receeding bond. > Is either option possible and, if so, how could I do it? There are a number of commands within RasMol that allow you to print out small molecule depictions similar to the one you describe. [Everything except the receeding bonds!] Try the following list of commands... # Ball & Stick Representation select all spacefill 100 wireframe 30 select hydrogen spacefill 80 # Generate the Postscript File select all color white background black set ambient 100 set vectps true write vectps temp.ps The Vector Postscript command is used to generate the output file. The "set vectps true" option instructs RasMol to output black lines around each object, much like a cartoon. The "set ambient 100" saturates the colours of each object, which is interpreted in the vectps routines as a flat sphaded spheres and bonds. By coloring the spheres and bonds white this means only the cartoon outlines are visible. The perfect black background instructs the vectps routine not to generate a background, but a white background should produce identical results except on colored paper or on transparencies. You might also consider "color bonds black". Roger -- Roger Sayle, E-mail: roger@metaphorics.com Bioinformatics Group, Metaphorics, WWW: http://www.metaphorics.com/ 419 East Palace Avenue, Tel: (+1) 505-984-0613 Santa Fe, New Mexico, 87501. Fax: (+1) 505-989-1200 boundary="----=_NextPart_000_004A_01BEBFEF.590F0C80" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 ++++------+------+------+------+------+------+------+------+------+------+ From: "VAN DE WIELE" Subject: selecting helix by color after dispaying "group" Date: Sat, 26 Jun 1999 16:17:12 -0000 To: "Rasmol list" This is a multi-part message in MIME format. ------=_NextPart_000_004A_01BEBFEF.590F0C80 charset="x-user-defined" Thanks to Dr Mueller and Dr Reichert for their quick reply. . After displaying by "group" and with "cartoon", I see on the screen = several helix colored by "group"...I wanted to take a short-cut and to try a = special command of this style: "select helix[255,0,0] " to obtain a restrict view of this red helix ....But it does not work ! I can take the way by displaying "sticks" and after "set picking ident" on the end and on the beginning of the helix... but it is long ! May be, there is a possibility ? Annie avandewiele@nordnet.fr=20 ------=_NextPart_000_004A_01BEBFEF.590F0C80 charset="x-user-defined"
Thanks to Dr Mueller and Dr = Reichert=20 for their quick reply.
.
After displaying by "group" and = with=20 "cartoon", I see on the screen several
helix colored by=20 "group"...I wanted to take a short-cut and to try a = special
command=20 of this style:

"select helix[255,0,0] "

to = obtain a=20 restrict view of this red  helix ....But it does not work !
I = can take=20 the way by displaying "sticks"
and after "set picking=20 ident" on the end and on the beginning of the
helix... but it is = long=20 !
May be,  there is a possibility ?

Annie
avandewiele@nordnet.fr=20

------=_NextPart_000_004A_01BEBFEF.590F0C80-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Fwd: rasmol <-> linux 2.2.x Date: Tue, 29 Jun 1999 20:14:58 -0400 To: rasmol@dhcp-srv2.oit.umass.edu I am forwarding this for linux users (which I am not) and to make Andreas' solution part of the email archives on the web. -Eric Martz >At 6/28/99, "Andreas Bohne" wrote: >>dear eric, >> >>today i wanted to compile rasmol with the latest version of linux but i run on >>some errors. i am using a linux system with : (uname -a) >>Linux Helios 2.2.5 #17 Thu May 20 11:24:08 CEST 1999 i586 unknown >> >>find attached my solution of this problem: >>(rasmol.c) >> >>#ifdef TERMIOS >>#include >>#include >> >>#ifdef esv >>#include >>#else >>#ifdef __FreeBSD__ >>#include >>#include >>#define TCSETAW TIOCSETAW >>#define TCGETA TIOCGETA >>#else >>#ifdef _CONVEX_SOURCE >>#include >>#include "/usr/sys/base/h/ioctl.h" >>#define TCSETAW TIOCSETAW >>#define TCGETA TIOCGETA >>#else >> >> >>#ifdef linux >>#include >>#include >>#endif /* _LINUX_ kernel >2.2.x */ >> >> >>#include >>#endif /* _CONVEX_SOURCE */ >>#endif /* __FreeBSD__ */ >>#endif /* esv */ >> >> >>----------------------------------------- >>(rasmol.h) >>#ifdef linux >>#define USE_FD_SET_TYPE >>#endif /* _LINUX_ */ >>----------------------------------------- >> >> >>the #ifdef linux is made by the Imake ( -Dlinux -D__i386__ ). >>of course a version number would be more helpful. >> >>bye and i hope you will include this to help other linux users with the >>installation of radmol of a linux platform. >> >>andreas >> >>-- >>+--------------------------------------------------- >>| Andreas Bohne >>| German Cancer Research Centre >>| Central Unit of Spectroscopy >>| WG: Molecular Modeling >>| Im Neuenheimer Feld 280 Tel: 06221 / 42-4541 >>| D-69120 Heidelberg Fax: 06221 / 42-2995 >>| E-Mail: a.bohne@dkfz-heidelberg.de >>| URL: http://www.dkfz-heidelberg.de/spec/ >> - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE OR UNSUBSCRIBE, GO TO THE ABOVE ADDRESS. ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Fwd: Re: Rasmol 2.6++ (rasmol.org?) Date: Tue, 29 Jun 1999 23:22:04 -0400 To: rasmol@dhcp-srv2.oit.umass.edu I am forwarding this to the RasMol email list since the question of the future of RasMol is obviously of great interest to many subscribers. I'll comment further in a message immediately following. -Eric Martz >X-Sender: yaya@epsilon.pair.com >Date: Tue, 29 Jun 1999 08:07:53 -0400 >To: "Andreas Bohne" , roger@metaphorics.com >From: "Herbert J. Bernstein" >Subject: Re: Rasmol 2.6++ >Cc: a.mueller@icrf.icnet.uk, emartz@microbio.umass.edu > >Andreas, > Thank you for your query. The situation is as follows: With Roger's >kind agreement, I am coordinating the next few releases of RasMol. You can >find the sources of the most recent release (2.7.0.1) at any of the IUCr >web site mirrors. In your case I would suspect you would get the best >response from the Swiss mirror: > >http://www.ch.iucr.org/iucr-top/cif/software/rasmol/ > >or you can pick it up from my site: > >http://www.bernstein-plus-sons.com/software/rasmol > >or > >ftp://ftp.bernstein-plus-sons.com/software/rasmol > >RasMol most certainly is _not_ dead. The next release (2.7.1) is almost >ready to go out, and there should be another release in late September or >early October. I would be very happy to have access to your changes and to >see if they can be incorporated with the 2.7.n series. > >On the specific subject of Linux -- I do my primary development for the >2.7.n series on a Linuxppc system, so hopefully you will not have any >serious problems with the 2.7.n releases under an Intel-based Linux, but if >you do, please let me know and we will get it straightened out. If you can >provide Linux binaries of 2.7.n to add to the 2.7.n releases, I will be >happy to include them. I am sure they will be well used, but please be >careful to identify the exact Linux version you use (esp. with respect to >the level of glibc). > >I am cc'ing this message to Eric Martz so he can be aware of your concerns. >The primary focus of his site seems to be Chime these days. I think your >idea of a new "www.rasmol.org" is sensible. RasMol is Roger's program, so >he would have to make the decision on that issue. If Roger agrees with >your idea, I would be willing to try to arrange the hosting of such a site. > >Even with the current arrangements, I have gotten a steady stream of source >code change contributions. It is my intention to try to combine all the >major RasMol variants for which source is openly available into one solid, >working release with source code over the next several months. There have >been so many solid contributions, I expect the 2.7.n series to run part way >into the year 2000. I think science is best done with tools that are >completely documented, and for software, the source code is an important >part of the documentation. These days, RasMol is an essential scientific >tool. > >Regards, > Herbert > > >P.S. I have not posted this to any of this lists, since it is a bit long >and rambling, but if any of the recipients wish to stimulate discussion >with bits and pieces, feel free. -- HJB > > >At 8:58 AM +0000 6/29/99, Andreas Bohne wrote: >>herb, >> >>(eric wrote:) >>>Actually, I have never used the source code at all. >>>You should send it to Herb Bernstein who has recently made version 2.7, and >>>send the information to the rasmol list, because then it will be archived >>>in the web-searchable history. >>>Also to Roger Sayle in case he updates his source again. >>>roger@metaphorics.com, yaya@bernstein-plus-sons.com >> >>o.k. i will do this. >> >>before i got this infomation that there is a version higher 2.6x2 i took the >>sourcecode from the http://www.umass.edu/microbio/rasmol/ page and start >>compiling it on a linux system (kernel 2.2.5 glibc) and run into problems. >> >>i fixed the source to be able to be compiled on a linux 2.2.5 system. >> >>furthermore i saw that there are much more output routines. i added these >>output routines to the graphical menu. >> >>at the moment i am working on a pdb-inline script. >>(e.g. in the pdb file: REMARK RASSCR: ribbon) >>with this feature it will be possible to use preselected displays of molecules >>on the web. >> >>i did this changes for my work. but i think if this is interesting for other >>people they should get the possibility of using the source too. >> >>my question: who is co-ordinating the source code developing of rasmol? >>from my point of view lot of people would help to develope new features to >>rasmol if they know that there is an interest and that someone is >>co-ordinating >>the development. >> >>why do have the .../microbio/rasmol/ page not the latest source (2.7)? >> >>where is the adress from where i can get the source 2.7? >> >>for further developement it would be nice if the feature of shuttere glasses >>(www.stereo3d.com) could be added to rasmol. >> >>what do you think of hosting www.rasmol.org? >> >>rasmol should not be dead!!! >> >>andreas >> >>-- >>+--------------------------------------------------- >>| Andreas Bohne >>| German Cancer Research Centre >>| Central Unit of Spectroscopy >>| WG: Molecular Modeling >>| Im Neuenheimer Feld 280 Tel: 06221 / 42-4541 >>| D-69120 Heidelberg Fax: 06221 / 42-2995 >>| E-Mail: a.bohne@dkfz-heidelberg.de >>| URL: http://www.dkfz-heidelberg.de/spec/ > > >===================================================== >**** BERNSTEIN + SONS >* * INFORMATION SYSTEMS CONSULTANTS >**** P.O. BOX 177, BELLPORT, NY 11713-0177 >* * *** >**** * Herbert J. Bernstein > * *** yaya@bernstein-plus-sons.com > *** * > * *** 1-516-286-1339 FAX: 1-516-286-1999 >===================================================== > - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE OR UNSUBSCRIBE, GO TO THE ABOVE ADDRESS. ++++------+------+------+------+------+------+------+------+------+------+ From: Eugene Leitl Subject: RasMol derivates with embedded scripting language? Date: Tue, 29 Jun 1999 20:32:42 -0700 (PDT) To: rasmol@dhcp-srv2.oit.umass.edu Are there RasMol derivates with embedded Python or Scheme for scripting languages out there? TIA, Eugene Leitl ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Rasmol 2.6++ (rasmol.org?) Date: Tue, 29 Jun 1999 23:51:39 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Here are my thoughts concerning the proposal for a new www.rasmol.org by Andreas Bohne and Herbert Bernstein, and the future of RasMol and its support in general. I am very delighted to see the recent collaborative efforts of Herbert, Roger Sayle, Arne Mueller and others which has led to the first new release of RasMol since 1996. I myself have never contributed directly to the source code of RasMol as I have kept busy with other forms of support. Spurred by this latest discussion, I have finally (a couple of months overdue with apologies) put a link to RasMol 2.7 at my site (www.umass.edu/microbio/rasmol/getras.htm). I have explained there that the documentation at my site will remain largely frozen at version 2.6-beta-2a and that all documentation for the changes in 2.7 will be found at the Bernstein site, http://www.bernstein-plus-sons.com/software/rasmol/. I am investing most of my personal efforts these days into the development of Chime resources. As I have commented previously on this list, I believe that for the most widely used (but certainly not all) purposes, the Protein Explorer I have developed is superior to RasMol (bearing in mind of course that it incorporates and builds upon most of RasMol's wonderful features). Most importantly, if I am able to continue to develop the Protein Explorer as planned ( = if I get the NSF grant I just applied for) I believe it can bring to students and educators greatly enhanced ease of access to 3D macromolecular structure. I will be happy if happy if Herbert et al. wish to start a www.rasmol.org but I have no interest in doing so myself. I will be happy to link to it from my site. Although my site www.umass.edu/microbio/rasmol was initially dubbed the "RasMol Home Page" (with Roger's blessing in November 1995) observant visitors will have noticed that more than a year ago the main page title was changed to "RasMol & Chime: Molecular Visualization Freeware". I am quite willing to relinquish the title "RasMol Home Page" whenever a new site becomes more deserving of that appellation. I am also happy to have RasMol documentation I have authored at my site copied and served from the proposed www.rasmol.org, provided authorship is acknowledged and these copies are adequately maintained by others. A plan was in the works to mirror my site through the BNL PDB site and its mirrors prior to the transition from BNL to RCSB. That plan is now on hold pending future discussions with RCSB. For the near future, I certainly plan to keep my site as it is. Despite the many ways it could be improved (but unfortunately will not be due to lack of funds, time and other priorities) the RasMol branch of my site has been visited steadily by over 5,000 people per week for most of the past year. I think this is largely due to the help and clear documentation I have provided for beginners, into which I have put a great deal of effort. Perhaps, at least initially, the focus of www.rasmol.org would gravitate naturally to cutting edge use of RasMol by experienced users, while my site would continue to provide basic help for novices (Quick Start, Select Commands, Colors, etc.). Chime derives much of its power and elegance from Roger's RasMol source code. This was possible because Roger placed NO restrictions on the use of RasMol's source code, which allowed it to be used even in a product developed in a for-profit context (notably MDL's ISIS/Chemscape; MSI's WebLab Viewer). In part because of its RasMol heritage, MDL has made the Chime plugin free to all users, including commercial users. We all have Roger's generosity and forsight to thank for this development. Not long ago, when Roger Sayle was still focusing more intensely upon RasMol development, I believe there was an agreement between Roger and MDL's Chime team to develop Chime and RasMol in parallel, so that enhancements to one could be built into the other. I myself would love to see this idea rejuvenated. RasMol 2.7 contains significant enhancements from which Chime could benefit. A number of bugs in RasMol's code (e.g. in the saving of scripts, see http://www.umass.edu/microbio/chime/explorer/right1tu.htm#chimake which refers to http://www.umass.edu/microbio/chime/shared/sshorten.htm; and in stereo) have been fixed in Chime, but not in RasMol, and Chime has many new features such as surfaces. -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE OR UNSUBSCRIBE, GO TO THE ABOVE ADDRESS. ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime 2.0a Mac bug: pick report not cleared Date: Wed, 30 Jun 1999 00:03:42 -0400 To: chime-feedback@mdli.com Cc: rasmol@dhcp-srv2.oit.umass.edu The following bug occurs only in the Macintosh version of Chime 2.0a (not in Windows Chime 2.0.2). If you click on an atom, generating a report such as "Atom: CA 1545 Group: LYS 45 Chain: B", and you are in 'debugscript=on' mode, and the next event is to issue a command such as "select 27:D", the message which comes back contains the previous pick message concatenated to the command, e.g. "Atom: CA 1545 Group: LYS 45 Chain: Bselect 27:D". The command is executed properly, only the message coming back is corrupted due apparently to failure to clear the pick report out of the buffer. I wrote the following javascript to fix this since I am using the pick report to trigger various automatic scripts, and the bug causes the triggering to occur twice, the second time with erroneous commands since the chain is parsed as e.g. "Bselect 27:D". This javascript is the first item in the MessageCallback function. (I am using it in the Noncovalent Bond Finder which I am making Mac-compatible prior to making it freely downloadable). I am copying this to the RasMol list in case others are developing code using pick reports. // Workaround for Mac Chime 2.0a bug which concatenates first debugscript // -echoed command onto end of previous pick message, e.g. this pick // report // Atom: CA 1545 Group: LYS 45 Chain: B // when followed by the command 'select 27:D' generates this message // Atom: CA 1545 Group: LYS 45 Chain: Bselect 27:D // This code cleans the redundant pick report off of the front of the // second message, changing it to the desired 'select 27:D'. if (message.indexOf("Atom: ") == 0 && top.client_os == "mac" && message.substring(0, last_msg.length) == last_msg) message = message.substring(last_msg.length); last_msg = message; -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Chime vs. RasMol Date: Wed, 30 Jun 1999 08:12:42 -0400 (EDT) To: rasmol@dhcp-srv2.oit.umass.edu Cc: roger@metaphorics.com, a.mueller@icrf.icnet.uk, emartz@microbio.umass.edu Eric Martz raised some interesting points in his recent message. I would like to comment on the relationship with Chime: Eric said: >> Chime derives much of its power and elegance from Roger's RasMol source >> code. This was possible because Roger placed NO restrictions on the use >> of RasMol's source code, which allowed it to be used even in a product >> developed in a for-profit context (notably MDL's ISIS/Chemscape; MSI's >> WebLab Viewer). In part because of its RasMol heritage, MDL has made >> the Chime plugin free to all users, including commercial users. We all >> have Roger's generosity and forsight to thank for this development. >> Not long ago, when Roger Sayle was still focusing more intensely upon >> RasMol development, I believe there was an agreement between Roger and >> MDL's Chime team to develop Chime and RasMol in parallel, so that >> enhancements to one could be built into the other. I myself would love >> to see this idea rejuvenated. RasMol 2.7 contains significant >> enhancements from which Chime could benefit. A number of bugs in >> RasMol's code (e.g. in the saving of scripts, see >> http://www.umass.edu/microbio/chime/explorer/right1tu.htm#chimake which >> refers to http://www.umass.edu/microbio/chime/shared/sshorten.htm; and >> in stereo) have been fixed in Chime, but not in RasMol, and Chime has >> many new features such as surfaces. If MDL wishes to contribute any of its improvements as source code to the RasMol 2.7.n series, I would be more than happy to incorporate them. As many commercial firms have learned from the growth of Linux, the supposed conflict between the commercial status of a product and having source available is an illusion. Indeed, open-source development environments produce much more robust, reliable products that do binary-only environments. All MDL has to do is to send me their code with a message accepting its incorporation into the RasMol 2.7.n series under the terms stated in the 2.7.n releases. As a practical matter, it would be simplest if they agreed to put out all of Chime as an open-source product under the same terms, but, as long as they respect the RasMol 2.7.n terms as written, they are welcome to make only a partial contribution of their efforts to sources available to the community. However, in order for MDL to back-incorporate the RasMol 2.7.n changes into a new version of Chime, the version of Chime would have to become an open-source product incorporating the RasMol terms and notices. I highly recommend this course of action. I believe it is the right thing to do for any scientific software, and that it would be good for MDL and for the community. I firmly believe that this would be the best way to "develop Chime and RasMol in parallel". Just for completeness, here is a copy of those terms: This version is based on RasMol version 2.6_CIF.2, on RasMol version 2.6x1 and on RasMol version 2.6.4. Please read the file NOTICE for important notices which apply to this package. If you are not going to make changes to RasMol, you are not only permitted to freely make copies and distribute them, you are encouraged to do so, provided you do the following: 1. Either include the complete documentation, especially the file NOTICE, with what you distribute or provide a clear indication where people can get a copy of the documentation; and 2. Please give credit where credit is due citing the version and original authors properly; and 3. Please do not give anyone the impression that the original authors are providing a warranty of any kind. If you would like to use major pieces of RasMol in some other program, make modifications to RasMol, or in some other way make what a lawyer would call a "derived work", you are not only permitted to do so, you are encouraged to do so. In addition to the things we discussed above, please do the following: 4. Please explain in your documentation how what you did differs from this version of RasMol; and 5. Please make your modified source code available. This version of RasMol is not in the public domain, but it is given freely to the community in the hopes of advancing science. If you make changes, please make them in a responsible manner, and please offer us the opportunity to include those changes in future versions of RasMol. The "file NOTICE" referred to above may be seen at http://www.bernstein-plus-sons.com/software/rasmol/doc/NOTICE.html ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-516-286-1339 FAX: 1-516-286-1999 ===================================================== References: <14201.36746.224860.54771@lrz.de> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: RasMol derivates with embedded scripting language? Date: Wed, 30 Jun 1999 13:46:54 +0100 To: rasmol@dhcp-srv2.oit.umass.edu Eugene Leitl wrote: > > Are there RasMol derivates with embedded Python or Scheme for > scripting languages out there? > > TIA, > > Eugene Leitl Hi, I also imagined what'll happen if rasmol contained a scripting language ... ;-) - maybe python. Alas, I've no idea how to implement python in rasmol. As far as I know there no such extensions for RasMol yet. By the way: For what do you like to use an embedded scripting language? Greetings, Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)171 2693405 | Fax : +44-(0)171 269 3258 email : a.mueller@icrf.icnet.uk | http://www.icnet.uk/bmm/ References: boundary="------------4285B271473D5D6F721928AA" X-Accept-Language: de ++++------+------+------+------+------+------+------+------+------+------+ From: " Dr. Frank Eblinger" Subject: Rasmol 2.7. bug for windows Date: Wed, 30 Jun 1999 14:59:16 +0200 To: rasmol@dhcp-srv2.oit.umass.edu Dies ist eine mehrteilige Nachricht im MIME-Format. --------------4285B271473D5D6F721928AA Dear Rasmol users, I think it was a very good idea to implement the export feature to povray inside vs. 2.7. But when I tried to export a povray file of a chiral compound (e.g. R-lactic acid) the resulting *.pov file is rendered to the S-enantiomer! (See attached file). Did anybody observe the same? How can one fix this? 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ABQAAgAIANqQ3SY76QW7OBUAAE0VAAANAAAAAAAAAAAAIAC2gaJEAABNaWxjaF9SYXMuR0lG UEsFBgAAAAACAAIAeQAAAAVaAAAAAA== --------------4285B271473D5D6F721928AA-- References: <14201.36746.224860.54771@lrz.de> <377A11BE.C4FE0777@icrf.icnet.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Eugene Leitl Subject: Re: RasMol derivates with embedded scripting language? Date: Wed, 30 Jun 1999 12:01:58 -0700 (PDT) To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu Arne Mueller writes: > I also imagined what'll happen if rasmol contained a scripting language > ... ;-) - maybe python. Alas, I've no idea how to implement python in > rasmol. As far as I know there no such extensions for RasMol yet. By the Peter McCluskey has some code here http://www.openchem.org/download/index.html which I am unfortunately unable to run yet. > way: For what do you like to use an embedded scripting language? I would like to have MMTK http://starship.python.net/crew/hinsen/mmtk.html http://www.python.org/workshops/1997-10/proceedings/hinsen.html running within RasMol instead of just using it as a display engine. For another illustration what can be done with Python see MDTools http://www.ks.uiuc.edu/~jim/mdtools/ . As you probably now, it is very simple to extend Python with C modules using SWIG http://www.swig.org . For an illustration, see SPaSM http://bifrost.lanl.gov/MD/MD.html , for more look under http://ftp.swig.org/papers.html There are obviously lots of excellent reasons why RasMol should speak Python ;) -- Eugene ++++------+------+------+------+------+------+------+------+------+------+ Beginning July 1, 1999: ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Noncovalent Bond Finder works on Macs and is Downloadable Date: Thu, 01 Jul 1999 11:46:41 -0400 To: rasmol@dhcp-srv2.oit.umass.edu, pdb-l@rcsb.org My Noncovalent Bond Finder has just been upgraded. You can select any moiety within a PDB file, such as a ligand or an alpha helix, and the Finder will visually display all atoms within bonding distance. This is as easy as pressing the [FIND] button. On each [FIND] press, it moves out to a larger shell, highlighting the found atoms with a dot surface. The steps are 0.1 Angstrom by default, but you can specify larger step sizes. You can display the entire residue to which a found atoms belongs with a single mouse click. Several crystallographers who have seen the Finder responded that it allows them to discover noncovalent bonding relationships with greater ease, and clearer visualization, than does commercial software already at their disposal. Each immediately asked for a copy, and one (surrounded by SGI's) bought a notebook computer to enable him to use it regularly. To simplify the image, you can find only designated categories of atoms in a given pass. For example, in one series of [FIND] clicks, you can specify "find only (carbon and hydrophobic and sidechain)" (using RasMol command syntax), or you could specify "don't find water". You can change the target atom(s) dynamically. Thus, once you find a water molecule bound to the initial target (ligand), you can temporarily make that water the target, press [FIND], and thus "walk out on the water bridge" to the other side. A snapshot of the Finder in action may be seen at http://www.umass.edu/microbio/chime/find-ncb/preview.htm and the Finder itself is at http://www.umass.edu/microbio/chime/find-ncb The Finder includes a click-by-click tutorial/demonstration with a built-in example molecule (peptide bound to MHC). I have just released version 1.5 of the Finder. It now works as well on Macintoshes as on Windows, and can be freely downloaded for local installation. Downloaded copies include complete source code (javascript and chemical script language) and could be modified or enhanced as desired. The Finder is copyrighted. It may be used freely, including installation in local computer labs. You may put a link to the Finder site at your website as long as there is no fee to access your website. You may NOT redistribute copies or derivatives of the Finder from your website, from a CD, or by other means without permission. In other words, all copies must be obtained from my website. If you have a fast connection to the Internet, it is not necessary to download the Finder in order to use it -- it works on the molecule of your choice directly from my website. Temporarily, you will need a local copy of the PDB file since at this moment of transition between the BNL and RCSB PDB's, there is no longer any URL which can work with Chime to fetch a PDB file directly via Internet (this will hopefully be fixed very soon - a request has been made to RCSB). The Finder requires Chime 2, and therefore works only on Windows 95/98/NT or Macintosh PPC computers (sorry, not linux, Irix, etc. -- beyond my control as Chime 2 is the proprietary freeware of MDLI). I'd like to thank the Division of Undergraduate Education of the US National Science Foundation for support. -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - UMass Chime Resources: www.umass.edu/microbio/chime Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Brian Salter-Duke Subject: animation in scripts Date: Fri, 2 Jul 1999 14:02:58 +1100 To: RasMol List I am using Chime to animate molecular vibrations etc and I have looked at various examples from various sites. In the button stuff in the script " ... ", I see examples such as:- anim on anim off animation direction +1 animation direction -1 anim frame next I can get these to work fine. My question is this - where is this documented? I want to see a full syntax for anim and animation (which I assume are the same). I have searched the chime pages, various rasmol pages and so on, but I can not find this. There is the list of embed commands, but that is not what I want. Any ideas? Cheers, Brian. -- Associate Professor Brian Salter-Duke (Brian Duke) Chemistry, Faculty of Science, IT and Education, Northern Territory University, Darwin, NT 0909, Australia. Phone 08-89466702. Fax 08-89466847 b_duke@lacebark.ntu.edu.au http://www.smps.ntu.edu.au/chemistry/compchem.html ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: animation in scripts Date: Fri, 02 Jul 1999 11:33:25 -0700 To: rasmol@dhcp-srv2.oit.umass.edu Cc: chime-feedback@mdli.com Here are some notes on the animation command: "show animation", or "animation info" - show anim info "animation" | "anim" - either can be used for command "frame next" | "frame -1" - advance to next frame "frame #" - set the animation frame to the frame # specified "on" - starts animation playing "off" - stops animation "mode" - sets animation mode while playing "loop" - loop from start to end, over and over "once" - loop from start to end ONCE "palindrome" - loop start to end, then end to start, over and over "direction" - sets current play direction: "+1" - forward "-1" - backward "fps" "#" of frames per second "info" - prints anim info (see above, you can also use 'show animation" Hope that helps.. -tim At 02:02 PM 7/2/99 +1100, you wrote: > >I am using Chime to animate molecular vibrations etc and I have looked >at various examples from various sites. In the button stuff >in the script " ... ", I see examples such as:- > >anim on >anim off >animation direction +1 >animation direction -1 >anim frame next > >I can get these to work fine. My question is this - where is this >documented? I want to see a full syntax for anim and animation (which >I assume are the same). I have searched the chime pages, various rasmol >pages and so on, but I can not find this. There is the list of embed >commands, but that is not what I want. > >Any ideas? > >Cheers, Brian. >-- > Associate Professor Brian Salter-Duke (Brian Duke) >Chemistry, Faculty of Science, IT and Education, Northern Territory University, > Darwin, NT 0909, Australia. Phone 08-89466702. Fax 08-89466847 >b_duke@lacebark.ntu.edu.au http://www.smps.ntu.edu.au/chemistry/compchem.html > ++++------+------+------+------+------+------+------+------+------+------+ From: Ross Feldberg Subject: running a ras script in chime Date: Fri, 02 Jul 1999 15:25:18 -0400 To: rasmol@dhcp-srv2.oit.umass.edu I am a relative newcomer to using Chime and am trying to prepare a new Chime tutorial. I have put together a series of Ras script files into a master script. When I call up this master script file using a Chime button, I see the files listed as loading in the status line at the bottom of the Navigator page, but no images appear until the last image. I have gotten this type of button to work before and I can't see what I am doing different. Can any one suggest what I am doing wrong? Also, is this the "correct" way to do this in Chime. In this script file I am showing the sequential secondary structure elements from N to C terminus. By using a series of ras script files, Chime needs to reload the entire structure each time. Is there a more efficient way to do carry out this type of action? Ross Feldberg Dept Biology Tufts University ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: running a ras script in chime Date: Fri, 02 Jul 1999 18:11:49 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Cc: rfeldber@emerald.tufts.edu At 7/2/99, you wrote: >I am a relative newcomer to using Chime and am trying to prepare a new >Chime tutorial. > >I have put together a series of Ras script files into a master script. When >I call up this master script file using a Chime button, I see the files >listed as loading in the status line at the bottom of the Navigator page, >but no images appear until the last image. I have gotten this type of >button to work before and I can't see what I am doing different. Can any >one suggest what I am doing wrong? > >Also, is this the "correct" way to do this in Chime. In this script file I >am showing the sequential secondary structure elements from N to C >terminus. By using a series of ras script files, Chime needs to reload the >entire structure each time. Is there a more efficient way to do carry out >this type of action? > >Ross Feldberg >Dept Biology >Tufts University Dear Ross: I urge you to download the template from www.umass.edu/microbio/chime/prsswc which has extremely detailed instructions for "presenting RasMol-saved scripts in Chime", plus troubleshooting steps. In general, rather than putting a master script on a Chime button, I think you probably will get a better result putting each individual script on a separate button. If you need to show intermediate images in a script, the command to do that is 'refresh' or 'delay N' (N seconds) or 'pause' (wait for a keystroke) but again, most likely this is NOT the best way to do this -- one button per image/script is best. By putting a master script on one Chime button you lose all the random access and backing up control which makes Chime so much better for presentations than RasMol. Don't worry about reloading the molecule for each image. Chime is intelligent about this: if given a load command, if the pdb file specified in the load command is already loaded, it doesn't actually load the molecule -- it just resets as though it had so the script works properly thereafter. So it is very efficient with no effort on your part. Regards, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Morpher Downloadable with Methods Date: Sun, 04 Jul 1999 23:54:31 -0400 To: rasmol@dhcp-srv2.oit.umass.edu, pdb-l@rcsb.org I have put a new version of my Protein Morpher on the web. The new features are that it works fully on Macintoshes, it is downloadable for local installation, and that the methods are documented to enable others to prepare morphs viewable in Chime. As in the previous version, there are morph "movies" of the conformational changes of recoverin binding calcium and extruding myristic acid, influenza hemagglutinin (not very satisfactory), integrin CD11b changing the affinity of its ligand binding site by changing the charge environment of a metal ion, calmodulin (one morph binding calcium, a second binding peptide), and cAMP kinase. Thanks to the Morph Server of Mark Gerstein and Werner Krebs at Yale U which generated some of the "semi-plausible" morphs displayed here in Chime. -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - UMass Chime Resources: www.umass.edu/microbio/chime Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: Re: animation in scripts Date: Mon, 5 Jul 1999 17:38:34 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Cc: chime-feedback@mdli.com Here are some notes on the animation command: "show animation", or "animation info" - show anim info "animation" | "anim" - either can be used for command "frame next" | "frame -1" - advance to next frame "frame #" - set the animation frame to the frame # specified "on" - starts animation playing "off" - stops animation "mode" - sets animation mode while playing "loop" - loop from start to end, over and over "once" - loop from start to end ONCE "palindrome" - loop start to end, then end to start, over and over "direction" - sets current play direction: "+1" - forward "-1" - backward "fps" "#" of frames per second "info" - prints anim info (see above, you can also use 'show animation" Hope that helps.. -tim At 02:02 PM 7/2/99 +1100, you wrote: > >I am using Chime to animate molecular vibrations etc and I have looked >at various examples from various sites. In the button stuff >in the script " ... ", I see examples such as:- > >anim on >anim off >animation direction +1 >animation direction -1 >anim frame next > >I can get these to work fine. My question is this - where is this >documented? I want to see a full syntax for anim and animation (which >I assume are the same). I have searched the chime pages, various rasmol >pages and so on, but I can not find this. There is the list of embed >commands, but that is not what I want. > >Any ideas? > >Cheers, Brian. >-- > Associate Professor Brian Salter-Duke (Brian Duke) >Chemistry, Faculty of Science, IT and Education, Northern Territory University, > Darwin, NT 0909, Australia. Phone 08-89466702. Fax 08-89466847 >b_duke@lacebark.ntu.edu.au http://www.smps.ntu.edu.au/chemistry/compchem.html > _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ Frieda Reichsman, Ph.D. _/_/_/_/_/ Biochemistry and Molecular Biology _/_/_/_/_/ University of Massachusetts _/_/_/_/_/ Amherst, MA 01003 _/_/_/_/_/ Phone: (413) 545-4029 _/_/_/_/_/ Fax: (413) 545-3291 _/_/_/_/_/ http://www.bio.umass.edu/biochem/reichsman _/_/_/_/_/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: animation in scripts Date: Mon, 5 Jul 1999 17:38:33 -0400 To: RasMol List I am using Chime to animate molecular vibrations etc and I have looked at various examples from various sites. In the button stuff in the script " ... ", I see examples such as:- anim on anim off animation direction +1 animation direction -1 anim frame next I can get these to work fine. My question is this - where is this documented? I want to see a full syntax for anim and animation (which I assume are the same). I have searched the chime pages, various rasmol pages and so on, but I can not find this. There is the list of embed commands, but that is not what I want. Any ideas? Cheers, Brian. -- Associate Professor Brian Salter-Duke (Brian Duke) Chemistry, Faculty of Science, IT and Education, Northern Territory University, Darwin, NT 0909, Australia. Phone 08-89466702. Fax 08-89466847 b_duke@lacebark.ntu.edu.au http://www.smps.ntu.edu.au/chemistry/compchem.html _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ Frieda Reichsman, Ph.D. _/_/_/_/_/ Biochemistry and Molecular Biology _/_/_/_/_/ University of Massachusetts _/_/_/_/_/ Amherst, MA 01003 _/_/_/_/_/ Phone: (413) 545-4029 _/_/_/_/_/ Fax: (413) 545-3291 _/_/_/_/_/ http://www.bio.umass.edu/biochem/reichsman _/_/_/_/_/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: Noncovalent Bond Finder works on Macs and is Downloadable Date: Mon, 5 Jul 1999 17:38:35 -0400 To: rasmol@dhcp-srv2.oit.umass.edu, pdb-l@rcsb.org My Noncovalent Bond Finder has just been upgraded. You can select any moiety within a PDB file, such as a ligand or an alpha helix, and the Finder will visually display all atoms within bonding distance. This is as easy as pressing the [FIND] button. On each [FIND] press, it moves out to a larger shell, highlighting the found atoms with a dot surface. The steps are 0.1 Angstrom by default, but you can specify larger step sizes. You can display the entire residue to which a found atoms belongs with a single mouse click. Several crystallographers who have seen the Finder responded that it allows them to discover noncovalent bonding relationships with greater ease, and clearer visualization, than does commercial software already at their disposal. Each immediately asked for a copy, and one (surrounded by SGI's) bought a notebook computer to enable him to use it regularly. To simplify the image, you can find only designated categories of atoms in a given pass. For example, in one series of [FIND] clicks, you can specify "find only (carbon and hydrophobic and sidechain)" (using RasMol command syntax), or you could specify "don't find water". You can change the target atom(s) dynamically. Thus, once you find a water molecule bound to the initial target (ligand), you can temporarily make that water the target, press [FIND], and thus "walk out on the water bridge" to the other side. A snapshot of the Finder in action may be seen at http://www.umass.edu/microbio/chime/find-ncb/preview.htm and the Finder itself is at http://www.umass.edu/microbio/chime/find-ncb The Finder includes a click-by-click tutorial/demonstration with a built-in example molecule (peptide bound to MHC). I have just released version 1.5 of the Finder. It now works as well on Macintoshes as on Windows, and can be freely downloaded for local installation. Downloaded copies include complete source code (javascript and chemical script language) and could be modified or enhanced as desired. The Finder is copyrighted. It may be used freely, including installation in local computer labs. You may put a link to the Finder site at your website as long as there is no fee to access your website. You may NOT redistribute copies or derivatives of the Finder from your website, from a CD, or by other means without permission. In other words, all copies must be obtained from my website. If you have a fast connection to the Internet, it is not necessary to download the Finder in order to use it -- it works on the molecule of your choice directly from my website. Temporarily, you will need a local copy of the PDB file since at this moment of transition between the BNL and RCSB PDB's, there is no longer any URL which can work with Chime to fetch a PDB file directly via Internet (this will hopefully be fixed very soon - a request has been made to RCSB). The Finder requires Chime 2, and therefore works only on Windows 95/98/NT or Macintosh PPC computers (sorry, not linux, Irix, etc. -- beyond my control as Chime 2 is the proprietary freeware of MDLI). I'd like to thank the Division of Undergraduate Education of the US National Science Foundation for support. -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - UMass Chime Resources: www.umass.edu/microbio/chime Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ Frieda Reichsman, Ph.D. _/_/_/_/_/ Biochemistry and Molecular Biology _/_/_/_/_/ University of Massachusetts _/_/_/_/_/ Amherst, MA 01003 _/_/_/_/_/ Phone: (413) 545-4029 _/_/_/_/_/ Fax: (413) 545-3291 _/_/_/_/_/ http://www.bio.umass.edu/biochem/reichsman _/_/_/_/_/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.0810.800 ++++------+------+------+------+------+------+------+------+------+------+ From: "Tjaard Pijning" Subject: Chime and Netscape Date: Wed, 7 Jul 1999 08:13:50 +0200 To: "RasMol Mailing List" I am using a Chime with Netscape, using data files (PDBs etc.) stored on my harddisk. When running Chime this way is it possible for other people to "see" or retrieve the information displayed in Chime in any way ? Or is it enough to run Netscape offline ? If not, is there another way to secure my files ? Thanks for your help, ----------------------------------------------------- //// . . / - Ing. Tjaard Pijning Protein Crystallography Group University of Groningen Nijenborgh 4 9747 AG Groningen tel : (31)(0)50 3634385 email : pijning@chem.rug.nl ----------------------------------------------------- charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 ++++------+------+------+------+------+------+------+------+------+------+ From: "Ronald Frisch" Subject: COLO records / User colours in Rasmol Date: Wed, 7 Jul 1999 11:37:49 +0200 To: "RasMol List" Hi all, trying to visualize certain protein atom properties like accessible surface / solvation contact I came upon the "user color" menu option in RasMol. I found how to build those COLO records and quickly implemented into my project so that the result is a PDB file with a COLO record for each atom. I have found that RasMol accepts no more than roughly 25 COLO records, otherwise it won't display the PDB file giving this error message: "Too many color records in file." Is there a way to make RasMol display much more COLO records? (like 200) Thank you for your help, ---------------------------------------------------------- Ronald Frisch, student Ab initio protein structure prediction group Department of Computer Science V University of Mannheim Mannheim, Germany email: ronald@frisch.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Brian White" Subject: Compiling RasMol on RedHat Linux 5.2 Date: Wed, 07 Jul 1999 11:52:13 -0400 To: "rasmol@lists.umass.edu" Hi all - With help from Andreas Bohne, I just got RasMol 2.6 to compile & run on RedHat Linux 5.2. It required the following: 0) Make sure you've installed all the relevant X11 libraries on your machine. 1) Get the files explictly for UNIX. Get 'em from: http://www.dkfz-heidelberg.de/spec/sweet2/doc/plugin/ - click on the link to "netscape 4" "step-by-step ... UNIX" - in the top line of the window that appears, click "Linux (2.0.x)" - you'll need to gunzip & tar the file 2) Fix the Makefile because Linux puts the libraries in a strange place. - add "-L/usr/X11R6/lib" to the LIBS lines. Changed lines are shown below: # -lXi required if using DIALBOX EXTLIBS = -lm -L/usr/X11R6/lib -lXext -lXi -lX11 # Normal Libraries LIBS = -lm -L/usr/X11R6/lib -lXext -lX11 3) Fix the rasmol.h for linux; altered lines are indicated by *** /* rasmol.h * RasMol2 Molecular Graphics * Roger Sayle, August 1995 * Arne Mueller, Mai 1998 * Version 2.6x1 */ /*===========================*/ /* User Definable Options! */ /*===========================*/ /* #define IBMPC */ /* #define APPLEMAC */ /* #define DIALBOX */ #define TERMIOS #define SOCKETS #define MITSHM #define LINUX *** - added this line /* #define MMIOLIB */ /* #define OMLCOMMS */ /* #define CEXIOLIB */ #if !defined(EIGHTBIT) && !defined(THIRTYTWOBIT) && !defined(SIXTEENBIT) /* #define THIRTYTWOBIT */ /* #define SIXTEENBIT */ #define EIGHTBIT *** - un-commented this line #endif /* define ´USE_FD_SET_TYPE´ if you get compilations */ /* errors in ´rasmol.c´ claiming about ´WaitSet´ */ /* and OrigWaitSet´ (happens on newer linux systems) */ #define USE_FD_SET_TYPE *** un-commented this line 4) Fix rasmol.c; altered lines are indicated by *** /* rasmol.c * RasMol2 Molecular Graphics * Roger Sayle, August 1995 * Arne Mueller, Mai 1998 * Version 2.6x1 */ #ifndef sun386 #include #endif #include #include #include #include #include #define RASMOL #include "rasmol.h" #include "graphics.h" #include "molecule.h" #include "infile.h" #include "abstree.h" #include "transfor.h" #include "command.h" #include "render.h" #include "repres.h" #include "pixutils.h" #include "outfile.h" #ifdef USE_FD_SET_TYPE *** these 5 lines were added #define fd_set fd_set *** #else *** #define fd_set struct fd_set *** #endif *** #ifdef TERMIOS #include #include #ifdef esv #include #else #ifdef __FreeBSD__ #include #include #define TCSETAW TIOCSETAW #define TCGETA TIOCGETA #else #ifdef _CONVEX_SOURCE #include #include "/usr/sys/base/h/ioctl.h" #define TCSETAW TIOCSETAW #define TCGETA TIOCGETA #else #ifdef LINUX *** these 4 lines were added #include *** #include *** #endif /*linux */ *** #include *** this was changed from "termio.h" to "termios.h" #endif /* _CONVEX_SOURCE */ #endif /* __FreeBSD__ */ #endif /* esv */ For the moment, all the modified files & a compiled version of rasmol can be found at: ftp://lab032-10.bio.umb.edu/pub/ Enjoy & thanks to Andreas Brian -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://omega.cc.umb.edu/~bwhite/ References: <14201.36746.224860.54771@lrz.de> <377A11BE.C4FE0777@icrf.icnet.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: "Peter C. McCluskey" Subject: Re: RasMol derivates with embedded scripting language? Date: Thu, 8 Jul 1999 10:38:47 -0700 To: rasmol@dhcp-srv2.oit.umass.edu eugene.leitl@lrz.uni-muenchen.de (Eugene Leitl) writes: >Arne Mueller writes: > > > I also imagined what'll happen if rasmol contained a scripting language > > ... ;-) - maybe python. Alas, I've no idea how to implement python in > > rasmol. As far as I know there no such extensions for RasMol yet. By the > >Peter McCluskey has some code here http://www.openchem.org/download/index.html >which I am unfortunately unable to run yet. > > > way: For what do you like to use an embedded scripting language? > >I would like to have MMTK http://starship.python.net/crew/hinsen/mmtk.html >http://www.python.org/workshops/1997-10/proceedings/hinsen.html >running within RasMol instead of just using it as a display I don't think running MMTK within RasMol is a very practical goal. I've designed my python interface to RasMol so that you ought to be able use Python code while running RasMol by having the RasMol code return to the Python code that called it, letting Python manipulate things, and then call the RasMol code again to update the display. I think I've done most of the work to enable this, but haven't tried to make use of this feature. If you're using the RasMol code from the openchem site, the most recent version is: ftp.openchem.org/openchem0.0.8.tar.gz but it isn't usable as a program (I announced that only to Chris and John because I thought they were on the verge of integrating it into something usefull, but I've heard virtually nothing from them since). The interface available in my MMTK extensions at http://www.rahul.net/pcm/mmtk/index.html is simpler and probably as close to what you want. -- ------------------------------------------------------------------------ Peter McCluskey | Critmail (http://crit.org/critmail.html): http://www.rahul.net/pcm | Accept nothing less to archive your mailing list ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: COLO records / User colours in Rasmol Date: Thu, 08 Jul 1999 20:04:48 -0400 To: rasmol@dhcp-srv2.oit.umass.edu The most likely source for an answer is Roger Sayle -- or maybe Herbert Bernstein if he is familiar with this zone of the source code. Meanwhile, please enlighten the rest of us about the format for COLO records! Send a description to the list, please. I have never used COLO records and neither has anyone else I know of because in most cases a simple script with select commands followed by color commands does the job more effectively. For an example, see http://www.umass.edu/microbio/rasmol/makescrp.htm#allmol -Eric At 7/7/99, you wrote: >Hi all, > >trying to visualize certain protein atom properties like accessible surface >/ solvation contact I came upon the "user color" menu option in RasMol. I >found how to build those COLO records and quickly implemented into my >project so that the result is a PDB file with a COLO record for each atom. >I have found that RasMol accepts no more than roughly 25 COLO records, >otherwise it won't display the PDB file giving this error message: "Too many >color records in file." > >Is there a way to make RasMol display much more COLO records? (like 200) > >Thank you for your help, > > >---------------------------------------------------------- >Ronald Frisch, student >Ab initio protein structure prediction group >Department of Computer Science V >University of Mannheim >Mannheim, Germany >email: ronald@frisch.com > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: "Brian W. Beck" Subject: Re: COLO records / User colours in Rasmol Date: Fri, 9 Jul 1999 10:16:25 -0500 (CDT) To: rasmol@dhcp-srv2.oit.umass.edu Eric Martz wrote: > > ... > Meanwhile, please enlighten the rest of us about the format for COLO > records! Send a description to the list, please. > ... > > >Ronald Frish wrote: > > ... > >I have found that RasMol accepts no more than roughly 25 COLO records, > >otherwise it won't display the PDB file giving this error message: "Too many > >color records in file." > > > >Is there a way to make RasMol display much more COLO records? (like 200) > > If you read the Rasmol source or look in the Raster3d distribution (mycolours.pdb), I believe the COLO record is something like the following: 1-6 COLOUR 7-30 ATOM and/or SEQ and/or CHAIN MASK (Mask format same as ATOM) 31-54 Red(F8.3),Blue(F8.3),Green(F8.3) (0-1 range) 55-60 ??Radius(F6.2)?? (I don't know that it's actually radius) eg. COLOUR#######C################ 1.000 1.000 1.000 1.70 is equal to all carbons white with a radius of 1.70A COLOUR#######CA##GLY########## 0.200 1.000 0.200 2.00 is equal to all GLY alpha carbons greenish with a radius of 2.00A It seems also that the first mask to equate takes precedence over subsequent masks. Regarding the limit of 25 masks, alter MAXMASK in molecule.h. -Brian -- ============================================================== | Brian W. Beck |E-mail Address: beck@uh.edu | | Inst. Molec. Design| | | Univ. of Houston |URL: | | 220 Fleming |http://www.chem.uh.edu/pettitt/beck | | Houston, TX, USA |VOICE (713) 743-3264 | | 77204-5641 |FAX (713) 743-2709 | ============================================================== boundary="----=_NextPart_000_000B_01BECA44.CAB06FA0" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 ++++------+------+------+------+------+------+------+------+------+------+ From: "Sorin Pancotan" Subject: Totally different use of RasMol/Chime Date: Fri, 9 Jul 1999 19:54:01 +0300 To: This is a multi-part message in MIME format. ------=_NextPart_000_000B_01BECA44.CAB06FA0 charset="iso-8859-1" Hi ! I'm a medical student who is interested both in micro and macro cosmos . So I've combined the great chemistry program -Chime- with my studies on the surrounding stars and star systems .The result is a pretty nice (and exact) model of our Solar Neighbors up to 15 light years (about 40 stars). I was very surprised in a pleasant way ,about the simplicity and the flexibility of Chime, and it's implementation in Netscape .I find very few limitations and must congratulate the peoples who created it ,and helped so much the scientific community . I've attached a zip file with a pdb ,a script file and a simple html to visualize the model .The html works in 1024*768 ,and all the files was created under Windows 98 .I hope it will work even on Macs and Unix machines . If u are problems running it try to run directly the closest.spt file . 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It required the following: Hi - thanks for that - I did most of that in RH 6.0 - it seems to work fine, except that the only way to open a file is through the command line (when you go to file - open, there's no display of a file system, it just creates a rasmol prompt in an xterm window....is this normal?) Also, the screen changes color when the mouse focus goes off & on rasmol - is this a color rez mismatch? It's no big deal, but it'd be nice to know I'm getting full color on rasmol (in my case 16 bit). Thus: What's the command in x to see what your color resolution is? I'm pretty sure I have it set up for 16 bit color - you'd think I'd be able to tell, but some of the other graphics programs (gimp, etc.) seem to only have a 256 color palate, even though images seem to appear 16 bit. Thank you kindly........ ---- - - - - - - - - - - - - - - - - - - - - _ _ _ _ _ _ _ _ _ _ _ _ _ "I believe in the doctrine of non-violence as a weapon of the weak. I believe in the doctrine of non-violence as a weapon of the strongest. I believe that a man is the strongest soldier for daring to die unarmed" Mohandes Gandhi ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Please don't send attachments to this list! Date: Fri, 09 Jul 1999 23:48:00 -0400 To: rasmol@dhcp-srv2.oit.umass.edu I would like to remind our subscribers not to attach files to emails sent to this list. Not only does this waste Internet bandwidth for the majority who typically are not interested in the attachment, but many of our 450 subscribers connect via modem and must pay phone charges (and wait a long time) for _unwanted_ attached files to arrive. Furthermore, if you have a virus on your computer, you may be infecting everyone on the list! Please make any files you offer to the list downloadable from a server, or offer to attach them in direct emails to individuals who request them. Thanks, -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE OR UNSUBSCRIBE, GO TO THE ABOVE ADDRESS. ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Maffett Subject: Re: Please don't send attachments to this list! Date: Fri, 09 Jul 1999 22:45:38 -0700 To: rasmol@dhcp-srv2.oit.umass.edu In Sorin's defense a ZIP file attachment which contains *no executables*, only Chime/HTML pages and pdb files, CANNOT carry a virus to your machine. (Except of course if you are using Microsoft's Internet Explorer ;) - there seems to be no end to ways that microsoft introduces to bring virus's to one's machine ;) Eric's point regarding size about sending attachments in general to the mailing list is well taken though. -tim At 11:48 PM 7/9/99 -0400, you wrote: >I would like to remind our subscribers not to attach files to emails sent >to this list. Not only does this waste Internet bandwidth for the majority >who typically are not interested in the attachment, but many of our 450 >subscribers connect via modem and must pay phone charges (and wait a long >time) for _unwanted_ attached files to arrive. Furthermore, if you have a >virus on your computer, you may be infecting everyone on the list! > >Please make any files you offer to the list downloadable from a server, or >offer to attach them in direct emails to individuals who request them. > >Thanks, -Eric >- - - >Eric Martz, Professor (Immunology), Dept Microbiology >U Mass, Amherst MA US 01003-5720 > >RasMol Email List >TO SUBSCRIBE OR UNSUBSCRIBE, GO TO THE ABOVE ADDRESS. > charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 ++++------+------+------+------+------+------+------+------+------+------+ From: "Sorin Pancotan" Subject: Apologises and some questions about scripting Date: Sat, 10 Jul 1999 14:13:13 +0300 To: First I have to apologize to the persons who had trouble because of downloading my attachment ,but believe me I wouldn’t post that file if I wouldn’t sow in my inbox a another attachment (posted by Dr. Frank Eblinger on 30.06.1999) followed by no reactions about attached files although it was bigger than mine . Second ,I have a few words to those who reacted to my mail : -To Mr. Bob Bateman: I’ve downloaded already the new Kinemage so I will take a try on it soon . -To Mr. Ajit Jadhav: I’ll be grateful if u can help me find that OpenGL site .I’ve already tried a few 3D modeler progs with no significant results ,but a good OpenGL engine will provide a lot of power to my application .Thanks in advance . -to Mr. Thomas A. Manderfield: it’s wery kind of you offering me some space on a server .I wish to talk about this possibility in private so, here is my e-mail address: pancotan@oradea.iiruc.ro Thanks in advance . and now the Questions : -how can I set the center of the axes to the center of an individual atom not the center of the molecule ? (that's the reason why the Sun isn't in the center the axes -thanks to Mr. Mitch Miller ). -how can I reuse and refer the atom (and label) colors loaded from a script file , without reloading it . Sorin ++++------+------+------+------+------+------+------+------+------+------+ From: Margaret Wong Subject: Re: Please don't send attachments to this list! Date: Sun, 11 Jul 1999 11:09:53 -0700 To: rasmol@dhcp-srv2.oit.umass.edu Hello All In spite of attachments being frowned upon I probably would not have bothered to download something like this which turned out to be an interesting extension to the use of rasmol which I will show some of the astronomers in the physics department next week. I am sure they will be most impressed :) > In Sorin's defense a ZIP file attachment which contains *no > executables*, only > Chime/HTML pages and pdb files, CANNOT carry a virus to your machine. > Eric's point regarding size about sending attachments in general to the > mailing list > is well taken though. cheers Margaret _ Dr Margaret Wong V marg@freon.chem.swin.edu.au _-_|\ \_ (_)o Chemistry Dept ) ( mgw@stan.xx.swin.oz.au / \ <4.1.19990709223814.01bfb2b0@mind.net> ++++------+------+------+------+------+------+------+------+------+------+ From: Eugene Leitl Subject: Re: Please don't send attachments to this list! Date: Sat, 10 Jul 1999 19:37:54 -0700 (PDT) To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu Tim Maffett writes: > Eric's point regarding size about sending attachments in general to the > mailing list > is well taken though. -rw-r--r-- 1 eugene.l users 18671 Jul 9 16:24 closest.zip is easy enough even on people with modems. It was definitely a very interesting attachement! ;) Regards, Eugene Leitl References: <199907091516.KAA23227@Ba.Chem.UH.EDU> charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 ++++------+------+------+------+------+------+------+------+------+------+ From: "Ronald Frisch" Subject: Re: COLO records / User colours in Rasmol Date: Tue, 13 Jul 1999 11:51:58 +0200 To: "RasMol List" Hi all, thank you for the information, Brian, changing the MAXMASK constant in molecule.h definitely solved my problem. Usually it is 40, I think, I tried 400 and it works just fine. That way, 400 user colour masks can be applied to a molecule which is enough for me. The way I use the COLO records is like this, I create a mask for each atom I want to colour and also provide a default mask/colour for all atoms that are not described by a preceding mask. I have not figured out the use of the last value, you should be able to actually set something like a radius, since I don't need it, I just leave it away. .... ATOM 194 N THR 28 3.827 14.802 6.358 1.00 4.53 ATOM 195 CA THR 28 2.691 15.221 7.194 1.00 5.08 ATOM 196 C THR 28 1.672 14.132 7.434 1.00 4.62 ATOM 197 O THR 28 .947 14.112 8.468 1.00 7.80 ATOM 198 CB THR 28 1.986 16.520 6.614 1.00 6.03 COLO 194 N ### ##### 0.707 0.707 1.000 COLO 195 CA ### ##### 0.610 0.610 1.000 COLO 196 C ### ##### 0.617 0.617 1.000 COLO 197 O ### ##### 0.425 0.425 1.000 COLO 198 CB ### ##### 0.437 0.437 1.000 COLO ######################## 0.100 0.100 0.100 .... (For the mask, the atom number only would suffice of course, the atom type is not needed. the colours are values from white to blue, default is almost black...) Kind regards, Ronald Frisch Student University of Mannheim, Germany Department of Computer Science V Ab Initio Protein Structure Prediction Group ----- Original Message ----- Sent: Friday, July 09, 1999 5:16 PM From: Brian W. Beck Subject: Re: COLO records / User colours in Rasmol To: > Eric Martz wrote: > > > > ... > > Meanwhile, please enlighten the rest of us about the format for COLO > > records! Send a description to the list, please. > > ... > > > > >Ronald Frish wrote: > > > ... > > >I have found that RasMol accepts no more than roughly 25 COLO records, > > >otherwise it won't display the PDB file giving this error message: "Too many > > >color records in file." > > > > > >Is there a way to make RasMol display much more COLO records? (like 200) > > > > > > If you read the Rasmol source or look in the Raster3d > distribution (mycolours.pdb), I believe the COLO record is > something like the following: > > 1-6 COLOUR > 7-30 ATOM and/or SEQ and/or CHAIN MASK (Mask format same as ATOM) > 31-54 Red(F8.3),Blue(F8.3),Green(F8.3) (0-1 range) > 55-60 ??Radius(F6.2)?? (I don't know that it's actually radius) > > eg. > COLOUR#######C################ 1.000 1.000 1.000 1.70 > is equal to all carbons white with a radius of 1.70A > > COLOUR#######CA##GLY########## 0.200 1.000 0.200 2.00 > is equal to all GLY alpha carbons greenish with a radius of 2.00A > > It seems also that the first mask to equate takes precedence > over subsequent masks. > > Regarding the limit of 25 masks, alter MAXMASK in molecule.h. > > > -Brian > -- > ============================================================== > | Brian W. Beck |E-mail Address: beck@uh.edu | > | Inst. Molec. Design| | > | Univ. of Houston |URL: | > | 220 Fleming |http://www.chem.uh.edu/pettitt/beck | > | Houston, TX, USA |VOICE (713) 743-3264 | > | 77204-5641 |FAX (713) 743-2709 | > ============================================================== > ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: COLO records / User colours in Rasmol Date: Tue, 13 Jul 1999 09:50:49 -0600 (MDT) To: rasmol@dhcp-srv2.oit.umass.edu > The way I use the COLO records is like this, I create a mask for each > atom I want to colour and also provide a default mask/colour for all > atoms that are not described by a preceding mask. I have not figured out > the use of the last value, you should be able to actually set > something like a radius, since I don't need it, I just leave it away. The final column in a COLOR record is indeed the radius. The appropriate RasMol command to use these radii is "spacefill user" or "cpk user". This behaves almost the same as "spacefill temperature" (or "cpk temperature") but in the later the radius is defined by the bfactor field in the PDB file. Roger -- X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: "Ari M. Siqueira" Subject: RasMol vs. MSI's WebLabViewer Date: Wed, 14 Jul 1999 13:46:47 -0300 To: rasmol@dhcp-srv2.oit.umass.edu Hi folks, Why is it that RasMol and MSI's WebLabViewer see the same pdb file differently? With WebLabViewer I see 2 beta-sheets while RasMol displays 3 well-defined beta-sheets plus 3 residues which are indicated to be also beta-sheets. If anybody would care to take a closer look I can send the original PDB file and 2 gifs prepared from WebLabViewer and RasMol displays of the same data. Thankfully, --- Ari M. Siqueira, PhD Associate Professor of Biochemistry, ICB-UFMG mailto:siqueira@icb.ufmg.br tel 55-31-499-2644, 9952-7470, fax 441-5963 References: <378CBEF7.7DC11F18@icb.ufmg.br> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: RasMol vs. MSI's WebLabViewer Date: Wed, 14 Jul 1999 18:04:09 +0100 To: Rasmol Mailinglist "Ari M. Siqueira" wrote: > > Hi folks, > > Why is it that RasMol and MSI's WebLabViewer see the same pdb file > differently? > With WebLabViewer I see 2 beta-sheets while RasMol displays 3 > well-defined beta-sheets plus 3 residues which are indicated to be also > beta-sheets. If anybody would care to take a closer look I can send the > original PDB file and 2 gifs prepared from WebLabViewer and RasMol > displays of the same data. must be a different algorithm for determining secundary structure in weblab then in rasmol (which uses DSSP). Normally a pdb-file contains already the secondary structure information like SHEET HELIX TURN and maybe it was generated bt a different algorithmn then DSSP. In RasMol try the command: select protein structure cartoons Does the secundary structure change? greetings, Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)171 2693405 | fax :+44-(0)171-269-3534 email : a.mueller@icrf.icnet.uk | http://www.icnet.uk/bmm/ ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Roseman Subject: Rasmol suggestion Date: Wed, 14 Jul 1999 14:17:52 -0400 (EDT) To: rasmol@dhcp-srv2.oit.umass.edu I suppose this might be directed to Herbert Bernstein and Roger Sayle, but I would certainly like to have an undo command available in RasMol, for I often find myself sending a command that I wish I hadn't, thus forcing me to redo an entire sequence of commands over. Does anyone desire this option? .. or perhaps it already exists and I just haven't found it yet.... -dan References: X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: Rasmol suggestion Date: Wed, 14 Jul 1999 20:13:15 +0100 To: rasmol@dhcp-srv2.oit.umass.edu Dan Roseman wrote: > > I suppose this might be directed to Herbert Bernstein and Roger Sayle, but > I would certainly like to have an undo command available in RasMol, for I > often find myself sending a command that I wish I hadn't, thus forcing me > to redo an entire sequence of commands over. Does anyone desire this > option? .. or perhaps it already exists and I just haven't found it > yet.... > > -dan Yes, in fact that's a nice feature but I think it is rather difficult to implement an undo in the current rasmol version. As a workaround I suggest to save the current rasmol session in a script (write script filename) so you can reload the script. For proper undo functionlity one would have to store all information about the loaded molecule and things you've manipulated like colour representation etc. in a datastructure. Each time something has changed a backup is created by copying that datastructure, and than when the undo function is called that backup replaces the current datastructure. Hm, I'm afraid rasmol's internal structure is not designed for such a concept, it's rather difficult without major changes in rasmol's internals. I'm looking forward to read from Herbert and Roger and off course others what they think about 'undo', maybe my point of view is too complicated and a simple solution is just around the corner ... greetings, Arne ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Fwd: Re: RasMol vs. WebLabViewer Date: Wed, 14 Jul 1999 22:22:08 -0400 To: rasmol@dhcp-srv2.oit.umass.edu >Date: Wed, 14 Jul 1999 19:46:48 GMT >To: siqueira@cenapad.ufmg.br >CC: pdb-l@rcsb.org, support@msi.com >Subject: Re: RasMol vs. WebLabViewer >From: Ethan Benatan >Sender: owner-pdb-l@rcsb.org > >>>> "Ari" == Ari M Siqueira writes: > > Ari> Why is it that RasMol and MSI's WebLabViewer see the same pdb > Ari> file differently? With WebLabViewer I see 2 beta-sheets while > Ari> RasMol displays 3 well-defined beta-sheets plus 3 residues which > Ari> are indicated to be also beta-sheets. > >I don't have WebLabViewer but I'll take a wild guess: it is easy to >forget that secondary structure is not "real" in the sense that the >protein doesn't have a helix that starts here and ends there. The >protein has a structure; we *label* parts of it with *names* for our >convenience. Helices, leucine zippers, type II turns, etc. are our >labels for bits of structure that have certain loosely defined >characteristics (no slur intended here!). > >How a program (or a human) decides to go about labeling a structure >involves making choices, and there is no universally accepted (much >less "correct") way of deciding if a part of a structure deserves a >label such as "helix" or "strand". I suspect that your two programs >simply took different approaches to deciding. RasMol, last I looked, >uses author assignments if available, else assignments by DSSP's >algorithm (the latter can also be forced). > >An important corollary is that when assigning these labels we should >always be careful to state how we reached the decision--by eye, or >algorithmically, and if so which algorithm. I consider this to be a >real failing in the current PDB format, particularly for those of us >who wish to automatically process large numbers of structures. I've >been meaning to learn more about mmCIF's metadata support for some time, >but haven't yet; if anyone has thoughts or pointers to share I'd be >grateful. > >Yours truly, > >Ethan >_____________ >Ethan Benatan ethan+@pitt.edu http://www.pitt.edu/~ethan > > > *** Details on how to be removed from this list as well as an *** > *** archive of recent postings are available at *** > *** http://www.rcsb.org/pdb/forum.html *** > X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Boshoff Subject: AIX 4.3.2 Binaries Date: Thu, 15 Jul 1999 08:37:15 -0400 To: rasmol@dhcp-srv2.oit.umass.edu I'm having trouble compiling Rasmol under AIX 4.3.2. Does anyone else perhaps run Rasmol on IBM RISC/6000 with AIX 4.3.2? I was hoping someone could provide me with the precompiled binaries. Thanks! Jan mmciflist@ndbdev.rutgers.edu ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: RasMol 2.7.1 Release Date: Thu, 15 Jul 1999 08:21:02 -0400 To: pdb-l@rcsb.org, rasmol@dhcp-srv2.oit.umass.edu, The current rasmol release has been updated. When you access: http://www.bernstein-plus-sons.com/software/rasmol you should get the new RasMol 2.7.1 release. You may need to flush the cache on your browser to access the new version. It may take a little while for the mirror sites to catch up with this change. The important changes in release 2.7.1 are: * The ability to automatically mark non bonded atoms in wireframe and stick displays. Our thanks to R. Curtis Haltiwanger for suggesting this change. * The ability to use a proportionally spaced font and to draw labels with heavier strokes. Our thanks to Eric Martz for suggesting this change. * The ability to auto-recognize PDB vs. CIF and mmCIF datasets. * Extensive updating to the manual. Our thanks to William McClure, Margaret Wong, Eric Martz and Frances Bernstein. * Updating the canvas title with the PDB ID code and EXPDTA information, so models will be clearly distinguished from experimental data. Our thanks to Helen Berman for suggesting this change. * The ability to report coordinates. * Additions to the list of pre-defined colours. * Improved accuracy of coordinates in pseudo-PDB output. * Fixes to the centering logic. To mark non-bonded atoms: set bondmode not bonded before doing a wireframe To make fancy labels set fontsize 24 PS set fontstroke 2 To load a cif -- just do it -- it should be accept just as if it was a PDB file. The manual has been extensively updated. I hope to have a frames version for the release in September, buts its content will be exactly the same as the monolithic html version in this release. We still have to work in Arne's color mods, fix stereo, and the many, many very useful source code contributions that are in the queue, but we hope you will find release 2.7.1 an useful addition to the series of RasMol releases. If you require access to the previous version, it is still available at: http://www.bernstein-plus-sons.com/software/RasMol_2.7.0.1 ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-516-286-1339 FAX: 1-516-286-1999 ===================================================== References: ++++------+------+------+------+------+------+------+------+------+------+ From: Kjeld Olesen Subject: Re: RasMol 2.7.1 Release Date: Thu, 15 Jul 1999 15:41:56 +0200 To: rasmol@dhcp-srv2.oit.umass.edu Dear Dr. Bernstein: Thank you for the info on the updated version of Rasmol. One thing that I have been wanting to suggest, but never got around to, is: When writing to a povray output file (or a PDB file for that matter), the output is oriented according to the orientation of the original PDB file, not according to the orientation of the current rotation of the loaded molecule. Would it be easy to correct this behaviour? Best regards, Kjeld Olesen Herbert J. Bernstein wrote: > The current rasmol release has been updated. > When you access: > http://www.bernstein-plus-sons.com/software/rasmol > > you should get the new RasMol 2.7.1 release.-- *************************************************************** Kjeld Olesen, Ph.D. Phone: (+45) 3327 5309 Carlsberg Research Laboratory Fax: (+45) 3327 4764 Department of Yeast Breeding E-mail: kol@crc.dk Gamle Carlsberg Vej 10 DK-2500 Copenhagen Valby D E N M A R K *************************************************************** References: <378DE524.E1465CA7@crc.dk> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: RasMol 2.7.1 Release Date: Thu, 15 Jul 1999 15:24:17 +0100 To: rasmol@dhcp-srv2.oit.umass.edu Kjeld Olesen wrote: > > Dear Dr. Bernstein: > > Thank you for the info on the updated version of Rasmol. > > One thing that I have been wanting to suggest, but never got around to, is: > > When writing to a povray output file (or a PDB file for that matter), the output is oriented > according to the orientation of the original PDB file, not according to the orientation of the > current rotation of the loaded molecule. Would it be easy to correct this behaviour? Hi Kjeld, under unix it is save to use the 'write povray3 filename' command to save the molecule in the current rotation, translation and magnification. Under windows this command produces still the wrong transformation (yes I know ... ;-( ) greetings, Arne mmciflist@ndbdev.Rutgers.EDU ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: RasMol 2.7.1 Manual Date: Thu, 15 Jul 1999 12:27:07 -0400 To: pdb-l@rcsb.org, rasmol@dhcp-srv2.oit.umass.edu, My apologies for a temporarily dead link to the new rasmol manual in the 2.7.1 release. Thanks to a prompt report from Kurt Giles, that problem has been fixed. If you tried to access http://www.bernstein-plus-sons.com/software/rasmol/doc/rasmol.html and got a "Not Found" message, please try again. -- Herbert J. Bernstein ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-516-286-1339 FAX: 1-516-286-1999 ===================================================== ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Using Chime 2 on linux, SGI, etc! Date: Thu, 15 Jul 1999 23:10:13 -0400 To: rasmol@dhcp-srv2.oit.umass.edu, pdb-l@rcsb.org Yesterday at the San Diego Supercomputer Center I observed Chime 2 functioning well in Netscape Communicator 4.5 on an ***SGI workstation***. Netscape and Chime were actually running on a remote Windows NT server, with the display, mouse and keyboard control coming from the SGI. Performance including rotation of complex molecular structures in Chime was quite satisfactory. This was made possible by MetaFrame software from Citrix (www.citrix.com). The NT server requires three software licenses (costs are approximate educational discount costs): Terminal Server for NT Server (about $300), Citrix MetaFrame Server (about $4,000 for 15 concurrent sessions) and Windows NT Terminal Server Client Access, roughly $1,000 for access by about 150 workstations. The Citrix client software is free and can be downloaded from their site. This system supports not only SGI but most unix platforms, including Solaris and linux. Installation on the server, I am told by the person who did it at SDSC, is "not trivial" but straightforward -- she found the Citrix support forum useful. Not all applications work in this mode via NT Terminal Server, but Netscape and Chime appear to work perfectly. Thus, people who normally work on unix systems, and who are fortunate enough to be at institutions with sufficient resources, could take advantage of Chime 2-dependent visual exploration software such as STING (http://trantor.bioc.columbia.edu/STING), the Noncovalent Bond Finder and the Protein Explorer (www.umass.edu/microbio/chime) without leaving their preferred unix workstations, via the Citrix software. -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - UMass Chime Resources: www.umass.edu/microbio/chime Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: <004701becac5$40d7b8c0$9691e2c1@za-komputtah> X-Accept-Language: en,tr ++++------+------+------+------+------+------+------+------+------+------+ From: Sinasi Ellialtioglu Subject: Fixing the axes to real coordinates Date: Fri, 16 Jul 1999 16:06:06 +0300 To: rasmol@dhcp-srv2.oit.umass.edu I also would like to have a control of fixing the axes either at a given atom (at 000 for instance), or fix the positin of the corner of the bounding box so that when I use RasWin-ucb to load more than one pdb file, they will have the same origin. TIA Sinasi Sorin Pancotan wrote: .... [cut] > pancotan@oradea.iiruc.ro > Thanks in advance . > > and now the Questions : > > -how can I set the center of the axes to the center of an individual atom > not the center of the molecule ? (that's the reason why the Sun isn't in the center > the axes -thanks to Mr. Mitch Miller ). > -how can I reuse and refer the atom (and label) colors loaded from a script > file , without reloading it . > > Sorin ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Roseman Subject: picture to chime Date: Fri, 16 Jul 1999 12:21:05 -0400 (EDT) To: rasmol@dhcp-srv2.oit.umass.edu Perhaps someone has a solution-- I have recently set a web page using two frames, the right side being the chime window and the left side containing text and pictures. All the buttons work great, sending over scripts etc over to the chime window.. Is it possible to have one of the pictures in the left frame clickable so that it appears in the right side? I've had some success using javascript and adding a third, blank frame, while sending a script to the chime window, but I'm thinking there must be an easier way to accomplish this..either with HTML or javascripting. thanks, dan mmciflist@ndbdev.rutgers.edu ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: AIX 4.3.2 RasMol 2.7.1 binaries Date: Fri, 16 Jul 1999 15:09:53 -0400 To: pdb-l@rcsb.org, rasmol@dhcp-srv2.oit.umass.edu, Jan Boshoff has contributed an 8-bit RasMol 2.7.1 binary for IBM RS/6000's running AIX 4.3.2. The binary is at: ftp://ftp.bernstein-plus-sons.com/software/RasMol_2.7.1.RS6K/rasmol.gz or at http://www.bernstein-plus-sons.com/software/RasMol_2.7.1.RS6K/rasmol.gz Links from other pages will be added in the future, but we did not want to delay access to this binary. ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-516-286-1339 FAX: 1-516-286-1999 ===================================================== mmciflist@ndbdev.rutgers.edu ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Fix for -nodisplay bug Date: Fri, 16 Jul 1999 22:46:37 -0400 To: pdb-l@rcsb.org, rasmol@dhcp-srv2.oit.umass.edu, Xiang-Jun Lu has reported a bug in RasMol 2.7.1 when the -nodisplay command line option is used on X-windows versions of RasMol. The same bug can arise if RasMol 2.7.1 is used on an X-windows system set to a pixel bit depth which differs from the RasMol compilation settings. The bug relates to the new code which automatically sets the display title. The code in x11win.c does not test for Interactive mode before trying to set the title. Here is a quick patch: *** x11win.c 1999/07/16 22:33:08 1.3 --- x11win.c 1999/07/16 22:34:31 *************** *** 1924,1930 **** void SetCanvasTitle( char *ptr ) { ! XStoreName(dpy,MainWin,ptr); } --- 1924,1930 ---- void SetCanvasTitle( char *ptr ) { ! if ( Interactive) XStoreName(dpy,MainWin,ptr); } --------------------------------------------------------- A more complete patch will be included in the September release, but this patch, hopefully, will allow those who need a version of RasMol 2.7.1 which will work without a display on a X-windows system to make use of RasMol 2.7.1. Some people work in this mode when generating export images to save time and memory. Since this bug does not affect operation for most people, and since the RasMol 2.7.0.1 binaries will do almost the same things as RasMol 2.7.1 for most users who are working without a display, we will not update the 2.7.1 binaries at this time, but wait until more bug fixes have accumulated. ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-516-286-1339 FAX: 1-516-286-1999 ===================================================== X-Authenticated: wm0p by cyrus.andrew.cmu.edu X-Licensed-To: Site License ++++------+------+------+------+------+------+------+------+------+------+ From: "Will McClure" Subject: Re: chime 2 menu explanation Date: Sat, 17 Jul 1999 11:26:38 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Cc: rule --On Fri, Jun 4, 1999 1:43 PM -0400 "Judy Voet" wrote: > Does anyone know where to find a good explanation of the functions in the > chime 2 menu that students can be referred to? All the references I've > been able to find to the chime menu are for early versions of chime. My colleague, Gordon Rule , has written a Chime 2 tutorial that we plan to use in the Fall '99 semester of our Intro Biochem course. In addition to the basics, it illustrates the rationale of the cascading menu selections under the Chime 2 'Select' heading. It is not an exhaustive description of everything possible under 'Select'; instead we hope that with the examples provided, the student will be able to extend their experience from the tutorial to the additional manipulations assigned in problem sets. http://stingray.bio.cmu.edu/~rule/chime_tut/chime.html -Will McClure ++++------+------+------+------+------+------+------+------+------+------+ From: Wayne M Barnes Subject: chime plugin source? Date: Mon, 19 Jul 1999 10:48:37 -0500 (CDT) To: rasmol@dhcp-srv2.oit.umass.edu Dear Chimers, Well, I finally decided to try this, and the link to the Netscape plugin (the link on the web page below, which is the same as the one the Netscape offers) just says "MSQL server has gone away". Is there another source for the chime plugin? Wayne M. Barnes, Ph.D. wayne@barnes1.wustl.edu Biochemistry Dept. 8231 Washington Univ. Medical School 314.362.3351 fax 7183 660 South Euclid Ave., St. Louis, MO 63110 http://barnes1.wustl.edu Just plain Taq is old tech anymore. > --On Fri, Jun 4, 1999 1:43 PM -0400 "Judy Voet" > wrote: > > > Does anyone know where to find a good explanation of the functions in the > > chime 2 menu that students can be referred to? All the references I've > > been able to find to the chime menu are for early versions of chime. > > My colleague, Gordon Rule , has written a Chime 2 > tutorial that we plan to use in the Fall '99 semester of our Intro Biochem > course. In addition to the basics, it illustrates the rationale of the > cascading menu selections under the Chime 2 'Select' heading. It is not an > exhaustive description of everything possible under 'Select'; instead we > hope that with the examples provided, the student will be able to extend > their experience from the tutorial to the additional manipulations assigned > in problem sets. > > http://stingray.bio.cmu.edu/~rule/chime_tut/chime.html > > -Will McClure > info@rcsb.org ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: PDB Lite lives ... Date: Tue, 20 Jul 1999 21:50:19 -0400 To: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu Cc: helgew@SDSC.EDU, badger@SDSC.EDU, bourne@SDSC.EDU, kenneth@SDSC.EDU, The main point of this message is that PDB Lite remains available from the following BNL PDB mirror sites. As of July 15, the 7 sites listed below not only offered a functional PDB Lite but had kept their database up with the latest releases at the PDB. Australia, Sydney http://molmod.angis.org.au/pdb/ Australia, Melbourne http://pdb.wehi.edu.au/pdb/ India http://202.41.70.33/ Israel http://pdb.weizmann.ac.il/ Poland http://pdb.icm.edu.pl/ UK, Cambridge http://pdb.ccdc.cam.ac.uk/ UK, EBI Hinxton http://www2.ebi.ac.uk/pdb Other sites may be OK too but when checked on July 15 had not installed the July 13 update. Some sites not listed may have up to date data but no longer have PDB Lite working. None of the three US mirror sites have chosen to continue to offer PDB Lite with an up to date database. As many of you noticed, the Brookhaven National Lab Protein Data Bank (BNL PDB) website closed June 30. The old URL, www.pdb.bnl.gov, now takes you to the new PDB. Operated by the Research Collaboratory for Structural Bioinformatics (RCSB, www.rcsb.org), the new PDB began offering search access to the PDB dataset earlier in the year. Their SearchLite interface is all new, but does not yet offer all of the features available in PDB Lite aimed at nonspecialists and occasional users. It does offer the simple Chime viewer which was available for the past year at BNL. The new PDB has made and is continuing to make significant improvements in the database, and their SearchFields interface can already do some things which were not possible with the BNL interface (such as finding entries which contain only RNA atoms). Whether you wish to continue using PDB Lite for some searches or begin doing all of your searches in SearchLite/SearchFields is a matter of personal preference. The new PDB is working very actively to set up mirrors around the world. The arrangements and new technology being established will guarantee that the new mirrors are always fully functional and up to date. A related issue is support for the URL which hands PDB files to my Noncovalent Bond Finder and Protein Explorer. This is needed when you type a PDB ID code into the slot and press Load, expecting the PDB file to come through the Internet. For technical reasons which will eventually be resolved, there is no URL at the new PDB which is compatible. Only four of the above 7 old BNL PDB mirror sites continue to provide this compatible URL (India, Israel, Poland, and UK Cambridge). I have updated the page for selecting the site used by the above Chime resources (shared/mirror.htm) to list these 4 sites. The updated file is on the website only -- if you have downloaded and installed local copies, you may wish to go to www.umass.edu/microbio/chime/shared/mirror.htm, then do a File, Save As and replace the old shared/mirror.htm file in your shared folder. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ boundary="----=_NextPart_000_004B_01BED42B.FE541C80" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 ++++------+------+------+------+------+------+------+------+------+------+ From: "Scott Lammas" Subject: Compiling rasmol Date: Thu, 22 Jul 1999 10:21:42 +0100 To: This is a multi-part message in MIME format. ------=_NextPart_000_004B_01BED42B.FE541C80 charset="iso-8859-1" I'm trying to compile rasmol to run under windows NT/95 using Microsoft = Visual C++ version 4.2. The source files seem to compile without any = errors or warnings, however when the linker kicks in all sorts of = problems occur e.g : SCRIPT.OBJ : error LNK2001: unresolved external symbol = _InvalidateCmndLine MOLECULE.OBJ : error LNK2001: unresolved external symbol = _InvalidateCmndLine RENDER.OBJ : error LNK2001: unresolved external symbol = _InvalidateCmndLine OUTFILE.OBJ : error LNK2001: unresolved external symbol _LabelList SCRIPT.OBJ : error LNK2001: unresolved external symbol _LabelList RENDER.OBJ : error LNK2001: unresolved external symbol _LabelList COMMAND.OBJ : error LNK2001: unresolved external symbol _LabelList COMMAND.OBJ : error LNK2001: unresolved external symbol _MonitList OUTFILE.OBJ : error LNK2001: unresolved external symbol _MonitList SCRIPT.OBJ : error LNK2001: unresolved external symbol _MonitList I'm fairly sure this has something to do with options that can be set in = rasmol.h. Can anybody advise me as to what options need to be set in = this file to compile for win32. ------=_NextPart_000_004B_01BED42B.FE541C80 charset="iso-8859-1"
I'm trying to compile rasmol to run = under windows=20 NT/95 using Microsoft Visual C++ version 4.2.  The source files = seem to=20 compile without any errors or warnings, however when the linker kicks in = all=20 sorts of problems  occur e.g :
 
SCRIPT.OBJ : error LNK2001: unresolved external = symbol=20 _InvalidateCmndLine
MOLECULE.OBJ : error LNK2001: unresolved external = symbol=20 _InvalidateCmndLine
RENDER.OBJ : error LNK2001: unresolved external = symbol=20 _InvalidateCmndLine
OUTFILE.OBJ : error LNK2001: unresolved external = symbol=20 _LabelList
SCRIPT.OBJ : error LNK2001: unresolved external symbol=20 _LabelList
RENDER.OBJ : error LNK2001: unresolved external symbol=20 _LabelList
COMMAND.OBJ : error LNK2001: unresolved external symbol=20 _LabelList
COMMAND.OBJ : error LNK2001: unresolved external symbol=20 _MonitList
OUTFILE.OBJ : error LNK2001: unresolved external symbol=20 _MonitList
SCRIPT.OBJ : error LNK2001: unresolved external symbol=20 _MonitList
 
I'm fairly sure this has something to do with = options that=20 can be set in rasmol.h.  Can anybody advise me as to what options = need to=20 be set in this file to compile for win32.
------=_NextPart_000_004B_01BED42B.FE541C80-- References: X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Joseph Fioretti Subject: pdb compression?? Date: Thu, 22 Jul 1999 14:29:36 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Greetings, fellow RasMol users! I am writing in hopes that one of you can help me out with the issue of compressing a pdb file so that it is the smallest possible size but so that it maintains accessibility on both the Windows and Macintosh Platforms... I have access to a Windows 98 machine, but my primary machine for creating RasMol/Chime visualizations is a Macintosh. What is the best type of compression to use (if any!) on pdb files that will 1) keep the pdb file able to be seen in browsers on Windows AND Mac platforms, 2) make the file as small as possible to reduce download times on slow connections, and 3) maintain full functionality of the pdb file on the web (meaning that it will automatically load the Chime plugin and then open the rotating molecule in the browser as normal)?? I appreciate any and all feedback that anyone can provide. Thank you for your time, Joseph Fioretti fioretti@panther.middlebury.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: pdb compression?? Date: Thu, 22 Jul 1999 15:44:42 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Cc: fioretti@panther.middlebury.edu At 7/22/99, Joseph Fioretti wrote: >I am writing in hopes that one of you can help me out with the issue of >compressing a pdb file so that it is the smallest possible size but so >that it maintains accessibility on both the Windows and Macintosh >Platforms... As long as you don't want to open the compressed pdb file in RasMol, you should gzip it. Chime automagically g-unzips pdb files which it receives gzipped; Chime does not recognize any other form of compression. Full details on how to do this are in the FAQ at http://www.umass.edu/microbio/rasmol/faq_em.htm Gzip achieves about 3.5-fold compression of the typical PDB file. This is much more compression than is achieved by unix compress, and about the same as that achieved by other algorithms such as winzip/pkzip. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - UMass Chime Resources: www.umass.edu/microbio/chime Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: <14201.36746.224860.54771@lrz.de> <377A11BE.C4FE0777@icrf.icnet.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: Re: RasMol derivates with embedded scripting language? Date: Fri, 23 Jul 1999 21:11:37 -0700 To: rasmol@dhcp-srv2.oit.umass.edu Hi - I recently compiled rasmol for linux (RH 6.0). Thanks to referencs from this list, it seems to work fine. One thing however - when the cursor slides off & on the rasmol window, the rest of the x-windows apps change color....is this because I've compiled rasmol with a different color resolution? So far I haven't gotten x to change color resolution (more hacking needed), and rasmol seems to work ok....It'd be good to know what's going on though....thank you kindly! ---- - - - - - - - - - - - - - - - - - - - - _ _ _ _ _ _ _ _ _ _ _ _ _ "I believe in the doctrine of non-violence as a weapon of the weak. I believe in the doctrine of non-violence as a weapon of the strongest. I believe that a man is the strongest soldier for daring to die unarmed" Mohandes Gandhi ++++------+------+------+------+------+------+------+------+------+------+ From: "walter g. rothschild" Subject: conect statement Date: Sat, 24 Jul 1999 22:55:51 -0400 To: rasmol@dhcp-srv2.oit.umass.edu --------------BBAB42768068A95E9085F640 I made up a .pdb file of the coordinates of an organic tree molecule (no loops) of 292 atoms (C, H, N) with about the proper bond lengths and correct atomic orbital directions. Each bond (all single) is identified by its CONECT statement and, as far as I can see, there are no unconnected atoms. (The structure is a portion of a four-stage Dendrimer molecule and, once equilibrated, will be helpful in making sense of low-frequency Raman data taken with the modern equipment offered by my long-time friends at the University of Bordeaux.) Nevertheless, RasMol gives me ten additional bonds of no chemical sense (as much as 10 angstrom distance and radiating out, as two bundles of six and four, from two C atoms) between pairs of carbon atoms on different branches of the tree, carbon atoms that are properly connected to all of their four neighbors and would now be pentavalent or more! (Whether I put into the command line "set connect false" or not makes no difference.) Working on a comment by by E. Martz, I succeeded in turning the ten bonds off by putting all the (eight) C atoms involved into a separate group (# 2) and then adding the two command lines "select 2", "wireframe off". This works visually but when building up beyond the wireframe representation (sticks and balls), the atoms in group 2 remain mere points and I have problems with different coloring; the bond count still lists the additional ten bonds as present. I addition, "Information" tells me that I have twelve (!) groups (292 atoms, and 301 bonds) although all atoms are either in group 1 (284) or group 2 (8). I searched the e-mail history but did not find (or overlooked) anything specifically helping me. Roger also gave me advice but my mail system malfunctioned and his second communication was gone with the wind before I read it. I hate to bother him again and perhaps someone else in the group ought to be able to help me. In other words: (1) How do I turn the bonds off without any further damage? (2) How do I tell Rasmol not to connect any atoms except those solely mentioned in CONECT statements? (3) Must I add the MASTER record? Please be specific; I have a talent of not seeing the obvious in help files and Instruction Manuals. Regards, Walter --------------BBAB42768068A95E9085F640 I made up a .pdb file of the coordinates of an organic tree molecule (no loops) of 292 atoms (C, H, N) with about the proper bond lengths and correct atomic orbital directions. Each bond (all single) is identified by its CONECT statement and, as far as I can see, there are no unconnected atoms. (The structure is a portion of a four-stage Dendrimer molecule and, once equilibrated, will be helpful in making sense of low-frequency Raman data taken with the modern equipment offered by my long-time friends at the University of Bordeaux.) Nevertheless, RasMol gives me ten additional bonds of no chemical sense (as much as 10 angstrom distance and radiating out, as two bundles of six and four, from two C atoms) between pairs of carbon atoms on different branches of the tree, carbon atoms that are properly connected to all of their four neighbors and would now be pentavalent or more! (Whether I put into the command line "set connect false" or not makes no difference.) Working on a comment by by E. Martz, I succeeded in turning the ten bonds off by putting all the (eight) C atoms involved into a separate group (# 2)  and then adding the two command lines "select 2", "wireframe off". This works visually but when building up beyond the wireframe representation (sticks and balls), the atoms in group 2 remain mere points and I have problems with different coloring; the bond count still lists the additional ten bonds as present. I addition, "Information"  tells me that I have twelve (!) groups (292 atoms, and 301 bonds) although all atoms are either in group 1 (284) or group 2 (8). I searched the e-mail history but did not find (or overlooked) anything specifically helping me. Roger also gave me advice but my mail system malfunctioned and his second communication was gone with the wind before I read it. I hate to bother him again and perhaps someone else in the group ought to be able to help me.
In other words: (1) How do I turn the bonds off without any further damage? (2) How do I tell Rasmol not to connect any atoms except those solely mentioned in CONECT statements? (3) Must I add the MASTER record? Please be specific; I have a talent of not seeing the obvious in help files and Instruction Manuals.
      Regards,  Walter
 
 
  --------------BBAB42768068A95E9085F640-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: PDB Lite lives ... Date: Sun, 25 Jul 1999 22:17:14 -0400 To: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu On July 20 I listed seven former BNL PDB mirror sites which still supported PDB Lite and which were keeping their database up with new releases. Immediately after posting that message, I realized that a bug in PDB Lite (a bug which was my fault) was preventing the file-save operation. When you click on "Express Save for Experts" or "Open the Save As Dialog", you get "The PDB has moved ..." rather than the file save dialog. Thanks to the quick cooperation of Jaim Prilusky in Israel who verified my fix, I then sent a fix for this bug to all of the former BNL mirror sites. I am happy to report that four of the seven 'working' PDB Lite sites installed the fix immediately. These four sites support PDB Lite, have fixed the file-download bug, and have their databases up to date with new releases: India http://202.41.70.33/ Israel http://pdb.weizmann.ac.il/ UK, Cambridge http://pdb.ccdc.cam.ac.uk/ UK, EBI Hinxton http://www2.ebi.ac.uk/pdb I hope that Australia (2 sites) and Poland will install the fix soon, but they have not done so yet. -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE OR UNSUBSCRIBE, GO TO THE ABOVE ADDRESS. X-Authenticated: wm0p by cyrus.andrew.cmu.edu X-Licensed-To: Site License ++++------+------+------+------+------+------+------+------+------+------+ From: "Will McClure" Subject: Re: conect statement Date: Tue, 27 Jul 1999 15:01:46 -0400 To: rasmol@dhcp-srv2.oit.umass.edu --On Sat, Jul 24, 1999 10:55 PM -0400 "walter g. rothschild" wrote: > In other words: (1) How do I turn the bonds off without any further damage? (2) How do I tell Rasmol not to connect any atoms except those solely mentioned in CONECT statements? (3) Must I add the MASTER record? Please be specific; I have a talent of not seeing the obvious in help files and Instruction Manuals. Walter, Pasted below is a PDB file with CONECT lines that are necessary to prevent spurious bonds between oxygens. What I've noticed for small molecules is that it helps to fill in all columns with zeros if they do not specify a bonded neighbor, e.g. oxygens at ATOMNO=15-21. You could look at this model with and without some (or all) of the CONECT lines to see whether your problem is similar. -Will ***** COMPND ATP.pdb from Klotho. ATOM 1 C1* 1 -2.558 -0.880 0.320 1.00 0.02 ATOM 2 O 1 -1.181 -0.535 0.150 1.00 0.02 ATOM 3 C4* 1 -0.501 -1.645 -0.441 1.00 0.02 ATOM 4 C3* 1 -1.586 -2.370 -1.260 1.00 0.02 ATOM 5 O 1 -1.645 -3.739 -0.850 1.00 0.02 ATOM 6 C2* 1 -2.929 -1.689 -0.938 1.00 0.02 ATOM 7 O 1 -3.951 -2.650 -0.660 1.00 0.02 ATOM 8 C5* 1 0.662 -1.192 -1.322 1.00 0.02 ATOM 9 O 1 1.620 -0.493 -0.523 1.00 0.02 ATOM 10 PA 1 2.845 0.001 -1.371 1.00 0.02 ATOM 11 O 1 3.856 0.759 -0.439 1.00 0.02 ATOM 12 PB 1 5.109 1.280 -1.230 1.00 0.02 ATOM 13 O 1 6.077 2.025 -0.244 1.00 0.02 ATOM 14 PG 1 7.354 2.572 -0.975 1.00 0.02 ATOM 15 O 1 8.219 3.257 -0.004 1.00 0.02 ATOM 16 O 1 8.119 1.408 -1.607 1.00 0.02 ATOM 17 O 1 6.933 3.558 -2.067 1.00 0.02 ATOM 18 O 1 5.840 0.096 -1.865 1.00 0.02 ATOM 19 O 1 4.672 2.208 -2.282 1.00 0.02 ATOM 20 O 1 3.543 -1.202 -2.009 1.00 0.02 ATOM 21 O 1 2.376 0.911 -2.426 1.00 0.02 ATOM 22 N9 1 -3.374 0.341 0.385 1.00 0.02 ATOM 23 C8 1 -3.448 1.332 -0.576 1.00 0.02 ATOM 24 N7 1 -4.297 2.277 -0.150 1.00 0.02 ATOM 25 C5 1 -4.780 1.940 1.054 1.00 0.02 ATOM 26 C4 1 -4.212 0.714 1.421 1.00 0.02 ATOM 27 N3 1 -4.539 0.158 2.595 1.00 0.02 ATOM 28 C2 1 -5.402 0.759 3.425 1.00 0.02 ATOM 29 N1 1 -5.965 1.933 3.105 1.00 0.02 ATOM 30 C6 1 -5.678 2.539 1.945 1.00 0.02 ATOM 31 N6 1 -6.275 3.767 1.625 1.00 0.02 ATOM 32 H 1 -2.677 -1.501 1.206 1.00 0.02 ATOM 33 H 1 -0.063 -2.297 0.312 1.00 0.02 ATOM 34 H 1 -3.252 -1.040 -1.749 1.00 0.02 ATOM 35 H 1 -1.371 -2.251 -2.320 1.00 0.02 ATOM 36 H 1 -2.912 1.343 -1.513 1.00 0.02 ATOM 37 H 1 -5.649 0.290 4.366 1.00 0.02 ATOM 38 H 1 -4.705 -2.513 -1.254 1.00 0.02 ATOM 39 H 1 -1.479 -4.320 -1.609 1.00 0.02 ATOM 40 H 1 0.291 -0.532 -2.103 1.00 0.02 ATOM 41 H 1 1.134 -2.061 -1.775 1.00 0.02 ATOM 42 H 1 -7.187 3.820 2.056 1.00 0.02 ATOM 43 H 1 -6.371 3.844 0.623 1.00 0.02 TER CONECT 1 2 6 22 32 CONECT 2 0 3 0 0 CONECT 3 0 4 8 33 CONECT 4 0 5 6 35 CONECT 5 0 39 0 0 CONECT 6 0 0 7 34 CONECT 7 0 38 0 0 CONECT 8 0 9 40 41 CONECT 9 0 10 0 0 CONECT 10 0 11 20 21 CONECT 11 0 12 0 0 CONECT 12 0 13 18 19 CONECT 13 0 14 0 0 CONECT 14 0 15 16 17 CONECT 15 0 0 0 0 CONECT 16 0 0 0 0 CONECT 17 0 0 0 0 CONECT 18 0 0 0 0 CONECT 19 0 0 0 0 CONECT 20 0 0 0 0 CONECT 21 0 0 0 0 CONECT 22 0 23 26 0 CONECT 23 0 24 36 0 CONECT 24 0 25 0 0 CONECT 25 0 26 30 0 CONECT 26 0 0 27 0 CONECT 27 0 28 0 0 CONECT 28 0 29 37 0 CONECT 29 0 30 0 0 CONECT 30 0 0 31 0 CONECT 31 0 42 43 0 END badger@SDSC.EDU, shoba@angis.org.au, mmhelp@angis.org.au ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Working PDB Lite Sites Date: Wed, 28 Jul 1999 22:20:45 -0400 To: edmolvis@dhcp-srv2.oit.umass.edu, rasmol@dhcp-srv2.oit.umass.edu Cc: lsprilus@weizmann.weizmann.ac.il, helgew@SDSC.EDU, kenneth@SDSC.EDU, I have created a new page which lists the 5 former BNL mirror sites which are keeping PDB Lite working, and keeping their databases up to date, at http://www.umass.edu/microbio/rasmol/pdblite.htm (You get to this page through the 'Molecules Galore' link at the main page.) This new page also lists the unique features of PDB Lite vis a vis the present implementation of RCSB's new SearchLite. None of the 3 former US mirrors of BNL are offering up to date, working PDB Lite, but recently Internet connections from within the USA to all of the working sites outside the USA have been fast, and ALL FIVE presently working sites generally have been giving quick responses. I'll do my best to keep the above page up to date when the situation changes. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: "Brian White" Subject: inline pdbs with chime Date: Thu, 05 Aug 1999 13:02:27 -0400 To: "rasmol@lists.umass.edu" Hi all - I'm creating a script to generate pdb's "on the fly". It generates the following button AOK, but this button does nothing!!! I'm running on netscape 4.08 or 4.5; mac OS 8.6; chime 2.0. I even put in the magical 6 'simulated header' lines. I looked at chime's documentation & they don't mention 'load pdb inline' - does this mean it doesn't exist? Has anybody gotten this to work? Any suggestions? Are there any cute html/javascript tricks to create a pdb file on the client that chime could load? Any help would be _greatly_ appreciated. Brian -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://omega.cc.umb.edu/~bwhite/ References: <3.0.5.32.19990621123233.007ec4d0@alunos.cc.fc.ul.pt> ++++------+------+------+------+------+------+------+------+------+------+ From: Judy Voet Subject: Prelim ASBMB Symposium Announcement Date: Mon, 9 Aug 1999 17:27:27 -0400 To: rasmol@dhcp-srv2.oit.umass.edu TimesMultimedia in Biochemistry and Molecular Biology Education Preliminary call for abstracts and Ideas ASBMB Meeting, Boston, June 4-8, 2000 Organizers: Judy Voet (jvoet1@swarthmore.edu) and Carl Rhodes (crhodes@leland.Stanford.EDU) The past year has seen a proliferation of multimedia resources for teaching biochemistry and molecular biology, from CD- and Web-based images, animations, tutorials, lecture and lesson outlines to on-line testing and feedback. Our session for the Boston 2000 meeting is designed to help find answers to the following questions: What's the best way to learn about current and new resources? How do you select the best multimedia elements and use them effectively in your own courses? How do you assess their utility and effectiveness? How do you obtain support for their use? How do you justify the cost and the effort of adopting these resources? How can you participate in the development of new and unique multimedia resources that you and your colleagues need? We plan to identity at least four speakers with experience in the development, deployment and assessment of a variety of multimedia approaches to learning biochemistry and molecular biology. We would also like to connect the session with a laptop-based "electronic poster" session which will allow participants to sample and discuss the variety of multimedia programs employed in teaching as well as those under development. We need your help. Please send us your ideas and preliminary abstracts for possible inclusion in this session. Thanks in advance, Judy Judith G. Voet, J. H. Hammons Professor Swarthmore College jvoet1@swarthmore.edu Department of Chemistry 610-328-8520 500 College Avenue FAX 610-328-7355 Swarthmore, PA 19081 Content-Disposition: inline X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id EAA01904 ++++------+------+------+------+------+------+------+------+------+------+ From: "Brendan O'Malley" Subject: How to make Rasmol always use CONECT statements Date: Tue, 17 Aug 1999 18:37:25 +1000 To: Is it possible with version 2.7 to force rasmol to use the conect information in an input pdb file even if the number of bonds is less than the number of atoms? If not is it a simple matter to modify the source code to make it so? We use rasmol for analysing molecular dynamics simulations of often model systems so the bond lengths used by rasmol have no meaning. Regards Brendan O'Malley (brendan.omalley@rmit.edu.au) Applied Physics RMIT ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: "Chime" or "Kime"? Date: Tue, 17 Aug 1999 11:27:39 -0400 To: rasmol@dhcp-srv2.oit.umass.edu On August 4, Michael Bruist asked: >Is the "ch" in chime pronounced hard as in chemistry? Most people I know, including those at MDL, say Chime as in Chime (sound of a bell)/Chimney/Chimpanzee/China. However, since "Chime" is a contraction of "Chemical MIME", it seems to me also perfectly acceptable to pronounce it "Kime" as in Chemistry/Chlorine/Chiral/Chi (greek letter). That's my 2 cents. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - UMass Chime Resources: www.umass.edu/microbio/chime Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: How to make Rasmol always use CONECT statements Date: Tue, 17 Aug 1999 11:36:52 -0400 To: rasmol@dhcp-srv2.oit.umass.edu On August 4, Michael F. Bruist asked how to show ligand-protein hbonds. This inspired me to start writing an explanation of how RasMol and Chime handle bonds. Today, Brendan O'Malley asked how to get CONECT records to be obeyed. This inspired me to finish said explanation (or at least get it into presentable form). So under my FAQ http://www.umass.edu/microbio/rasmol/faq_em.htm you will now find How do RasMol and Chime determine which atoms in a PDB file are covalently bonded? How can arbitrary bonds be added or hidden? Why don't RasMol or Chime show most of the hydrogen bonds? answered to the best of my ability at http://www.umass.edu/microbio/rasmol/rasbonds.htm Any suggestions for improvements or (gasp) corrections are welcome. I would be particularly grateful if someone who understands how RasMol assigns hbonds could write a short description of that process in nontechnical language. From examining RasMol's C source code, I was unable to grasp how this works. Ditto for secondary structure. (True, I've been too lazy so far to go to the library for a copy of Kabsch and Sander's paper -- nor have I been able to find it on the web.) -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: bond command needed in RasMol and Chime Date: Tue, 17 Aug 1999 11:40:21 -0400 To: rasmol@dhcp-srv2.oit.umass.edu, chime-feedback@mdli.com I'm aiming this primarily at the handful of people who are enhancing RasMol, and at the team at MDL working on Chime, but I'm sharing it with the list to see any comments it may evoke. I'd like to propose to the developers of RasMol and Chime that a 'bond' command be implemented which would allow specifying bonds between atoms, using atom serial numbers, with syntax similar to the PDB format CONECT record. Thus bond 213 222 225 307 would create bonds between atom serial number 213 and the other three. This would make it possible to write scripts which would, for example, show or hide categories of hydrogen bonds such as interchain vs. intrachain-nonbackbone or intrachain-backbone-to-sidechain. (Determining the serial numbers of bonded atoms to use in the scripts would require calculations or assignments external to RasMol or Chime as far as I know.) The only way it is possible to do this at present is by adding CONECT records to the PDB file and reloading it following a 'set connect save' command (see http://www.umass.edu/microbio/rasmol/rasbonds.htm). Rewriting the PDB file from a server is much more cumbersome, and generates much more network traffic, than just one line of script (or less) per new bond. Also, the CONECT records do not necessarily make it easy to show and hide arbitrary categories of hydrogen bonds, whereas a 'bond' command would give complete flexibility. I propose the name 'bond' because there is already a 'connect' command. Occasionally, RasMol may make bonds which are incorrect, particularly with molecules of under 255 atoms ('connect true' default). Here it is easy enough to select the two atoms in question and do 'wireframe off' to hide unwanted bonds. So no 'unbond' command is needed as far as I can see. The same mechanism can be used to hide groups of bonds added with the proposed 'bond' command. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Supplying the missing Hbonds to RasMol/Chime Date: Tue, 17 Aug 1999 11:53:33 -0400 To: rasmol@dhcp-srv2.oit.umass.edu, pdb-l@rcsb.org Neither RasMol nor Chime have built-in mechanisms to display most hydrogen bonds (the exceptions being backbone-to-backbone hbonds in regions of recognizable secondary structure). However, using CONECT records, it is possible to add arbitrary hbonds, provided the 'set connect save' command (implemented in Chime 2 but not in RasMol 2.6-beta-2a) is issued prior to loading the PDB file (see http://www.umass.edu/microbio/rasmol/rasbonds.htm). It is also possible to show arbitrary hbonds with monitor lines in both RasMol and Chime, though these cannot be rendered as cylinders (see http://www.umass.edu/microbio/rasmol/rasbonds.htm). Can someone suggest a public domain program which will read a PDB file and list hbonds? Such a program could be set up on a server to generate a script or a modified PDB file which would inform RasMol and Chime where to draw the missing hbonds. If someone wishes to volunteer to set up such a routine on a server, I'll be happy for some help. I would then like to add an option to the Protein Explorer (http://www.umass.edu/microbio/chime/explorer) which will request the script or CONECT-enhanced PDB file for display in Chime. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - UMass Chime Resources: www.umass.edu/microbio/chime Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: David Smith Subject: colour Date: Tue, 17 Aug 1999 15:26:47 -0400 To: rasmol@dhcp-srv2.oit.umass.edu I was wondering if anyone has come up with a color scheme for rasmol which allows viewing with 3-deminsional glasses. A simple color scheme allowing all close objects to be in the red range and the deeper in the picture one would look the colors would change through the spectrum until blue was at the farthest point in 3-demensional space. If you would like to see an example of this here is a web page that describes it better: www.Chromatek.com ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Full screen stereo under X11 Date: Tue, 17 Aug 1999 15:49:52 -0400 To: rasmol@dhcp-srv2.oit.umass.edu [I am forwarding this for Gert Vriend, Gert.Vriend@EMBL-Heidelberg.de --Eric Martz] Rolando Ridriguez has written some very simple code in WHAT IF to allow for full screen stereo viewing on PCs using cheap stereo devices that were developed mainly for the game computer industry. An article about this topic was submitted to J.Mol.Graph.Mod. last week, but the source code essentials can be found in the WHAT IF WWW pages: http://swift.embl-heidelberg.de/whatif/ and http://swift.embl-heidelberg.de/whatif/stereo/ The source code is given there too. Feel free to use it, but don't forget from where you got it! Have 3D fun Gert Vriend ++++------+------+------+------+------+------+------+------+------+------+ From: Suzanne Sirois Subject: CHIME and IRIX 6.5 Date: Tue, 17 Aug 1999 15:47:09 -0400 (EDT) To: rasmol@dhcp-srv2.oit.umass.edu Dear Ercik, our systems have been upgraded to IRIX 6.5 With the 6.2 unix system the Chime plugins were working fine. However with the 6.5 unix system upgrade I can't visualize anything. Is it normal? Suzanne Sirois, ++++------+------+------+------+------+------+------+------+------+------+ From: Albion Baucom Subject: Re: CHIME and IRIX 6.5 Date: Tue, 17 Aug 1999 13:50:28 -0700 To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu Suzanne, I too have recently upgraded our SGI's to 6.5. I can still use the Chime 0.99z plug-in using Netscape Communicator 4.51. Remember that you must use 8-bit color in Netscape when you start it as follows netscape -visual pseudocolor& Also, be sure that in the process of upgrading that the plugin libchimeplugin.so is still on your computer in directory /usr/local/lib/netscape/plugins I do encounter frequent crashes if I push the browser with scripts and errors from netscape claiming it can't display colors that are outside its 8-bit palette. Albion Albion E. Baucom http://tito.ucsc.edu/baucom http://c4.cabrillo.cc.ca.us '71 R75/5 '74 R90/6 On Tue, 17 Aug 1999, Suzanne Sirois wrote: > Dear Ercik, our systems have been upgraded to IRIX 6.5 > With the 6.2 unix system the Chime plugins were working fine. > However with the 6.5 unix system upgrade I can't visualize anything. > Is it normal? > > Suzanne Sirois, > ++++------+------+------+------+------+------+------+------+------+------+ From: Suzanne Sirois Subject: Re: CHIME and IRIX 6.5 Date: Tue, 17 Aug 1999 16:54:37 -0400 (EDT) To: rasmol@dhcp-srv2.oit.umass.edu Thank you Albion, I will forward your answer to our system administrator and see what he can do. kind regards, Suzanne Sirois References: X-Accept-Language: German/Germany, de-DE, en ++++------+------+------+------+------+------+------+------+------+------+ From: jr Subject: Re: CHIME and IRIX 6.5 Date: Wed, 18 Aug 1999 11:33:50 +0200 To: rasmol@dhcp-srv2.oit.umass.edu Albion Baucom wrote: > netscape -visual pseudocolor& > /usr/local/lib/netscape/plugins I have installed ~/.netscape/plugins/libchimeplugin.so as indicated by about:plugins application/x-spt RASMol Script spt Yes but if I started netscape -visual pseudocolor I only get a blank netscape window (no error or crash) accessing a File MIME Type: application/x-spt which was handled by Embed: internal-external-plugin as indicated by page info of netscape Communicator 4.51 on IRIX64 6.5 Regards, Jan -- Snail to:Jan Reichert, IMB, D-07708 Jena, POB 100813. Voice:+49 3641 6562-05 (Fax:+49 3641 6562-10) mailto:jr@imb-jena.de http://www.imb-jena.de/~jr/index.shtml PDB Listserver ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: Post-doc: Bioinformatics Date: Wed, 18 Aug 1999 16:31:10 +0300 To: o-info@kaktus.imsb.au.dk, x-plor@net.bio.net, POSTDOC POSITION IN BIOINFORMATICS AVAILABLE AT THE ISRAELI EMBNET NODE, THE WEIZMANN INSTITUTE OF SCIENCE, REHOVOT, ISRAEL JOB DESCRIPTION: The successful candidate will: * Provide resources and training in databases and software related to macromolecular structure. The aim is to enable biological scientists to access this rich source of information. * Design tutorials, supplemented by lectures and exercises, for delivery at workshops (attended mainly by graduate students). * Act as administrator for INN, the Israeli National Node of EMBnet (http://il.embnet.org). DURATION: 1-3 years (depending on suitability) EFFECTIVE: Starting date, October 1999 QUALIFICATIONS: Recent Ph.D. (within 4 years) BENEFITS: Competitive salary plus individual grant for attending conferences LOCATION: The Department of Plant Sciences in collaboration with the Biological Computing Unit of Biological Services, Weizmann Institute of Science, Rehovot, Israel. * The Weizmann Institute is a premiere international science institution with a scientific staff of 1,700 and several hundred foreign visitors and post-docs on campus at any one time. All seminars, activities, etc. are run in English. Israel's largest science-based industrial park is right next door. * Rehovot is a university town of 100,000 located 30 min. from Tel Aviv, 50 min. from Jerusalem and 15 min. from the Mediterranean sea. Lots of activities on campus and lots of restaurants in town. RESPOND BY EMAIL: Include C.V. to: Leon Esterman (lsestern@weizmann.weizmann.ac.il) ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: uncoloring bonds? Date: Wed, 18 Aug 1999 14:37:57 -0400 To: rasmol@dhcp-srv2.oit.umass.edu In RasMol and Chime, after loading 1d66.pdb, the following commands color green all bonds connected to phosphorus atoms (in the DNA backbone). restrict none select all color cpk wireframe 0.15 spacefill 0.45 set bondmode or select phosphorus #selection must occur after bondmode is set! color bonds green Is there any way to restore these bonds back to their default 'split' CPK colors? (short of reloading and starting over) These don't work color bonds color bonds false color bonds atoms color bonds cpk color bonds default ???? (If there is no way, one should be added!) -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: uncoloring bonds? Date: Wed, 18 Aug 1999 18:29:32 -0600 (MDT) To: rasmol@dhcp-srv2.oit.umass.edu Hi Eric, > Is there any way to restore these bonds back to their default 'split' > CPK colors? (short of reloading and starting over) > (If there is no way, one should be added!) color bonds none Roger -- References: <3.0.5.32.19990621123233.007ec4d0@alunos.cc.fc.ul.pt> ++++------+------+------+------+------+------+------+------+------+------+ From: "Brian White" Subject: Re: Prelim ASBMB Symposium Announcement Date: Thu, 19 Aug 1999 10:24:15 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Judy - I would be very interested to present the mol vis stuff I've used in lecture & lab with intro bio students. I've also begun some investigation of what the students actually get from mol vis. I've also done some animations as well. What should I send to get signed up? Brian Judy Voet wrote: > Multimedia in Biochemistry and Molecular Biology Education > Preliminary call for abstracts and Ideas > ASBMB Meeting, Boston, June 4-8, 2000 > > Organizers: Judy Voet (jvoet1@swarthmore.edu) and Carl Rhodes (crhodes@leland.Stanford.EDU) > > The past year has seen a proliferation of multimedia resources for teaching > biochemistry and molecular biology, from CD- and Web-based > images, animations, tutorials, lecture and lesson outlines to on-line > testing and feedback. Our session for the Boston 2000 meeting is designed > to help find answers to the following questions: > > What's the best way to learn about current and new resources? > > How do you select the best multimedia elements and use them effectively in > your own courses? > > How do you assess their utility and effectiveness? How do you obtain > support for their use? > > How do you justify the cost and the effort of adopting these resources? > > How can you participate in the development of new and unique multimedia > resources that you and your colleagues need? > > We plan to identity at least four speakers with experience in the > development, deployment and assessment of a variety of multimedia > approaches to learning biochemistry and molecular biology. We would also > like to connect the session with a laptop-based "electronic poster" session > which will allow participants to sample and discuss the variety of > multimedia programs employed in teaching as well as those under development. > > We need your help. Please send us your ideas and preliminary abstracts for possible inclusion in this session. > > Thanks in advance, > > Judy > > Judith G. Voet, J. H. Hammons Professor Swarthmore College > jvoet1@swarthmore.edu Department of Chemistry > 610-328-8520 500 College Avenue > FAX 610-328-7355 Swarthmore, PA 19081 -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://omega.cc.umb.edu/~bwhite/ ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: Chime NAME/TARGET Date: Thu, 19 Aug 1999 19:11:19 +0300 To: RasMol list When using buttons to send RasMol scripts to Chime windows, is it possible to send a script to more than one Chime window at a time? If you give the Chime windows identical NAMEs, the script is only sent to the first one. Is it possible to list more than one NAME in a TARGET command, or duplicating the TARGET commands? All the ways I've tried fail. Kurt -- -------------------------------------------------------------- Dr. Kurt Giles kurt@il.embnet.org Israeli National Node Biological Computing Unit Tel: +-972-8-9342614 Weizmann Institute of Science Fax: +-972-8-9466269 Rehovot 76100, Israel http://inn-prot.weizmann.ac.il -------------------------------------------------------------- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Chime NAME/TARGET Date: Thu, 19 Aug 1999 12:38:41 -0400 To: rasmol@dhcp-srv2.oit.umass.edu The trick I've used is to use a javascript button which calls a function, instead of an embed button which targets a single Chime. The function can do as many things as you want, including sending scripts to multiple Chimes (almost) simultaneously. At http://www.umass.edu/microbio/chime/chimehow/chime_3.htm you can see simple examples of javascript buttons. I also use them profusely throughout my Protein Explorer. None of these do exactly what you want, but all you need to do is put in the button function e.g. function button1() { chime_graphics.executeScript(script); chime2_graphics.executeScript(script); } The button can be either a form button e.g. or a hyperlink, e.g. Show Secondary Structure Have fun, -Eric At 8/19/99, you wrote: >When using buttons to send RasMol scripts to Chime windows, is it possible >to send a script to more than one Chime window at a time? > >If you give the Chime windows identical NAMEs, the script is only sent to >the first one. >Is it possible to list more than one NAME in a TARGET command, or >duplicating the TARGET commands? All the ways I've tried fail. > >Kurt > >-- >-------------------------------------------------------------- >Dr. Kurt Giles kurt@il.embnet.org >Israeli National Node >Biological Computing Unit Tel: +-972-8-9342614 >Weizmann Institute of Science Fax: +-972-8-9466269 >Rehovot 76100, Israel http://inn-prot.weizmann.ac.il >-------------------------------------------------------------- > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu Molecular visualization in bioscience education at the RasMol Home Page - - - - - - - - - - - - - - - - - - - - - - - - - - - */ X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id MAA11618 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: rasmol atomic radii Date: Thu, 19 Aug 1999 12:48:00 -0400 To: "Edwin Landale" Cc: rasmol@dhcp-srv2.oit.umass.edu At 8/19/99, Edwin Landale wrote: > > where can I find out what atomic radii (Van der Waals radii?) rasmol uses? > and can the user change them? > I do not see this information in FAQs or using 'site search'. > thanks, Edwin Landale  >   I summarized the vdW radii used by RasMol/Chime for the major elements in www.umass.edu/microbio/r asmol/rasbonds.htm That document also has a link to the source code and a reference to where you can find the list for all elements in the source code. The covalent radii (used internally for assigning bonds) are also listed. There are two ways to make custom radii that I know about: 1. Select groups of atoms and use the command 'spacefill n' where n is the desired radius. If in Angstroms, n must include a decimal point! 2. 'spacefill temperature', provided you have put the desired radii in the 'temperature' field of the PDB file. From www.umas s.edu/microbio/rasmol/distrib/rasman.htm#spacefill "The temperature option sets the radius of each sphere to the value stored in its temperature field. Zero or negative values have no effect and values greater than 2.0 are truncated to 2. The user option allows the radius of each sphere to be specified by additional lines in the molecule's PDB file using Raster 3D's COLOR record extension." - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 To unsubscribe from the RasMol Email List, change your address, etc., see X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 ++++------+------+------+------+------+------+------+------+------+------+ From: Henry Brzeski Subject: RE: Chime NAME/TARGET Date: Thu, 19 Aug 1999 17:44:41 +0100 To: rasmol Kurt >When using buttons to send RasMol scripts to Chime windows, is it possible >to send a script to more than one Chime window at a time? You should first download the JavaScript which allows you to use a command line with Chime. This has a function called sendRasmolScriptToChime() (written by Eric in collaboration with MDL) which will send commands to a Chime window. You can get this command line interface from Eric's site, MDL or try one of my pages that uses this eg http://www.herts.ac.uk/natsci/Bio/pst/pst.htm (this page will load pst2.htm that contains the relevant javascript). You should then put a standard HTML button on your page (NOT a Chime button) and then do the rest with JavaScript. Write a function eg 2scripts() which includes two calls to sendRasmolScriptToChime() each diverting your script to a different window in turn. I think this should work. h Henry Brzeski Department of Biosciences University of Hertfordshire College Lane Hatfield AL10 9AB Phone +44 (0)1707 284554 Fax +44 (0)1707 285046 References: <37BA7DFE.F896E579@imb-jena.de> X-Accept-Language: German/Germany, de-DE, en ++++------+------+------+------+------+------+------+------+------+------+ From: jr Subject: Re: CHIME and IRIX 6.5 Date: Fri, 20 Aug 1999 09:30:10 +0200 To: rasmol@dhcp-srv2.oit.umass.edu After updating to Netscape® Communicator 4.61 SGI chime works on IRIX64 6.5: > I have installed > ~/.netscape/plugins/libchimeplugin.so > I started netscape -visual pseudocolor > Regards, Jan -- Snail to:Jan Reichert, IMB, D-07708 Jena, POB 100813. Voice:+49 3641 6562-05 (Fax:+49 3641 6562-10) mailto:jr@imb-jena.de http://www.imb-jena.de/~jr/index.shtml ++++------+------+------+------+------+------+------+------+------+------+ From: "Suzanne W. Slayden" Subject: MIME types Date: Mon, 23 Aug 1999 16:18:56 -0400 (EDT) To: rasmol@dhcp-srv2.oit.umass.edu Just as many of you have done, I've set up a web site for my students to access files to view on RasMol or WebLab (Chime is not an issue here). For their browsers to be able to launch one of these as an external viewer, chemical/x-pdb and chemical /x-mol MIME types must be configured on the server. I've read past e-mail on the list, and the only thing I can find is that "your system administrator should know". Unfortunately, he doesn't! This is what he has said to me: "Basically, I am looking for the authoritative source for chemical mime types. We are running a Netscape Enterprise 3.x server at the moment but plan to replace it with a Apache server, perhaps 1.3.9." He's found http://www.ch.ic.ac.uk/chemime/ but it doesn't seem to help. Can any of you tell us exactly what to do, or where to go, to find the information we need? Thanks, Suzanne Slayden ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Suzanne W. Slayden sslayden@gmu.edu Chemistry Department MSN 3E2 George Mason University (703) 993-1071 Fairfax, Va. 22030 (703) 993-1055 (FAX) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: uncoloring bonds? 2.7.1 Date: Thu, 26 Aug 1999 09:25:32 -0400 To: rasmol@dhcp-srv2.oit.umass.edu [I am forwarding this to the list for Shoba to circumvent technical difficulties. -Eric] Hi, Roger Sayle wrote: > > Hi Eric, > > Is there any way to restore these bonds back to their default 'split' > > CPK colors? (short of reloading and starting over) > > (If there is no way, one should be added!) > > color bonds none > > Roger This is not working: I am using Rasmol2.7.1 32_BIT for the SGI: I do the following: 1. load 1crn.pdb 2. select backbone 3. ribbon 3. colour group Now I want to show the sidechain and c-alpha of residue 13, coloured by atom type (i.e. cpk) 4. select 13 and (sidechain or alpha) 5. wireframe 80 6. colour cpk ! does not work! (Warning: Unable to allocate shade!) nether does "color bonds none", "color atoms cpk" etc. For residue 13, the "group" colour is cyan: this colour is also default for "monochrome" "cpk" and "chain". "structure" shows red (instead of magenta). Just as a check, I re-ran the above on the 8-bit Rasmol (SGI executable) and the Phe-13 residue is coloured yellow in cpk, gold in monochrome and chain and red in structure. If I select all and then colour structure, I get the default rasmol colouring but residue 13 coloured by cpk appears greyish (this is OK!). ribbon or cartoon coloured by structure, temperature or shapely are able assign cpk colours to specific residues but not ribbon coloured by group! "colour bonds none" doesn't work in any of these cases. Is there a workaround or has this bug been fixed already? Shoba ======================================================================= Shoba Ranganathan, Ph D Tel:+61-2-9351-1870 ANGIS, Bay 16, Suite 104 Toll free:1-800-728-028 Australian Technology Park Fax:+61-2-9351-1878 Eveleigh NSW 1430 Australia Personal URL: http://molmod.angis.org.au/~shoba ================MolMod Home Page: http://molmod.angis.org.au=========== ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Shapely color scheme & DNA; standard colors for nucleotides? Date: Thu, 26 Aug 1999 10:13:37 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Cc: phyllismartz@hotmail.com The Shapely color scheme built into RasMol/Chime applies colors which distinguish the 4 bases of DNA. Can anyone refer me to the original published description of this scheme? Or can anyone explain the rationale or mnemonic for the colors employed for nucleotides? I have been using the following color scheme for nucletides which was designed to be easy to remember. Also within DNA, the complementary pairs are 'opposite' colors. If there are other standard color schemes for nucleotides, I'd like to know about them. Azure (blue) Carmine (red) Green Tweety bird (yellow)* Umber (brown)** -Eric *Thanks to my wife, Phyllis Martz, for coming up with this one! ** Thanks to Tim Driscoll and Frieda Reichsman. - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 To unsubscribe from the RasMol Email List, change your address, etc., see ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: workaround for 'unable to allocate shade' Date: Thu, 26 Aug 1999 10:15:46 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Cc: chime-feedback@mdli.com Shoba Ranganathan inquired about the 'unable to allocate shade' issue in RasMol/Chime. A workaround I have often used successfully is: 1. Clear the palette by 'select all; color white' (or any single color). 2. Reserve any special colors needed, e.g. do cpk or other coloring first. 3. Apply palette-greedy schemes last, such as group or amino. The problem is that the greedy schemes will use all available colors in the internal memory reserved for palette, due to the subtle shading which requires many colors (and makes the images so beautiful!). After these greedy schemes have been applied, there are no colors left for adding new colors. However, I have never been able to get the super-greedy Shapely scheme to work on Windows without a long list of 'unable to allocate shade' messages, even if I clear the palette first and reserve no other colors. Does it work properly on unix or Macs? Apparently this problem is not easily fixed. Below I have reproduced a message from Roger Sayle which discusses this issue. It is excerpted from a message I sent to the list on Dec 22 98 which discusses a related bug affecting the group color scheme in NMR files. If you are interested in the latter, please see the email history file ftp://marlin.bio.umass.edu/pub/shareware/rasmol/email-history/98.11-12 ------------- Roger Sayle's explanation of the palette limitations in RasMol (and Chime) sent 12/21/98: BEGIN QUOTE OF ROGER SAYLE These limits are defined in "transfor.h". The two numbers that are defined are "ColourDepth" (the number of intensity levels per shade) and "LastShade" (the number of available shades). Multiply these two numbers together to give the number of spacefilling colours. For completeness three extra colours are also required (for the background, the bounding box or axes, and the labels). Finally the apple macintosh must always reserve one extra colour, and the X Windows version requires five extra colours (for the menus etc). Hence the number of colours available is: System Colour Depth * Last Shade + Extra = Total 8bit PC 16 15 3 243 8bit Mac 16 14 4 228 8bit UNIX 16 15 8 248 Other PC? 32 31 3 995 Other Mac 32 31 4 996 Other UNIX 32 31 8 1000 All eightbit platforms must use less than 256 colours (or else). The only thing that I'd recommend changing is to set last shade to 63 on sixteen, twentyfour or thirtytwo bit display depths. Colour depths have to be a power of two, and are probably already smooth enough on spheres and ribbons. However this still doesn't solve the problem. As soon as you try group colours it will use all the available shades. For example, every residue of crambin will become a slightly different shade. END QUOTE OF ROGER SAYLE - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 To unsubscribe from the RasMol Email List, change your address, etc., see X-Authenticated: wm0p by cyrus.andrew.cmu.edu X-Licensed-To: Site License ++++------+------+------+------+------+------+------+------+------+------+ From: "Will McClure" Subject: Re: uncoloring bonds? 2.7.1 Date: Thu, 26 Aug 1999 10:29:08 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Shoba, Whenever I want one of the "rainbow color schemes" (Group, Temp., etc) in a display, I first color individual residues as CPK, etc, specifically. Then I put the rainbow coloring on at the end (i.e. after selecting all of model not defined previously for the specific coloring). (Maybe the rainbow coloring "uses up" all of the shades.) -Will McClure --On Thu, Aug 26, 1999 9:25 AM -0400 "Eric Martz" wrote: > This is not working: I am using Rasmol2.7.1 32_BIT for the SGI: > I do the following: > > 1. load 1crn.pdb > 2. select backbone > 3. ribbon > 3. colour group > > Now I want to show the sidechain and c-alpha of residue 13, coloured > by atom type (i.e. cpk) > > 4. select 13 and (sidechain or alpha) > 5. wireframe 80 > > 6. colour cpk ! does not work! (Warning: Unable to allocate shade!) > > nether does "color bonds none", "color atoms cpk" etc. > > For residue 13, the "group" colour is cyan: this colour is also default > for "monochrome" "cpk" and "chain". "structure" shows red (instead of > magenta). > > Just as a check, I re-ran the above on the 8-bit Rasmol (SGI executable) > and the Phe-13 residue is coloured yellow in cpk, gold in monochrome and chain > and red in structure. > > If I select all and then colour structure, I get the default rasmol colouring > but residue 13 coloured by cpk appears greyish (this is OK!). > > ribbon or cartoon coloured by structure, temperature or shapely are able > assign cpk colours to specific residues but not ribbon coloured by group! > "colour bonds none" doesn't work in any of these cases. > > Is there a workaround or has this bug been fixed already? > > Shoba ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Re: workaround for 'unable to allocate shade' Date: Thu, 26 Aug 1999 11:02:52 -0400 To: rasmol@dhcp-srv2.oit.umass.edu On all kinds of Macintoshes, I have never been able to get around the "unable to allocate shade" problem. Cheers! ***************************** "Some people place favorite quotations at the end of their e-mails, but I don't." Anonymous, Greece, 3rd century BC. Gale Rhodes mailto:rhodes@usm.maine.edu http://www.usm.maine.edu/~rhodes/GRHomePage.html Professor of Chemistry Chemistry Department University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 Phone: (207)780-4734 Fax: (207)780-5607 ++++------+------+------+------+------+------+------+------+------+------+ From: Suzanne Sirois Subject: Re: CHIME and IRIX 6.5 Date: Thu, 26 Aug 1999 11:17:31 -0400 (EDT) To: rasmol@dhcp-srv2.oit.umass.edu After upgrating my IRXI to 6.5 I have made netscape -visual pseudocolor and it didn't work. After removing the preferences.js file in .netscape and restarting netscape -visual pseudocolor it works. Hope this is the solution to the upgrading of IRIX. Suzanne Sirois, Ph.D. ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: PDB nomenclature for inorganic crystals Date: Thu, 26 Aug 1999 11:26:22 -0400 To: I.Dance@unsw.edu.au (Ian Dance) Cc: rasmol@dhcp-srv2.oit.umass.edu, badger@SDSC.EDU Ian Dance wrote concerning his example file yubyoj881.pdb: >After opening this I cannot figure out how to use the select command of >Rasmol to select individual atoms or sequences of atoms. I have seen >somewhere the use of square parentheses for heteros, but I can't get that >to work either. I cannot find anything in the manuals. You can select atoms by atom serial number, e.g. 'select atomno=47', 'select atomno=2,atomno=47', 'select atomno<12', 'select atomno>=22,atomno<=44'. See http://www.umass.edu/microbio/rasmol/seleccmd.htm You cannot select by group name, group number, or chain because none are specified in your PDB file. The square brackets syntax is needed for group names containing digits: 'select po3' fails while 'select [po3]' succeeds (provided some atoms in the PDB file are designated as belonging to a group named PO3). >In crystal packing there is a heirarchy of >units. >(1) Atoms, collected in (2) chemical groups (such as phenyl rings which are >of interest to me), collected further into (3) molecules, and the molecules >are collected into (4) the crystal lattice. The analogy would be that (2) >is the residue, (3) is the chain, (4) is the full protein. First of all, formats other than PDB, such as MDL .mol, may be more appropriate for your inorganic crystals. I am not qualified to advise on this and I hope others will contribute, so I have posted this to the rasmol list (http://www.umass.edu/microbio/rasmol/raslist.htm). Your inquiry would seem also well suited to the PDB list and I suggest that you subscribe and post it there (http://www.rcsb.org/pdb/forum.html). That list has much less than one message per day; the rasmol list has about 1/day on average. Both RasMol and Chime can read several formats. For RasMol 2.6 (see http://www.umass.edu/microbio/rasmol/techintr.htm) "Currently supported input file formats include Brookhaven Protein Databank (PDB), Tripos' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XMol XYZ format and CHARMm format files.". The list for Chime can be seen in Netscape (Help, About Plugins) and includes several more. RasMol 2.7 (http://www.bernstein-plus-sons.com/software/rasmol/) but not RasMol 2.6 (http://www.umass.edu/microbio/rasmol/getras.htm) nor Chime 2 can read mmCIF, which however is also designed for macromolecules. It is my impression that the PDB file format was designed for proteins and nucleic acids, and hence is not well adapted to inorganic molecules. For example, RasMol knows about the 20 standard amino acids and the 5 standard nucleotides, and knows how to draw backbone traces for chains of these. Members of all other groups are supposed to be designated HETATM instead of ATOM (see http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html). However it is common to include HETATM's in the chains to which they belong (even tho they have no backbone rendering), and indeed often the water is given its own separate chain designation for convenience. The term 'group' is used in RasMol (and inherited by Chime) to mean residue, but can be used in a broader sense, e.g. a metal ion or ligand molecule. Thus, following normal PDB usage, molecules in your crystals should be given group names, and distinguished by group numbers. So the example you attached, which contains two identical molecules, would use one group name for all atoms, and two group numbers, 1 and 2. This does not however allow for convenient selection (without specifying a list of atom serial numbers) of sub-groups such as phenyl rings. So indeed you could assign different group names to portions of molecules, yet give all sub-groups in the same molecule the same residue number. This would allow you to select a whole residue easily by group number (but not a category of residues by name, which may be less important in your cases). As you suggest, chain designators could be used to designate categories of residues. In the case you provided, phenyl rings could be selected with 'select not (boron or fluorine)'. But perhaps it will not usually be so simple. Another approach is to write scripts which define terms. For example (for just two of your phenyl rings) select atomno>=21 and atomno<=26 # an easy one select selected and atomno=19,atomno=75,atomno=88, (atomno>=42 and atomno<=44) #must have been numbered by a computer! define phenyl selected Now you can use the term 'phenyl' in select commands. It seems to me that it would ge good for the journal CrystEngComm to recommend that RasMol scripts include a series of select and define commands which define arbitrary terms appropriate to the crystal in question. This bypasses the constraints of the group and chain designators, and makes them optional. For example they would not be needed in the example you supplied since 'select not boron' or 'select not (boron or fluorine)' cover all categories. It could also be recommended that all defined terms be listed in 'echo' commands, e.g. echo "phenyl" has been defined and may be used in select commands. Finally, on another topic, I am puzzled why the CONECT records in your example include a bond between the boron atoms with a length of 8.8 Angstroms. RasMol does not assign such a bond when you force it to ignore the CONECT records with 'connect true' (http://www.umass.edu/microbio/rasmol/rasbonds.htm). - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 To unsubscribe from the RasMol Email List, change your address, etc., see References: <199908261406.KAA05452@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: Re: Shapely color scheme & DNA; standard colors for nucleotides? Date: Thu, 26 Aug 1999 11:38:37 -0400 To: rasmol@dhcp-srv2.oit.umass.edu > >Azure (blue) >Carmine (red) Just a thought- IMHO, the terms Cardinal or Crimson are more likely to be understood/easy to associate as "red" by undergrads. >** Thanks to Tim Driscoll and Frieda Reichsman. d:-) Frieda _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ Frieda Reichsman, Ph.D. _/_/_/_/_/ Biochemistry and Molecular Biology _/_/_/_/_/ University of Massachusetts _/_/_/_/_/ Amherst, MA 01003 _/_/_/_/_/ Phone: (413) 545-4029 _/_/_/_/_/ Fax: (413) 545-3291 _/_/_/_/_/ http://www.bio.umass.edu/biochem/reichsman _/_/_/_/_/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Fwd: Error Condition Re: Chime webpage Date: Fri, 27 Aug 1999 08:40:46 -0400 To: sl1160@messiah.edu, rasmol@dhcp-srv2.oit.umass.edu >Dear List, > I am trying to make a chime webpage with a multienzyme complex. When I >load the page directly from the file everything works ok. However, when I >try to load the same file through the world wide web >(http://webstu.messiah.edu/~sl1160/chime/monomer_frameset.htm), I get an >error message saying, "error adding MIME value type." I am then promted to get >the plug-in even though I already have it. I will be grateful to anyone who >knows whats up with that. > >Steve Lenhert sl1160@messiah.edu >skateboard.about.com > I have finally gotten around to adding the answer to the FAQ at http://www.umass.edu/microbio/rasmol/faq_em.htm#mimes Remember to reload or clear your cache if you have visited the FAQ recently. -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 To unsubscribe from the RasMol Email List, change your address, etc., see ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Fwd: Use of Internet Explorer with Chime Date: Fri, 27 Aug 1999 09:21:00 -0400 To: rasmol@dhcp-srv2.oit.umass.edu, ray.harper@luton.ac.uk >From: "RAY HARPER Rm_C216f EXT_2195" >Organization: University of Luton >To: emartz@microbio.umass.edu >Date: Fri, 27 Aug 1999 11:43:16 GMT >Subject: Feedback from Chime Resources - Use of Internet Explorer >Priority: normal > >Hello, >In september 1998 the university changed its browser from Netscape 3 >to Internet Explorer 4 (IE4) and in september of this year is moving >to IE5. As you can imagine I was not pleased since Chime resorces >were no longer available to the students. > >I have since been trying to find out what can be done with Chime in >IE. Althought your site correctly states that all the resources >available fail with IE3/4 (and I expect IE5 also) it does not >indicate what can be achieved. > >I attach a zip of some files which show how to run Chime/Rasmol >scripts in IE5 or Netscape in a browser independent manner. I have >not checked IE4. > >These may be useful for people who have to use IE or who require >cross browser compatibility. The routines involve redisplaying the >chime pdb, I don't think the pdb files are cached so they will be >downloaded each time. The routines are therefore probably more >appropriate for an intranet where bandwidth is less of a problem than >the internet. However, I do not find it takes more than a few seconds >for most chime pdb's to display across the internet and I doubt most >users would notice any difference between these routines and the >normal ones. > >You may use the files in any way you wish including making them >avaiable for ftp downloading. > >Thank you for providing such a useful site. I hope maintaining it >does not become too arduous. > >Best wishes, > >Dr Ray Harper >Senior Lecturer >Department of Biology and Health Science >University of Luton, Park Square, Luton. LU1 3JU >Tel: 00 44 (0) 1582 734111 ext 2195. e-mail: ray.harper@luton.ac.uk > I myself think a compelling case can be made that no University should fail to offer Netscape, based both on the importance of Chime in education, and the importance of not allowing Microsoft to control ever more aspects of our lives. But I realize that this is too steep an uphill battle on some campuses. Well, obviously maintaining my site requires more time than I can devote to it since some important areas of it are so sadly out of date. And the NSF has said they won't support such maintenance efforts, despite visits by thousands of educators and students per week. So I focus on what I think will do the most good and hope visitors will forgive me for the parts of the site which are out of date. Indeed some Chime resources can be made to work in IE despite the fact that Microsoft refuses to implement full plugin support in IE. Exactly what does and doesn't work, I don't have the time to test and document. What I do know is that resources which use only static/constant scripts (scripts which are always the same) can probably be made to work in IE, using the mechanism Using javascript, it is possible to construct such buttons on the fly, inserting variable scripts into the embed tags. How well this works in IE I don't know. One crucial thing which doesn't work in IE5 is liveconnect. Liveconnect is quite useful for sending variable scripts to Chime by mechanisms other than buttons. By variable scripts, I mean scripts whose contents depend on the state or previous actions. Such scripts can readily be constructed in javascript as string variables, and sent to Chime 2 via liveconnect with document.chime_graphics.executeScript(script_string_variable_name) in Netscape, but IE5 does not support liveconnect. This precludes resources such as my Noncovalent Bond Finder, Protein Explorer, and Protein Morpher from working in IE5. For those interested, I have placed Ray Harper's examples where you can get them at http://www.umass.edu/microbio/chime/beta/ray_harper/chimeie5.zip (Macintosh users: unzipping instructions are at http://merckx.chem.amherst.edu/connlab/machowto/macdecom.html) -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 To unsubscribe from the RasMol Email List, change your address, etc., see ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: PDB nomenclature for inorganic crystals Date: Fri, 27 Aug 1999 18:33:48 -0400 To: rasmol@dhcp-srv2.oit.umass.edu This is the message from Ian Dance which prompted my reply (which the list already received due to a technical snafu). The message below includes the very pretty PDB crystal file. Subject: Time:2:25 PM OFFICE MEMO Query about RasMol Date:990826 Dear Dr Martz, Can you help with a RasMol question? I am Professor of Inorganic Chemistry at the University of New South Wales in Sydney. I have been using RasMol for some time for biological macrolecules from the pdb. I now am moving into the use of RasMol for non-biological macromolecules. One reason for this is that the new electronic journal of the Royal Society of Chemistry, called CrystEngComm (I am on the advisory board) will accept structures for electronic publication as RasMolScripts, to go to Chime. This looks good to me, but need to make it work effectively. I am preparing such files, but need help. I will be displaying complex crystal packing diagrams, with many atoms. The issue is how to use constructively, the pdb concepts of residues and chains. As an example, I generate (via Chem3D) the following (and enclosed) .pdb file based simply on atom coordinates and bonds. After opening this I cannot figure out how to use the select command of Rasmol to select individual atoms or sequences of atoms. I have seen somewhere the use of square parentheses for heteros, but I can't get that to work either. I cannot find anything in the manuals. There are some analogies between the pdb format and what I want to do, and I hope you can advise on this. In crystal packing there is a heirarchy of units. (1) Atoms, collected in (2) chemical groups (such as phenyl rings which are of interest to me), collected further into (3) molecules, and the molecules are collected into (4) the crystal lattice. The analogy would be that (2) is the residue, (3) is the chain, (4) is the full protein. Within RasMol I would like to be able to define, select, and manipulate my systems at each level of the heirarchy. In essence my problem is that I do not fully understand the pdb file format when it does not use all fields, or the way RasMol deals with non-standard pdb files. Can you help, or point me in the direction of a description of what I want to do. Thanks you very much for your time. With best regards Ian Dance Professor of Inorganic Chemistry University of NSW Sydney 2052 Australia fax 612 9385 6141 ____________________________________________________ COMPND yubyoj881.pdb HETATM 1 F -8.4341 2.0037 2.3734 HETATM 2 B 4.4112 0.1725 0.0802 HETATM 3 F -2.2220 4.3430 2.0175 HETATM 4 F -4.1139 2.5058 2.0914 HETATM 5 C -5.5085 0.0991 1.3983 HETATM 6 C -7.5057 1.0456 2.3508 HETATM 7 C -7.5849 -0.0187 3.2411 HETATM 8 C -6.6278 -1.0252 3.2090 HETATM 9 C -5.5896 -0.9662 2.2875 HETATM 10 F -8.6052 -0.0949 4.1309 HETATM 11 F -6.7090 -2.0700 4.0520 HETATM 12 F -4.7672 -1.9980 2.2956 HETATM 13 C -1.2166 -2.9949 0.1161 HETATM 14 C -1.3044 -2.0360 1.1178 HETATM 15 C -2.3461 -1.1129 1.1084 HETATM 16 F -0.1841 -3.8774 0.1136 HETATM 17 F -0.3596 -1.9750 2.0612 HETATM 18 F -2.4250 -0.2788 2.1055 HETATM 19 C 5.5793 1.3823 -0.1686 HETATM 20 F 2.3687 -1.9139 -0.2570 HETATM 21 C 5.4232 -1.2198 0.2815 HETATM 22 C 6.3302 -1.1540 1.3330 HETATM 23 C 7.2315 -2.1919 1.5394 HETATM 24 C 7.2238 -3.2973 0.6956 HETATM 25 C 6.3168 -3.3633 -0.3558 HETATM 26 C 5.4174 -2.3240 -0.5623 HETATM 27 F 6.3503 -0.1637 2.1667 HETATM 28 F 8.1565 -2.1157 2.5074 HETATM 29 F 8.0712 -4.3352 0.9208 HETATM 30 F 6.3056 -4.4391 -1.1343 HETATM 31 C 3.3459 0.3633 1.3841 HETATM 32 C 3.1428 -0.6060 2.3582 HETATM 33 C 2.1048 -0.4643 3.2734 HETATM 34 C 1.2735 0.6462 3.2142 HETATM 35 C 1.4749 1.6167 2.2404 HETATM 36 C 2.5128 1.4752 1.3256 HETATM 37 F 3.8592 -1.6900 2.4936 HETATM 38 F 1.8694 -1.4138 4.1787 HETATM 39 F 0.2500 0.7818 4.0867 HETATM 40 F 0.6632 2.6834 2.1825 HETATM 41 F 2.6225 2.4203 0.4057 HETATM 42 C 5.7592 2.4803 0.6640 HETATM 43 C 6.7834 3.3859 0.4092 HETATM 44 C 7.6259 3.1921 -0.6780 HETATM 45 F 5.0370 2.7092 1.7288 HETATM 46 F 6.9668 4.4391 1.1916 HETATM 47 B -4.4035 0.1727 0.0806 HETATM 48 C -3.3305 1.4888 0.0886 HETATM 49 C -2.3624 1.4754 -0.9085 HETATM 50 C -1.3527 2.4313 -0.9117 HETATM 51 C -1.3131 3.4016 0.0836 HETATM 52 C -2.2814 3.4149 1.0806 HETATM 53 C -3.2891 2.4606 1.0828 HETATM 54 F -2.3695 0.6396 -1.8947 HETATM 55 F -0.3900 2.4064 -1.8375 HETATM 56 F -0.3286 4.3433 0.0854 HETATM 57 C -6.4674 1.1046 1.4293 HETATM 58 F -6.4545 2.1334 0.6169 HETATM 59 C -3.2943 -1.1494 0.0938 HETATM 60 C -3.2064 -2.1084 -0.9080 HETATM 61 C -2.1667 -3.0306 -0.8968 HETATM 62 F -4.0219 -2.1823 -1.9293 HETATM 63 F -2.0519 -3.9452 -1.8462 HETATM 64 C -5.4626 0.2063 -1.2747 HETATM 65 C -6.3825 -0.8334 -1.3669 HETATM 66 C -7.3666 -0.8056 -2.3472 HETATM 67 C -7.4309 0.2618 -3.2353 HETATM 68 C -6.5127 1.3004 -3.1441 HETATM 69 C -5.5286 1.2723 -2.1628 HETATM 70 F -6.3720 -1.8600 -0.5515 HETATM 71 F -8.2525 -1.8069 -2.4178 HETATM 72 F -8.4150 0.2937 -4.1787 HETATM 73 F -6.5878 2.3264 -3.9989 HETATM 74 F -4.7324 2.3230 -2.1489 HETATM 75 C 6.4217 1.1885 -1.2559 HETATM 76 F 6.2887 0.1967 -2.0700 HETATM 77 C 3.3051 0.0502 -1.2318 HETATM 78 C 2.3816 -0.9881 -1.2027 HETATM 79 C 1.3650 -1.0420 -2.1500 HETATM 80 C 1.2756 -0.0578 -3.1272 HETATM 81 C 2.1975 0.9819 -3.1557 HETATM 82 C 3.2123 1.0345 -2.2082 HETATM 83 F 0.4754 -2.0450 -2.1405 HETATM 84 F 0.2858 -0.1219 -4.0566 HETATM 85 F 2.0936 1.9346 -4.0840 HETATM 86 F 4.0336 2.0490 -2.3337 HETATM 87 F 4.6538 -2.4348 -1.6151 HETATM 88 C 7.4459 2.0940 -1.5107 HETATM 89 F 8.6052 4.0880 -0.9563 HETATM 90 F 8.2723 1.9032 -2.5490 CONECT 1 6 CONECT 2 19 21 31 47 CONECT 2 77 CONECT 3 52 CONECT 4 53 CONECT 5 9 47 57 CONECT 6 1 7 57 CONECT 7 6 8 10 CONECT 8 7 9 11 CONECT 9 5 8 12 CONECT 10 7 CONECT 11 8 CONECT 12 9 CONECT 13 14 16 61 83 CONECT 14 13 15 17 CONECT 15 14 18 59 CONECT 16 13 CONECT 17 14 33 34 CONECT 18 15 CONECT 19 2 42 75 CONECT 20 78 CONECT 21 2 22 26 CONECT 22 21 23 27 CONECT 23 22 24 28 CONECT 24 23 25 29 CONECT 25 24 26 30 CONECT 26 21 25 87 CONECT 27 22 CONECT 28 23 CONECT 29 24 CONECT 30 25 CONECT 31 2 32 36 CONECT 32 31 33 37 CONECT 33 17 32 34 38 CONECT 34 17 33 35 39 CONECT 35 34 36 40 CONECT 36 31 35 41 CONECT 37 32 CONECT 38 33 CONECT 39 34 CONECT 40 35 51 52 CONECT 41 36 CONECT 42 19 43 45 CONECT 43 42 44 46 CONECT 44 43 88 89 CONECT 45 42 CONECT 46 43 CONECT 47 2 5 48 59 CONECT 47 64 CONECT 48 47 49 53 CONECT 49 48 50 54 CONECT 50 49 51 55 CONECT 51 40 50 52 56 CONECT 52 3 40 51 53 CONECT 53 4 48 52 CONECT 54 49 CONECT 55 50 80 81 CONECT 56 51 CONECT 57 5 6 58 CONECT 58 57 CONECT 59 15 47 60 CONECT 60 59 61 62 CONECT 61 13 60 63 83 CONECT 62 60 CONECT 63 61 CONECT 64 47 65 69 CONECT 65 64 66 70 CONECT 66 65 67 71 CONECT 67 66 68 72 CONECT 68 67 69 73 CONECT 69 64 68 74 CONECT 70 65 CONECT 71 66 CONECT 72 67 CONECT 73 68 CONECT 74 69 CONECT 75 19 76 88 CONECT 76 75 CONECT 77 2 78 82 CONECT 78 20 77 79 CONECT 79 78 80 83 CONECT 80 55 79 81 84 CONECT 81 55 80 82 85 CONECT 82 77 81 86 CONECT 83 13 61 79 CONECT 84 80 CONECT 85 81 CONECT 86 82 CONECT 87 26 CONECT 88 44 75 90 CONECT 89 44 CONECT 90 88 END mmciflist@ndbdev.rutgers.edu ++++------+------+------+------+------+------+------+------+------+------+ Beginning Sep 1, 1999: ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: torsion angles in RasWin 2.7.1 Date: Thu, 2 Sep 1999 23:39:29 -0400 To: pdb-l@rcsb.org, rasmol@dhcp-srv2.oit.umass.edu, Professor Kurt Berndt has reported a bug in the torsion angle calculations made by the windows version of RasMol 2.7.1 The problem has been traced to a bad routine (acos) in the math libraries used for the windows build. This routine is used for calculations of omega and phi, but not for calculation of psi (atan2, which seems to be working correctly, is used for psi). The bad acos seems to be computing angles scaled down by a factor of approximately 1.4. We will code and test a replacement for the bad acos and replace the windows binary in a few days. Until then, the windows binary of RasMol 2.7.1 should not be used for torsion angle calculations. Our thanks to Professor Berndt for reporting the problem, and our apologies for any inconvenience caused to windows users. -- Herbert J. Bernstein ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-516-286-1339 FAX: 1-516-286-1999 ===================================================== References: <0FDO006AZTLBD9@rfd1.oit.umass.edu> <3.0.5.32.19990621123233.007ec4d0@alunos.cc.fc.ul.pt> ++++------+------+------+------+------+------+------+------+------+------+ From: Duane Sears Subject: Re: Prelim ASBMB Symposium Announcement Date: Fri, 03 Sep 1999 17:32:59 -0700 To: rasmol@dhcp-srv2.oit.umass.edu Cc: sears@lifesci.lscf.ucsb.edu Dear Judy, Below is my preliminary abstract for the Multimedia in Biochemistry and Molecular Biology Education session of the ASBMB meeting. Thank you for considering the abstract. Duane ---------------------------------------------------------------------------- ----------------- TITLE: Inquiry-Based Biochemistry: Critical Thinking Skills Taught By Interactive Multimedia ABSTRACT: A web-based biochemistry curriculum has been created with interactive multimedia exercises designed to teach students fundamental biochemical concepts following the methodology of the scientific process. Specifically, students are guided into the "discovery" of protein structure/function relationships, first by observing structural and/or functional data; then by drawing conclusions and making inferences about the observations; and finally by testing the validity of hypotheses against the observations. Some of the customized features of the computer exercises will be discussed, including Javascript enhancements for optimizing the Chime browser plugin for molecular image analysis on the web; dynamic Excel data charts for detailed analysis of protein functional data; enhancing instruction with asynchronous streaming videos; creating self-grading with Authorware and with browser "cookies;" and creating instructor-graded quizzes with Access database-linked active server pages (ASPs). A rigorous educational assessment of the curriculum is currently underway with the primary aims being to evaluate and compare basic knowledge understanding and retention for two groups of students: students who have completed the biochemistry laboratory course as well as a traditional biochemistry lecture course offered concurrently; and students who have only taken the lecture course only and not the computer lab. Preliminary results from this assessment will be discussed. ABOUT PROF. SEARS: Prof. Sears has taught biochemistry and immunology for over twenty years. In the last four years he has focussed on designing inquiry-based, multimedia instructional activities to improve students' understanding of basic concepts taught in biochemistry and immunology. Earlier stages of the biochemistry project have been presented at an annual American Chemical Society meeting workshop and portions of the immunology project have been published on the web by W.H. Freeman in conjunction with their textbook , "Immunology" by Janis Kuby. ---------------------------------------------------------------------------- ------------------------------------- At 05:27 PM 8/9/1999 -0400, you wrote: >Multimedia in Biochemistry and Molecular Biology Education >Preliminary call for abstracts and Ideas >ASBMB Meeting, Boston, June 4-8, 2000 > >Organizers: Judy Voet (jvoet1@swarthmore.edu) and Carl Rhodes >(crhodes@leland.Stanford.EDU) > >The past year has seen a proliferation of multimedia resources for teaching >biochemistry and molecular biology, from CD- and Web-based >images, animations, tutorials, lecture and lesson outlines to on-line >testing and feedback. Our session for the Boston 2000 meeting is designed >to help find answers to the following questions: > >What's the best way to learn about current and new resources? > >How do you select the best multimedia elements and use them effectively in >your own courses? > >How do you assess their utility and effectiveness? How do you obtain >support for their use? > >How do you justify the cost and the effort of adopting these resources? > >How can you participate in the development of new and unique multimedia >resources that you and your colleagues need? > >We plan to identity at least four speakers with experience in the >development, deployment and assessment of a variety of multimedia >approaches to learning biochemistry and molecular biology. We would also >like to connect the session with a laptop-based "electronic poster" session >which will allow participants to sample and discuss the variety of >multimedia programs employed in teaching as well as those under development. > >We need your help. Please send us your ideas and preliminary abstracts for >possible inclusion in this session. > >Thanks in advance, > >Judy > > > Judith G. Voet, J. H. Hammons Professor Swarthmore College >jvoet1@swarthmore.edu Department of Chemistry >610-328-8520 500 College Avenue >FAX 610-328-7355 Swarthmore, PA 19081 > > > __________________________________________________________ Professor Duane W Sears Department of Molecular, Cellular and Developmental Biology University of California Santa Barbara, CA 93106 Phones: 805-893-3499 (Office) 805-893-4272(Lab) 805-893-4724(FAX) E-mail: sears@lifesci.ucsb.edu Instructional web sites @ Immunology -- http://mentor.lscf.ucsb.edu/mcdb133/ Biochemistry -- http://mentor.lscf.ucsb.edu/mcdb108a/ mmciflist@ndbdev.rutgers.edu ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: New RasWin 2.7.1 binary Date: Sat, 4 Sep 1999 12:07:46 -0400 (EDT) To: pdb-l@rcsb.org, rasmol@dhcp-srv2.oit.umass.edu, The binary of raswin.exe at http://www.bernstein-plus-sons.com/software/rasmol has been replaced in order to correct the problem in computing torsion angles under windows. Since the change was to a compiler header file rather than to rasmol, the same version number and release dates still apply. To be certain you have a corrected version, load the pdb file of 3CRO and do the command show phipsi The last two lines should read: Chain: R Group: TYR 61 (H) Phi = -121.5 Psi = -135.1 Chain: R Group: GLY 61 (C) Phi = -161.9 If these last three angles are very different, such as Phi = -112.9, Psi = -118.5, and Phi = -124.2, you have a version of the raswin binary with a defective copy of acos. If you wish to rebuild from source, an effective fix is to change the definition of acos in math.h to be: #define acos(x) atan2(sqrt(1.-(x)*(x)),(x)) Note that math.h is _not_ part of the rasmol release, but should be one of the headers provided with your compiler. Note that it may take a while for the corrected binary to be picked up by the various mirror site. Note that this fix should not be needed for mac or unix users. -- H. J. Bernstein ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-516-286-1339 FAX: 1-516-286-1999 ===================================================== ++++------+------+------+------+------+------+------+------+------+------+ From: "Brian White" Subject: Folding proteins Date: Fri, 10 Sep 1999 15:26:51 -0400 To: "rasmol@lists.umass.edu" I would like to have my students explore the relationship between sequence and structure by finding a program that would take a short, user-defined, peptide sequence and fold it to some crude minimal energy configuration. It would not have to be perfect - I just want to have them make changes to the sequence & see how that effects the structure in a (hopefully) predictable, or at least explicable, way. Is there a program that will approximately fold short protein sequences that takes into account some simple side-chain interactions? Thanks Brian -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://omega.cc.umb.edu/~bwhite/ ++++------+------+------+------+------+------+------+------+------+------+ From: "m. ott" Subject: Re: Folding proteins Date: Fri, 10 Sep 1999 15:26:03 -0500 (CDT) To: rasmol@dhcp-srv2.oit.umass.edu A program named "Sybyl" will do that for you rather easily. Unfortunately, is is rather expensive and requires an SGI. So, if you have the money and already have the SGI, this would be a great option to explore. Michael Ott Grad Student for Professor Harold Goff U. of Iowa michael-ott@uiowa.edu On Fri, 10 Sep 1999, Brian White wrote: > I would like to have my students explore the relationship between > sequence and structure by finding a program that would take a short, > user-defined, peptide sequence and fold it to some crude minimal energy > configuration. It would not have to be perfect - I just want to have > them make changes to the sequence & see how that effects the structure > in a (hopefully) predictable, or at least explicable, way. Is there a > program that will approximately fold short protein sequences that takes > into account some simple side-chain interactions? > > Thanks > > Brian > > -- > Prof. Brian White > Biology Department > University of Massachusetts, Boston > 100 Morrissey Blvd > Boston MA 02125 > (617) 287-6630 > fax:(617) 287-6650 > brian.white@umb.edu > http://omega.cc.umb.edu/~bwhite/ > References: <37D95B76.E8DB6F03@umb.edu> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Christopher Hogue Subject: Re: Folding proteins Date: Fri, 10 Sep 1999 18:59:44 -0500 To: rasmol@dhcp-srv2.oit.umass.edu http://bioinfo.mshri.on.ca/conform.html may be what you are looking for. Paste in a sequence and give it a try. You can download the cgi-bin or command line versions from ftp://bioinfo.mshri.on.ca/pub/TraDES /conform is the cgi version /foldtraj is the command-line version. Oh, and it is free to academics. --------------------------------------- Christopher W.V. Hogue, Ph.D. Samuel Lunenfeld Research Institute Mt. Sinai Hospital 600 University Ave. Toronto Ontario Canada M5G 1X5 (416) 586-4800 xt2866 fax (416) 586-8857 hogue@mshri.on.ca http://bioinfo.mshri.on.ca Brian White wrote: > > I would like to have my students explore the relationship between > sequence and structure by finding a program that would take a short, > user-defined, peptide sequence and fold it to some crude minimal energy > configuration. It would not have to be perfect - I just want to have > them make changes to the sequence & see how that effects the structure > in a (hopefully) predictable, or at least explicable, way. Is there a > program that will approximately fold short protein sequences that takes > into account some simple side-chain interactions? > > Thanks > > Brian > > -- > Prof. Brian White > Biology Department > University of Massachusetts, Boston > 100 Morrissey Blvd > Boston MA 02125 > (617) 287-6630 > fax:(617) 287-6650 > brian.white@umb.edu > http://omega.cc.umb.edu/~bwhite/ .edu> References: <37D95B76.E8DB6F03@umb.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: Re: Folding proteins Date: Fri, 10 Sep 1999 17:22:56 -0700 To: rasmol@dhcp-srv2.oit.umass.edu At 03:26 PM 9/10/99 -0500, you wrote: >A program named "Sybyl" will do that for you rather easily. >Unfortunately, is is rather expensive and requires an SGI. So, if you >have the money and already have the SGI, this would be a great option to >explore. Has Sybyl been ported to Linux? If so, there's a cheap solution........ Linux is becoming easier to use all the time. ---- - - - - - - - - - - - - - - - - - - - - _ _ _ _ _ _ _ _ _ _ _ _ _ "I believe in the doctrine of non-violence as a weapon of the weak. I believe in the doctrine of non-violence as a weapon of the strongest. I believe that a man is the strongest soldier for daring to die unarmed" Mohandes Gandhi ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Re: Folding proteins Date: Fri, 10 Sep 1999 23:45:23 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Swiss-PdbViewer 3.5 includes energy minization using GROMOS routines. You should be able to import an arbitrary sequence in FASTA format and fold it into some arbitrary but compact conformation (by dragging dots on the Ramachandran diagram), and then minimize from there. Then use the mutate function to change residues, and minimize again to see the effects. The minimize functions are relatively new to SPV, and I have not tried them out. A few experiments with crambin should show you whether this is feasible. If you try it, please let me know the results. If you are not familiar with SPV, try my tutorial at http://www.usm.maine.edu/~rhodes/SPVTut/index.html Cheers! ***************************** "Some people place favorite quotations at the end of their e-mails, but I don't." Anonymous, Greece, 3rd century BC. Gale Rhodes mailto:rhodes@usm.maine.edu http://www.usm.maine.edu/~rhodes/GRHomePage.html Professor of Chemistry Chemistry Department University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 Phone: (207)780-4734 Fax: (207) 228-8288 ++++------+------+------+------+------+------+------+------+------+------+ From: "Brian White" Subject: Thanks Date: Mon, 13 Sep 1999 11:40:24 -0400 To: "rasmol@lists.umass.edu" Thanks to all who suggested software for folding proteins. I'll give them a try! Brian -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://omega.cc.umb.edu/~bwhite/ ++++------+------+------+------+------+------+------+------+------+------+ From: Andrew Henry Subject: Viewing Rasmol Scripts from Internet Explorer Date: Wed, 15 Sep 1999 13:16:16 +0100 (BST) To: rasmol@dhcp-srv2.oit.umass.edu he pages for viewing rasmol scripts from a WWW browser all tend to use Netscape. I need to use Internet Explorer instead (as decided by the IT department where I work) so I have been fiddling with it. I've got it so that it sort of works. --------------------------------------------------------------- To set up your PC to open a RasMol script from Windows Explorer or Internet Explorer from either Windows 98 or NT: Click on the "My Computer" icon on the desktop With Windows 98, select the menu With NT, select the menu Select the tab If there is already a RAS file type in the list, select it and click "edit". Otherwise click the "New" button to create one. The details for it should be: Description: RasMol script Content Type (MIME): application/x-rasmol Default Extension for Content Type: .ras Then click the "Edit" button In the "Application used to perform action", you need a full path to the RasWin.exe followed by '-script %1'. eg "c:\program files\utils\raswin.exe" -script %1 Once you have entered this correctly, click the OK buttons to close all of the windows. --------------------------------------------------------------- You need the " quotes in the pathname to the program it includes directories with spaces in the name (eg "program files"). With Netscape the %1 feeds the file that you're downloading to rasmol. However like this, whilst you can enter the %1 in the box, if you click the "OK" button and the "EDIT" again then the %1 has disappeared. I tried a few things like \%1 "%1" and '%1' instead of %1 but none worked. This works fine for viewing rasmol scripts on my own machine, but if I try and view a .ras script from somewhere on the Internet using RasMol 2.7.1, I get the startup stuff followed by: Error: File 'INTERNET' not found! and Error: File '"C:\WINDOWS\Temporary' not found! C:\WINDOWS\Temporary does exist on my machine. Does anyone have any ideas on what else to try. -- Andrew Henry ahenry@oxmol.co.uk ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Some Advice (No Charge) Date: Wed, 15 Sep 1999 08:53:01 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Tell your IT department to go to hell and provide you the tools you really need. Computer services departments should not dictate choices of software. The user, who is looking for the best and most efficient way to do the job, should make the choices, and the services departments should SERVE by providing and supporting them. You are the horse; get in front of the cart. Cheers! ***************************** "Some people place favorite quotations at the end of their e-mails, but I don't." Anonymous, Greece, 3rd century BC. Gale Rhodes mailto:rhodes@usm.maine.edu http://www.usm.maine.edu/~rhodes/GRHomePage.html Professor of Chemistry Chemistry Department University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 Phone: (207)780-4734 Fax: (207) 228-8288 ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Re: Viewing Rasmol Scripts from Internet Explorer Date: Wed, 15 Sep 1999 08:55:09 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Oops! I meant for that one to go only to Andrew Henry. Oh, well. It's a familiar battle, eh? Apologies. Cheers! ***************************** "Some people place favorite quotations at the end of their e-mails, but I don't." Anonymous, Greece, 3rd century BC. Gale Rhodes mailto:rhodes@usm.maine.edu http://www.usm.maine.edu/~rhodes/GRHomePage.html Professor of Chemistry Chemistry Department University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 Phone: (207)780-4734 Fax: (207) 228-8288 development commands ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: set delay, set move: undocumented Chime movie script Date: Sun, 19 Sep 1999 17:50:32 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Cc: chime-feedback@mdli.com I just remembered some very useful Chime movie script debugging commands which Tim Maffett was kind enough to implement at my request when he was working on Chime version 1 (and remain in Chime 2). The commands, which I note are undocumented at www.mdli.com/support/chime/rasmol.html, are set delay [off|on] set move [off|on] The 'off' modes make all delays last for 0 seconds, and all moves occur in 0 seconds, regardless of the numbers of seconds actually specified in these commands. Thus, the movie is run at maximum speed. When you are writing a script lasting 10 seconds or more, and debugging/enhancing the tail end, you don't want to have to wait for all the slow moves and delays every time you run the script to see how the latest changes look. So, for example, you can put 'set delay off;set move off' at the top of the script, and then when you get to the portion where you are debugging/adding, insert 'set delay on;set move on'. The movie runs full speed to the inserted 'on' commands, then runs at normal speed from there forward. When you are finished with the script, just comment out these commands, or delete them, and the whole thing runs with the intended timing. -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 To unsubscribe from the RasMol Email List, change your address, etc., see chime X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Alex Garcia Subject: help help!!! Date: Sun, 19 Sep 1999 22:13:40 -0500 To: "rasmol@lists.umass.edu" , I am having lots of problems with the netscape, I have allready instaled the CHIME plug-in, it is suppouse to be working with both browsers, and it is when I open a local page one in my HD) , but when I try to loa a pdb file from the internet the netscape can not do it, and it only happens with a site that I have just finished, but it works fine wen I load it from my HD..... but as soon as I try to load the pages from the net it just doesnot work.... can some one please tell me what did I do wrong??? the netscape loads my files, the ones I put in my website as text files..... and when I try to load the htm doc that has the code for the molecule it says it does not have the right plug-in... and the sme page works fine when I use explorer from MS....... and with other pages from the same site the explorer says that the datas from the complement have not been loaded.... what di I do wrong???? please someone give me a hand.... please please I need help. cheers. PS the site I mention above is http://www.accefyn.org.co/rasmol/dna_protein.htm#dna_protein the netscape says that there is not a plug in for this page but the explorer opens it fine http://www.accefyn.org.co/rasmol/chime/insulina/Indice.htm#inicio again the same with the netscpae and the same with explorer... http://www.accefyn.org.co/rasmol/chime/insulina/Chime_2.htm#insulina with this page it is even more unusuall.... the netscape keeps asking for the plug-in, and the explorer gives me an error msg.... please give me a hand!!!! chime References: <37E5A664.F0981D01@accefyn.org.co> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Alex Garcia Subject: help help!!! Date: Mon, 20 Sep 1999 01:21:49 -0500 To: "rasmol@lists.umass.edu" , Alex Garcia wrote: > I am having lots of problems with the netscape, I have allready instaled > the CHIME plug-in, it is suppouse to be working with both browsers, and > it is when I open a local page one in my HD) , but when I try to loa a > pdb file from the internet the netscape can not do it, and it only > happens with a site that I have just finished, but it works fine wen I > load it from my HD..... but as soon as I try to load the pages from the > net it just doesnot work.... can some one please tell me what did I do > wrong??? the netscape loads my files, the ones I put in my website as > text files..... and when I try to load the htm doc that has the code for > the molecule it says it does not have the right plug-in... and the sme > page works fine when I use explorer from MS....... and with other pages > from the same site the explorer says that the datas from the complement > have not been loaded.... what di I do wrong???? please someone give me a > hand.... please please I need help. cheers. > > PS the site I mention above is > http://www.accefyn.org.co/rasmol/dna_protein.htm#dna_protein > the netscape says that there is not a plug in for this page but the > explorer opens it fine > http://www.accefyn.org.co/rasmol/chime/insulina/Indice.htm#inicio > again the same with the netscpae and the same with explorer... > http://www.accefyn.org.co/rasmol/chime/insulina/Chime_2.htm#insulina > with this page it is even more unusuall.... the netscape keeps asking > for the plug-in, and the explorer gives me an error msg.... please give > me a hand!!!! References: <37E5A664.F0981D01@accefyn.org.co> x-mac-creator="4D4F5353" ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: help help!!! Date: Mon, 20 Sep 1999 08:05:18 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Alex, I am also unable to view the noted pages using Netscape 4.6 on Mac 8.1 OS, though I do have Chime 2.0a installed and working properly. Try a site that should definitely work - for example, http://www.umass.edu/microbio/chime/hemoglob/2frmcont.htm (Eric Martz's tutorial on hemoglobin). If you can view this site in Netscape, then I suggest a direct email to the author of the problem pages below, since it does not appear to be trouble with your setup. If this will help, I noticed in the source code of http://www.accefyn.org.co/rasmol/dna_protein.htm#dna_protein that the plug-in MIME type is not specified - this may be the cause of the trouble. The problematic code is I think there should be a type="chemical/x-pdb" following the embed src="1d66.pdb" I am not sure whether the double percent signs in the width and height definitions could be messing it up, though I doubt it. Also, I use semicolons to separate commands in the script="..." string; I don't know if their absence is a problem. Good luck! Tim Driscoll BTW: Chime is not supported by Internet Explorer, so be very careful of interpreting your computer's behavior based on this combination. Sometimes things work fine, sometimes they crash horrendously. Check out the Chime Home Page for more info (http://www.umass.edu/microbio/chime) or, more specifically on IE vs. NC and Chime, see http://www.umass.edu/microbio/chime/explorer/whynav.htm. Alex Garcia wrote: > I am having lots of problems with the netscape, I have allready instaled > the CHIME plug-in, it is suppouse to be working with both browsers, and > it is when I open a local page one in my HD) , but when I try to loa a > pdb file from the internet the netscape can not do it, and it only > happens with a site that I have just finished, but it works fine wen I > load it from my HD..... but as soon as I try to load the pages from the > net it just doesnot work.... can some one please tell me what did I do > wrong??? the netscape loads my files, the ones I put in my website as > text files..... and when I try to load the htm doc that has the code for > the molecule it says it does not have the right plug-in... and the sme > page works fine when I use explorer from MS....... and with other pages > from the same site the explorer says that the datas from the complement > have not been loaded.... what di I do wrong???? please someone give me a > hand.... please please I need help. cheers. > > PS the site I mention above is > http://www.accefyn.org.co/rasmol/dna_protein.htm#dna_protein > the netscape says that there is not a plug in for this page but the > explorer opens it fine > http://www.accefyn.org.co/rasmol/chime/insulina/Indice.htm#inicio > again the same with the netscpae and the same with explorer... > http://www.accefyn.org.co/rasmol/chime/insulina/Chime_2.htm#insulina > with this page it is even more unusuall.... the netscape keeps asking > for the plug-in, and the explorer gives me an error msg.... please give > me a hand!!!! -- ******************** Timothy Driscoll UMass Amherst Molecular and Cellular Biology Chemistry-Biology Interface Program * Department of Chemistry Amherst College Amherst, MA 01002 413 542 2738 * http://merckx.chem.amherst.edu/tdriscoll/ ******************** ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: help help!!! Date: Mon, 20 Sep 1999 09:27:56 -0400 To: rasmol@dhcp-srv2.oit.umass.edu At 9/19/99, Alex Garcia wrote: >it works fine wen I >load it from my HD..... but as soon as I try to load the pages from the >net it just doesnot work It sounds like maybe you didn't set the MIME types on the server. This is covered in the first FAQ at http://www.umass.edu/microbio/rasmol/faq_em.htm -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 To unsubscribe from the RasMol Email List, change your address, etc., see References: <37E5A664.F0981D01@accefyn.org.co> ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: Re: help help!!! Date: Mon, 20 Sep 1999 12:40:34 -0700 To: rasmol@dhcp-srv2.oit.umass.edu At 01:21 AM 9/20/99 -0500, you wrote: > > >Alex Garcia wrote: > >> I am having lots of problems with the netscape Try reinstalling - also, is your server set up for mime types pdb, xyz, etc? Check with your sysadmin - the exact lines to add to the script file are in the archive of this listserv at the rasmol site. ---- - - - - - - - - - - - - - - - - - - - - _ _ _ _ _ _ _ _ _ _ _ _ _ "I believe in the doctrine of non-violence as a weapon of the weak. I believe in the doctrine of non-violence as a weapon of the strongest. I believe that a man is the strongest soldier for daring to die unarmed" Mohandes Gandhi References: <37E5A664.F0981D01@accefyn.org.co> <3.0.6.32.19990920124034.0079f100@asis.com> x-mac-creator="4D4F5353" ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: help help!!! Date: Mon, 20 Sep 1999 15:52:09 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Alex, My apologies - I did not realize it was your own site you were having trouble posting. I thought you were trying to access someone else's webpage. So ignore my last message, since it won't make much sense anyway :-) Tim -- ******************** Timothy Driscoll UMass Amherst Molecular and Cellular Biology Chemistry-Biology Interface Program * Department of Chemistry Amherst College Amherst, MA 01002 413 542 2738 * http://merckx.chem.amherst.edu/tdriscoll/ ******************** X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Alex Garcia Subject: thanks and help again!!! Date: Mon, 20 Sep 1999 23:33:06 -0500 To: "rasmol@lists.umass.edu" thanks a lot but a ot lot foryour kind replys, I have allready checked the mime files on my server and it is working fine when it loads one page but does not work when it hs to load a frame..... why is it?? again I must ask what am I doing wrong? cheers and agan thanks a lot ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer 1.0 Available Date: Tue, 21 Sep 1999 10:17:34 -0400 To: rasmol@dhcp-srv2.oit.umass.edu, pdb-l@rcsb.org I have released Protein Explorer freeware version 1.0 at www.umass.edu/microbio/chime/explorer. It can be freely downloaded for local installations, but please ask my permission if you want to put it on a publically accessible web server. (It will shortly be available on all RCSB PDB mirror sites, and at EBI Hinxton UK.) It has been tested on both Windows 95/98/NT and Macintosh PPC, and has a new tutorial. PLEASE CLEAR YOUR NETSCAPE COMMUNICATOR CACHE BEFORE TRYING THE NEW VERSION! Edit, Preferences, Advanced, Cache. Clear both memory and disk caches (only the latter on Macs). The Protein Explorer (PE) is visualization freeware which offers a RasMol-like interface in Chime, but is easier to use and more powerful than RasMol. For example, the default initial view is maximally informative: it shows all chains as backbones, all hetero atoms, all disulfide bonds, and all models if NMR. PE has a form/button interface to make 'contact surfaces' colored by distance. These show an overview of all hydrogen bonds and hydrophobic interactions (see snapshot at http://www.umass.edu/microbio/chime/explorer/prev_cs.htm which was displayed in the RCSB PDB booth at IUCr in Glasgow in August). Surfaces can also be colored by electrostatic potential or lipophilicity potential. By using Chime 2 (thanks to MDLI) the powerful new selection menu of Chime 2 is available, including pick lists of all amino acids present (those absent are grayed out), all chains, all predefined terms (hydrophobic, aromatic, solvent, purine, etc.). The Comparator mode shows two molecules side by side for easy comparision. On Windows, they can be set to rotate and zoom in synchrony so they are always seen from the same perspective. (A bug in Macintosh Chime precludes synchronous rotation on Macs at this time.) PE has many convenience features, including a pick list of the 10 most recently loaded molecules; NMR model manipulation buttons (including the ability to step through the models as a movie); preferences which survive between sessions including your preferred PDB mirror site (both BNL and RCSB sites work); user customizable command aliases ("r n w" means "restrict not water"); explanation of the message you get when you click on an atom to identify it; buttons for common tasks such as spin on/off, zoom up/down, show/hide water, show/hide nonsolvent hetero atoms, stereo on/off; buttons which apply a hydrophobic/polar/charged color scheme to proteins or an ATGCU color scheme to DNA or RNA. You can set a 'project folder' which becomes the default for 'script' and 'load' commands, thereby acting like RasMol in this regard. New features added to version 1.0 (since version 0.992) include an extensive tutorial designed for beginners, which has been tested in my current class 'macromolecular visualization computer laboratory' (http://www.bio.umass.edu/micro/courses/molvis.html) and improved based on this experience (thanks to my students and Frieda Reichsman). It includes movies which play in PE at the press of a button. A count of atoms selected is shown at all times. One or two molecules can now be prespecified in a hyperlink to PE. A page of examples which pull diverse molecules from servers around the globe is at www.umass.edu/microbio/chime/explorer/links2pe.htm. This means educators can easily construct a page of links for a class which will show pre-selected molecules in PE. In the near future, I plan to make PE an open platform (not yet available). This means that a hyperlink will be able to specify a third party control page which can perform any desired operations of which PE is capable. For example, a CGI script could generate a molecule-specific page with a button for each functional site specified in the PDB file REMARK 800 and SITE records; molecules could be colored by frequency of mutation based on sequence alignments; a routine to assign hydrogen bonds can add CONECT records to a PDB file, load it, and provide buttons to show categories of hbonds; an educational quiz designed for a particular course can be inserted; an ambitious CGI program could allow the user to specify a mutation, and then display the energy-minimized mutant aligned with the wild type protein. I plan to provide a specification which will enable any third party to create such added-value control panels. Thanks to Phil Bourne, Helge Weissig, John Badger and Ken Yoshimoto for support and advice in interfacing to the RCSB PDB (www.rcsb.org), to Jaime Prilusky and Joel Sussman for support and advice in interfacing to the BNL PDB (www.umass.edu/microbio/rasmol/pdblite.htm), to Kim Henrick for interfacing at EBI Probable Quaternary Structures (http://msd.ebi.ac.uk/Services/Quaternary/quaternary.html), to Roger Sayle, to Tim Maffett, Franklin Adler, Tom Blackadar, and the MDLI Chime Team (www.mdli.com/support/chime), and to the NSF, to name a few! -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ X-Received: from localhost by iron2.ch.ch.ic.ac.uk; Thu, 23 Sep 1999 10:47:57 +0100 (bst) ++++------+------+------+------+------+------+------+------+------+------+ From: simon potter Subject: Running Rasmol on Redhat 6.0 Date: Thu, 23 Sep 1999 10:47:57 +0100 (bst) To: rasmol@dhcp-srv2.oit.umass.edu Hi, I'm having problems running Rasmol on my Linux box. It compiles fine but gives the "No suitable display" message when I run it, although it works fine when I access it remotely through a Silicon Graphics X server. (Before you ask, I have compiled with 8,16 and 32 bit options. I HAVE read the previous postings to the mailing list. The DISPLAY variable is set. The X server has access permission, etc...) I'm running RasMol2.6. I tried the new version (2.7.1) but that just core dumped when I ran it. It seems that others have successfully run RasMol under RH Linux. I've no idea why it's not working. Any suggestions? Many thanks, Simon /***************************************** * DR SIMON POTTER * * Structural Biology Group * * Imperial College, London SW7 2AY * * Tel. 0171 594 5280 Fax 0171 594 5317 * * spot@ic.ac.uk sc_potter@yahoo.com * * www.bc.ic.ac.uk/research/vanheel/group * *****************************************/ <"Running Rasmol on Redhat 6.0"@igr.fr> (Sep 23, 10:47am) References: ++++------+------+------+------+------+------+------+------+------+------+ From: REVET Bernard Subject: Re: Running Rasmol on Redhat 6.0 Date: Thu, 23 Sep 1999 14:17:18 -0600 To: rasmol@dhcp-srv2.oit.umass.edu On Sep 23, 10:47am, simon potter wrote: > Subject: Running Rasmol on Redhat 6.0 > Hi, > > I'm having problems running Rasmol on my Linux box. It > compiles fine but gives the "No suitable display" message > when I run it, although it works fine when I access it > remotely through a Silicon Graphics X server. > > (Before you ask, I have compiled with 8,16 and 32 bit > options. I HAVE read the previous postings to the mailing > list. The DISPLAY variable is set. The X server has access > permission, etc...) > > I'm running RasMol2.6. I tried the new version (2.7.1) but > that just core dumped when I ran it. > > It seems that others have successfully run RasMol under RH > Linux. I've no idea why it's not working. Any suggestions? > > > Many thanks, > > Simon > > > > /***************************************** > * DR SIMON POTTER * > * Structural Biology Group * > * Imperial College, London SW7 2AY * > * Tel. 0171 594 5280 Fax 0171 594 5317 * > * spot@ic.ac.uk sc_potter@yahoo.com * > * www.bc.ic.ac.uk/research/vanheel/group * > *****************************************/ > >-- End of excerpt from simon potter Dear Dr Simon Potter I installed Rasmol 2.7.1 from http://www.bernstein-plus-sons.com/software/rasmol the source under linux RedHat 6.0 and previuously under RedHat 5.2 Following the indications first you have to be sure of your display by the command xdpyinfo if for instance you have a 16bit ( you have to modify the line which correspond to your display) Go to the src directory of your Rasmol then xmkmf you edit the new Makefile go to line 687 ferw lines after Version 2.6.9 remove the # at DEPTHDEF = -DSIXTEENBIT i.e DEPTHDEF = -DSIXTEENBIT and do make This works for me. Tell us what went wrong if it does not work Best regards Bernard Revet mmciflist@ndbdev.rutgers.edu ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: i386 Linux RasMol 2.7.1 binaries Date: Fri, 24 Sep 1999 12:22:10 -0400 To: pdb-l@rcsb.org, rasmol@dhcp-srv2.oit.umass.edu, Jon Bruno has contributed 8-, 16-, and 32-bit RasMol 2.7.1 binaries for i386 Redhat 6.0 Linux. The gzipped binaries are at: ftp://ftp.bernstein-plus-sons.com/software/RasMol_2.7.1.LINUX/RedHat_6.0/i386 These binaries are available in either gzipped or un-gzipped form via new links on the rasmol web page at: http://www.bernstein-plus-sons.com/software/RasMol_2.7.1 Be sure to do any downloads in binary format. It may take a few days before these new links be reflected on mirror sites. Please report any problems to: rasmol@bernstein-plus-sons.com Many RasMol users have requested Linux binaries. Our thanks to Jon Bruno for this contribution. -- Herbert J. Bernstein ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-516-286-1339 FAX: 1-516-286-1999 ===================================================== X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Alex Garcia Subject: thanks/check please Date: Sat, 25 Sep 1999 16:04:04 -0500 To: "rasmol@lists.umass.edu" I would appreciate if you could please let me know if you can see the moleculs at http://www.accefyn.org.co/rasmol/insulina/Indice.htm Cheers PS I think the problem I was having is already solved, and for that I want to thank all the persons who mailed me, thanks a lot but a lot!! ++++------+------+------+------+------+------+------+------+------+------+ From: Richard Laing Subject: Re: thanks/check please Date: Sat, 25 Sep 1999 18:16:41 -0700 To: rasmol@dhcp-srv2.oit.umass.edu At 04:04 PM 9/25/99 -0500, you wrote: >I would appreciate if you could please let me know if you can see the >moleculs at >http://www.accefyn.org.co/rasmol/insulina/Indice.htm > >Cheers > >PS I think the problem I was having is already solved, and for that I >want to thank all the persons who mailed me, thanks a lot but a lot!! > > Looks great! Regards, Richard Laing Vancouver, CANADA rlaing@axionet.com rlaing@bigfoot.com http://members.tripod.com/rlaing/index.htm ********************************************************* "Much may be made of a Scotchman if he be caught young." Samuel Johnson (1709-1784) ********************************************************* References: <37ED38C4.B1C36DCF@accefyn.org.co> X-Accept-Language: ca ++++------+------+------+------+------+------+------+------+------+------+ From: Antoni Parra Subject: Re: thanks/check please Date: Sun, 26 Sep 1999 20:42:02 +0200 To: rasmol@dhcp-srv2.oit.umass.edu Yes. But, please, change the URL to http://www.accefyn.org.co/rasmol/Insulina/Indice.htm A first trial gave a File Not Found error. Tony BTW, replace Interacitvo by Interactivo When you will finish the sections at the end?: 'Manuales' and 'Creación de tutoriales como este' Alex Garcia ha escrit: > I would appreciate if you could please let me know if you can see the > moleculs at > http://www.accefyn.org.co/rasmol/insulina/Indice.htm > > Cheers > > PS I think the problem I was having is already solved, and for that I > want to thank all the persons who mailed me, thanks a lot but a lot!! References: <37ED38C4.B1C36DCF@accefyn.org.co> ++++------+------+------+------+------+------+------+------+------+------+ From: Trina Valencich Subject: Re: thanks/check please Date: Mon, 27 Sep 1999 10:08:44 -0600 To: rasmol@dhcp-srv2.oit.umass.edu When I called the site it could not be found. Trina At 06:16 PM 9/25/99 -0700, you wrote: >At 04:04 PM 9/25/99 -0500, you wrote: >>I would appreciate if you could please let me know if you can see the >>moleculs at >>http://www.accefyn.org.co/rasmol/insulina/Indice.htm >> >>Cheers >> >>PS I think the problem I was having is already solved, and for that I >>want to thank all the persons who mailed me, thanks a lot but a lot!! >> >> > >Looks great! > >Regards, > > >Richard Laing >Vancouver, CANADA >rlaing@axionet.com >rlaing@bigfoot.com >http://members.tripod.com/rlaing/index.htm >********************************************************* >"Much may be made of a Scotchman if he be caught young." > Samuel Johnson (1709-1784) >********************************************************* > > References: <37ED38C4.B1C36DCF@accefyn.org.co> <3.0.6.32.19990927100844.007e1590@selway.umt.edu> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Alex Garcia Subject: Re: thanks/check please Date: Mon, 27 Sep 1999 11:26:27 -0500 To: unlisted-recipients:; (no To-header on input) Cc: rasmol@dhcp-srv2.oit.umass.edu, rasmol@dhcp-srv2.oit.umass.edu the correct address is: http://www.accefyn.org.co/rasmol/Indice.htm PS again thanks a lot for your kind replys, cheers Trina Valencich wrote: > When I called the site it could not be found. Trina > > At 06:16 PM 9/25/99 -0700, you wrote: > >At 04:04 PM 9/25/99 -0500, you wrote: > >>I would appreciate if you could please let me know if you can see the > >>moleculs at > >>http://www.accefyn.org.co/rasmol/insulina/Indice.htm > >> > >>Cheers > >> > >>PS I think the problem I was having is already solved, and for that I > >>want to thank all the persons who mailed me, thanks a lot but a lot!! > >> > >> > > > >Looks great! > > > >Regards, > > > > > >Richard Laing > >Vancouver, CANADA > >rlaing@axionet.com > >rlaing@bigfoot.com > >http://members.tripod.com/rlaing/index.htm > >********************************************************* > >"Much may be made of a Scotchman if he be caught young." > > Samuel Johnson (1709-1784) > >********************************************************* > > > > ++++------+------+------+------+------+------+------+------+------+------+ From: Gerry Prody Subject: Re: thanks/check please Date: Mon, 27 Sep 1999 12:20:49 -0700 To: rasmol@dhcp-srv2.oit.umass.edu My computer says "file not found" gp At 04:04 PM 9/25/99 -0500, you wrote: >I would appreciate if you could please let me know if you can see the >moleculs at >http://www.accefyn.org.co/rasmol/insulina/Indice.htm > >Cheers > >PS I think the problem I was having is already solved, and for that I >want to thank all the persons who mailed me, thanks a lot but a lot!! > > Gerry A. Prody Associate Professor of Chemistry Western Washington University Bellingham, WA 98225-9150 (360) 650-3156 (360) 650-2826 fax References: <3.0.5.32.19990927122049.00f73300@atom.chem.wwu.edu> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: ACCEFYN Subject: Re: thanks/check please Date: Mon, 27 Sep 1999 14:40:03 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu the right address is http://www.accefyn.org.co/rasmol/Indice.htm Gerry Prody wrote: > My computer says "file not found" gp > > At 04:04 PM 9/25/99 -0500, you wrote: > >I would appreciate if you could please let me know if you can see the > >moleculs at > >http://www.accefyn.org.co/rasmol/insulina/Indice.htm > > > >Cheers > > > >PS I think the problem I was having is already solved, and for that I > >want to thank all the persons who mailed me, thanks a lot but a lot!! > > > > > Gerry A. Prody > Associate Professor of Chemistry > Western Washington University > Bellingham, WA 98225-9150 > > (360) 650-3156 > (360) 650-2826 fax ++++------+------+------+------+------+------+------+------+------+------+ From: Jeff Cohlberg Subject: selecting a domain? Date: Wed, 29 Sep 1999 14:37:44 -0700 To: rasmol@dhcp-srv2.oit.umass.edu Dear RasMolers, Is there any way to select a domain of a protein? I was examining the file 3GPD (human GA3P dehydrogenase). The header for this PDB file says that there are two domains designated B and C. Can I select them and color them differently? (I can do this by specifying the amino acid residues, but I'd like to know if there's a direct way to select domains.) One of the few features of Cn3D that I prefer to RasMol is that Domain is one of its color schemes. Thanks in advance for your help. Jeff Cohlberg ------------------ Jeffrey A. Cohlberg, Professor Department of Chemistry and Biochemistry California State University, Long Beach 1250 Bellflower Blvd Long Beach, CA 90840 phone: (5620 985-4944 fax (209) 821-4471 X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id RAA01718 ++++------+------+------+------+------+------+------+------+------+------+ From: Rick Lee Subject: Chime "load" & drive letters Date: Thu, 30 Sep 1999 14:09:48 -0700 To: rasmol@dhcp-srv2.oit.umass.edu I'm having a bit of unexpected trouble. I need to issue a Chime script of the form zap; load pdb ; ... where the pdb file is on a different disk than the HTML file. Neither strings like: E:/folder/file.pdb nor file:///E|/folder/file.pdb will work. I already have src="file:///E|/folder/file.pdb" in the embed tag, and that works fine. Perhaps the complication may be that the script is being passed to ScriptToChime() via another JavaScript function? The script is a string argument to the wrapper function. Thanks for your help. Rick Lee ******************************************** * New Area Code -- 858 ******************************************** *  Richard H. Lee, PhD *  Editor/Lead Scientist, Biochemistry *  rick@sciencemedia.com * *  ScienceMedia.com *  6540 Lusk Blvd., Suite C148 *  San Diego, CA 92121-2767 * *  TEL: 858/625-9261, Ext. 5 *  FAX: 858/625-9262 * *  http://www.sciencemedia.com ********************************************* X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id RAA01961 ++++------+------+------+------+------+------+------+------+------+------+ From: Rick Lee Subject: Re: Chime "load" & drive letters Date: Thu, 30 Sep 1999 14:57:11 -0700 To: rasmol@dhcp-srv2.oit.umass.edu Anticipating a suggestion, after posting my question, I did try to use a "\" as well as "/" without success. Rick ******************************************** * New Area Code -- 858 ******************************************** *  Richard H. Lee, PhD *  Editor/Lead Scientist, Biochemistry *  rick@sciencemedia.com * *  ScienceMedia.com *  6540 Lusk Blvd., Suite C148 *  San Diego, CA 92121-2767 * *  TEL: 858/625-9261, Ext. 5 *  FAX: 858/625-9262 * *  http://www.sciencemedia.com ********************************************* References: <3.0.6.32.19990930140948.008367d0@pop3.sciencemedia.com> X-Accept-Language: en X-MIME-Autoconverted: from 8bit to quoted-printable by james.amherst.edu id IAA18916 X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id IAA05515 ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Chime "load" & drive letters Date: Fri, 01 Oct 1999 08:04:42 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Rick, If I save a script using RasMac, it access the pdb using the following command: load pdb "PowerBook:Desktop Folder:Documents:molvis:centdogma.pdb" Notice that RasMac uses the actual name of the drive (PowerBook) and not any type of drive designation (like C:). You might try this test using RasMol on Windows, if that is your platform, to see if this provides you any information. Another thing to consider with Chime is whether the path to the pdb file has to be relative to the html document, and not an absolute path like RasMac uses in my above example. I don't work much with paths (Macs don't generally require this knowledge) , but I often run into related problems running scripts and loading pdb files. So you may be able to "back out" from the html doc to the top level, then access your E: drive. For example, if my pdb file is on the desktop and my html doc with Chime is nested two layers down in my disk dir, I have to use "../../mymol.pdb" in the load command of the Chime script. As long as the html doc with Chime is always in the same location relative to the pdb file, I don't see that it matters what (or how many) js functions send the script to Chime, unless one of them is altering the load command string. Hope one of these suggestions is helpful - there are people on the list who know a lot about Chime and dir structures (unlike me), so maybe you'll get a more definitive answer from one of them. Yeah, I'm throwing the gauntlet down a bit... Tim Driscoll Rick Lee wrote: > I'm having a bit of unexpected trouble. > > I need to issue a Chime script of the form > zap; load pdb ; ... > where the pdb file is on a different disk than the HTML file. Neither > strings like: > E:/folder/file.pdb > nor > file:///E|/folder/file.pdb > will work. > > I already have > src="file:///E|/folder/file.pdb" > in the embed tag, and that works fine. > > Perhaps the complication may be that the script is being passed to > ScriptToChime() via another JavaScript function? The script is a string > argument to the wrapper function. > > Thanks for your help. > > Rick Lee > > ******************************************** > * New Area Code -- 858 > ******************************************** > *  Richard H. Lee, PhD > *  Editor/Lead Scientist, Biochemistry > *  rick@sciencemedia.com > * > *  ScienceMedia.com > *  6540 Lusk Blvd., Suite C148 > *  San Diego, CA 92121-2767 > * > *  TEL: 858/625-9261, Ext. 5 > *  FAX: 858/625-9262 > * > *  http://www.sciencemedia.com > ********************************************* -- ********************************************* * Timothy Driscoll University of Massachusetts at Amherst Molecular and Cellular Biology Program Chemistry Biology Interface Program * Amherst College Department of Chemistry Amherst, MA 01002 ph 413-542-2738 fx 413-542-2735 tdriscoll@amherst.edu tpdscs@javanet.com http://merckx.chem.amherst.edu/tdriscoll * ********************************************* ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Chime "load" & drive letters Date: Fri, 01 Oct 1999 10:17:40 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Cc: rick@sciencemedia.com It should work, Rick. Sometimes things get messed up in the wrapper, tho. Put an alert just before your executeScript() and see what the string being sent to Chime actually is. (Hopefully you are using LiveConnect and not the old dummy immediate button mode, which is needed for Win3.1 but not Win32 or MacPPC). What error message are you getting? It works in Protein Explorer. You may find PE useful as a testing/debugging platform. Since Chime supports the javascript command, you can run js commands in immediate mode from PE's command slot, e.g. 'javascript alert(variable)', 'javascript var x = "something";', etc. Note that there are some aliases such as 'jsa' and 'js' to save typing, and you can of course add your own aliases in shared/alias.js. Also, in PE, you can issue the command alias 'db' to turn on full debugging mode. Among other things you'll see the exact string being used for load commands for local disk files. For example, in a local disk installation of PE (it is downloadable), issuing 'db', then pushing the [Protein:DNA] button achieves success with load pdb 'file:///C|/3F/CHIME/shared/1d66.pdb' Beware of very long paths -- Chime 2.0.3 should have fixed this problem. Are you working on Mac tho? It still has a 90 character limit. PE catches this and reports without crashing -- another reason to use PE as a testbed. And I'd like to remind people that when PE is installed on your local disk, you can set a project folder, after which 'script ...' and 'load ...' commands use the specified folder as a default with no leading path needed in the command. Also PE automatically tacks the .pdb or .spt onto the end of the command. Thus, 'sc image1' is expanded to 'script image1.spt'. The project folder is a (nonvolatile) preference setting, and you can have as many such folders as you wish. -Eric At 9/30/99, you wrote: >I'm having a bit of unexpected trouble. > >I need to issue a Chime script of the form > zap; load pdb ; ... >where the pdb file is on a different disk than the HTML file. Neither >strings like: > E:/folder/file.pdb >nor > file:///E|/folder/file.pdb >will work. > >I already have > src="file:///E|/folder/file.pdb" >in the embed tag, and that works fine. > >Perhaps the complication may be that the script is being passed to >ScriptToChime() via another JavaScript function? The script is a string >argument to the wrapper function. > >Thanks for your help. > >Rick Lee > >******************************************** >* New Area Code -- 858 >******************************************** >* Richard H. Lee, PhD >* Editor/Lead Scientist, Biochemistry >* rick@sciencemedia.com >* >* ScienceMedia.com >* 6540 Lusk Blvd., Suite C148 >* San Diego, CA 92121-2767 >* >* TEL: 858/625-9261, Ext. 5 >* FAX: 858/625-9262 >* >* http://www.sciencemedia.com >********************************************* > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id QAA07067 ++++------+------+------+------+------+------+------+------+------+------+ From: Rick Lee Subject: Re: Chime "load" & drive letters Date: Fri, 01 Oct 1999 13:55:15 -0700 To: rasmol@dhcp-srv2.oit.umass.edu At 10:17 AM 10/1/99 -0400, Eric Martz wrote: > (Hopefully you are using LiveConnect and not the >old dummy immediate button mode, which is needed for Win3.1 but not >Win32 >or MacPPC). Frankly, I'm not sure. We're using the same version of ScriptToChime() we've used for 3 years. It does in fact call writeln() to output an x-spt button. I take it that this is wrong? (Big oops!) Where is the documentation for the new method? I can't seem to find it on the site. Thanks, Rick ******************************************** * New Area Code -- 858 ******************************************** *  Richard H. Lee, PhD *  Editor/Lead Scientist, Biochemistry *  rick@sciencemedia.com * *  ScienceMedia.com *  6540 Lusk Blvd., Suite C148 *  San Diego, CA 92121-2767 * *  TEL: 858/625-9261, Ext. 5 *  FAX: 858/625-9262 * *  http://www.sciencemedia.com ********************************************* ++++------+------+------+------+------+------+------+------+------+------+ From: Ron Hurlbert Subject: Problems running Chime Date: Fri, 01 Oct 1999 14:25:39 -0700 To: rasmol@dhcp-srv2.oit.umass.edu I have been attempting to use Chime (2.0.3) to display linked images using IE 5.0 during my classrm lec. on a P90 computer with ~90K of memory without success. Chime images come up fine on Netscape 5.6 unless I am running IE at the same time, in which case it causes Netscape to crash so I'm unable to switch back and forth. The reason I don't just stick to Netscape is that I've written the material with Front Page 2000 and it doesn't always display well on Netscape. I can get these same images to work fine on my office computer (P5-166) in IE 5.0. Our local tech can not figure it out. Thanks in advance for any advice/suggestions. Ron http://www.wsu.edu/~hurlbert/pages/101hmpg.html Ronald E. Hurlbert Washington State University PO Box 644233 Department of Microbiology Pullman WA 99164-4233 Phone: 509-335-5108 Fax: 509-335-1907 E-mail: hurlbert@wsu.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Avoiding false misses in boolean searching; site_identifier Date: Sat, 02 Oct 1999 14:35:51 -0400 To: rasmol@dhcp-srv2.oit.umass.edu, pdb-l@rcsb.org I would like to share some solutions to issues which come up when using the RCSB and BNL search interfaces to the PDB. I'm sure these issues, all of which are known to RCSB, will be addressed in future revisions of SearchFields and SearchLite. In the interim the following information may be useful. The issues detailed below concern: 1. Parentheses 2. "but not" 3. "site_identifier" 4. Access to PDB Lite/3DB Browser via RCSB 5. "and not" vs. "not" vs. leading "not" 6. Alternate spellings 7. "1,6-bisphos" 8. Atom counts 9. Residue counts 10. Excluding one technique 11. Multiple spaces between terms 1. Do not use parentheses "()" in phrasing a query to SearchLite/SearchFields. While "hemoglobin" finds 150 entries, "(hemoglobin)" finds zero. Complex boolean searches can be done in SearchLite/SearchFields by starting with a simple query, and then using the 'Refine Your Query' option on the pull-down menu. Neither are parentheses consistently supported in 3DB Browser: they sometimes result in incorrect findings. In PDB Lite, if you use parentheses in a query, it requests that you rephrase your query without parentheses, and points out that precedence is left to right, giving the example "human or egg albumin" is interpreted as "(human or egg) and albumin". 2. When using 'Refine Your Query' at RCSB, be cautious with the "but not" option. For example, "protease not proteinase" gives 472 hits, while "protease" refined with [but not "proteinase"] gives 471. 3. In SearchLite/SearchFields, I have found no way to find remarks of a specific number (e.g. "REMARK 800"). It is apparently also impossible to search for a term which includes an underscore, such as "site_identifier" (a term required in REMARK 800). However, "site_identifier" works fine in PDB Lite/3DB Browser, from which you can learn that over 1,700 PDB entries designate functional sites (such as catalytic, regulatory, or metal-binding sites) in SITE records. 4. You can access "PDB 3DB Browser" or PDB Lite from the RCSB SearchLite/SearchFields forms via the link "Other PDB search interfaces and related databases are found here" at the top of either page. Several former BNL sites are updating their databases weekly from the RCSB server, and continuing to offer PDB Lite and 3DB Browser. A list of seven which offer a fully functional PDB Lite with weekly updates is at www.umass.edu/microbio/rasmol/pdblite.htm 5. Don't use "and not" or a leading "not" at RCSB. "milk and not lactalbumin" gives zero hits in SearchLite/SearchFields, while "milk not lactalbumin" works correctly. In PDB Lite/3DB Browser both queries give the same result. "not lactalbumin and milk" also fails in SearchLite/SearchFields, but works correctly in PDB Lite/3DB Browser. 6. Beware of cases where British and American spellings differ. For example "protease" finds 793 entries via RCSB while "protease or proteinase" finds 1099. Another case is "hemoglobin" vs. "haemoglobin". Thanks to Jaime Prilusky, PDB Lite and 3DB Browser automatically search for both spellings when only one term is given, although for reasons unclear to me they come up with a few less hits than does RCSB with the same query. RCSB does not yet deal with alternate spellings automatically. 7. 1A3W and many other entries contain "1,6-bisphosphat". At RCSB they cannot be found with the search term "1,6-bisphos" but they can be found with the term "1, 6-bisphos" (space after comma). However, "1, 6-bisphos" does not occur in the PDB header. Also, "1 6-bisphos" (no comma) finds 1A3W. "1 6 bisphos" finds zero records, thus dashes are required in query terms, and in this instance the comma was tolerated provided it was followed by a space, but the comma was not required. In PDB Lite/3DB Browser, "1,6-bisphos*" is interpreted as "1 or 6-bisphos*" so "6-bisphos*" gives a more useful result; a helpful feature is that search engine's interpretation of your query is always explicitly stated on the result screen of the BNL interface. 8. Be aware that the number of atoms reported on RCSB's Structure Explorer page excludes hydrogens, and in the case of NMR files, is per model, although neither is explictly stated on this page nor on the help page. For example, for 1jsa (24 models) contains 3056 atoms/model, and 1545 non-hydrogen atoms/model; the SE page reports only the latter. Similarly, the X-ray structure 1lfa (which contains modeled hydrogen atoms) contains 4526 atoms, 3257 of which are not hydrogen; the latter is reported on the SE page. Atom counts are not offered by the BNL interfaces. 9. The "residue" count given on the SE page apparently excludes water, but I'm not clear exactly what it is counting. For example 1lfa contains 365 amino acids and 316 HETATM groups, which include 2Mn and 2Cl plus 312 waters. The SE page reports "Residues: 374". Residue counts are not offered by the BNL interfaces. 10. In SearchFields, it is cumbersome to exclude one technique (e.g. excluding "theoretical model" requires "query_term not technique: theoretical model") whereas in 3DB Browser, each technique is an independent checkbox making the exclusion of one easy. However, 3DB browser has only three checkboxes (X-ray, nmr, theory) while RCSB distinguishes nine techniques. 11. When more than a single space character is between terms in a query, all 4 search interfaces respond gracefully: they give the same result as if only a single space had been present. I have by no means made an exhaustive study of the RCSB or BNL search interfaces -- if anomalies or solutions not mentioned above are known to subscribers to this list, please inform us. Also if any of the statements above are not the whole story, please enlighten. Sincerely, -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Alex Garcia Subject: inquiry Date: Sun, 03 Oct 1999 22:51:26 -0500 To: "rasmol@lists.umass.edu" I am trying to call ramol 2.6 from visual basic, so I can use rasmol thru friendly menus, but rasmol 2.6 does not accept this topic (remote control) , however raswin (ver ver 2.5) does allow it but does not load any script, how can I get a 2.5 rasmol ver that may open and run script files (.top) , or where can I get a 2.6 ras ml ver that may be handled with VB? please if my english is not clear enought for explaining this problem just ask I will be more than happy to ask again, cheers X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Alex Garcia Subject: rasmol en =?iso-8859-1?Q?espa=F1ol?= Date: Mon, 04 Oct 1999 01:07:39 -0500 To: "rasmol@lists.umass.edu" por favor a todos los que usen rasmol y hablen español, agradecere sus comentarios, les recuerdo deven leer primero el readme, y tener en cuenta que es una version beta!!!! super BETA!!! sean benevolos!!!! gracias http://www.accefyn.org.co/rasmol/rasmolsp-readme.txt http://www.accefyn.org.co/rasmol/rasmolsp.zip PS es nuestra intencion el hacer mas facil el uso de rasmol, sus comentarios son valiosos, por favor envienos sugerencias, ideas, todo para mejorarlo, gracias de antemano ++++------+------+------+------+------+------+------+------+------+------+ From: Jeff Cohlberg Subject: domains Date: Mon, 04 Oct 1999 08:29:07 -0700 To: rasmol@dhcp-srv2.oit.umass.edu Dear RasMolers, Last Wednesday I sent the following query: "Is there any way to select a domain of a protein? I was examining the file 3GPD (human GA3P dehydrogenase). The header for this PDB file says that there are two domains designated B and C. Can I select them and color them differently? (I can do this by specifying the amino acid residues, but I'd like to know if there's a direct way to select domains.) One of the few features of Cn3D that I prefer to RasMol is that Domain is one of its color schemes." I received three responses, all of which suggested that I "select *b". This doesn't work -- nothing is selected. This command works with chains but not with domains. Also, there are other PDB files with no information in the header about designation of domains, but Cn3D colors the domains differently with no problem. Can I assume from the lack of response that this just can't be done in RasMol? Is Protein Explorer or Swiss-PDB Viewer capable of selecting and color coding domains? Or is Cn3D the only program that will do it easily? Jeff Cohlberg ------------------ Jeffrey A. Cohlberg, Professor Department of Chemistry and Biochemistry California State University, Long Beach 1250 Bellflower Blvd Long Beach, CA 90840 phone: (5620 985-4944 fax (209) 821-4471 X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: AGC Subject: xraswin Date: Mon, 04 Oct 1999 14:34:12 -0500 To: "rasmol@lists.umass.edu" I am trying to load a script file using the rasmol 2.7.1 ver, but does not work.... just can not find any file.... does this ver acept the VB remote control topic? does this ver work with script files? where can I get the source code for the raswin32.exe ver 2.6.4?????? thanks a lot in advance, cheers ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Molecular Visualization Lessons Date: Mon, 04 Oct 1999 18:01:09 -0400 To: edmolvis@dhcp-srv2.oit.umass.edu, rasmol@dhcp-srv2.oit.umass.edu Cc: gharris@wellesley.edu I'm giving a workshop next week (http://www.umass.edu/microbio/chime/workshop/mactlac.htm) and I wanted to put together some ideas for lesson plans. My efforts so far are at http://www.umass.edu/microbio/chime/workshop/lessons.htm If anyone has other ideas to contribute, or specifics for a given lesson which they would be willing to share (perhaps via email only to other profs, not necessarily on the web) please contact me. I'll credit all contributors. For example, I've offered the sequence of the unknown protein which is used in the Amino Acid Quizzer, by email to profs only (http://www.umass.edu/microbio/chime/quizzer/index.htm). So far I've had only one such request. Gary Harris: do you have lists of sequences with information about each which you'd be willing to email to profs on request for the exercise you do at Wellesley? Thanks, -Eric P.S. The 90 participants in the workshops I gave summer 1997-summer 1999 may be interested to know that this will be the first workshop in which I don't use RasMol at all, but instead only the Protein Explorer and Chime. Advantages of the Protein Explorer vs. RasMol for interactive exploration are listed at http://www.umass.edu/microbio/chime/explorer/why_pe.htm#appendix The main 'gap' in the no-RasMol approach is that I haven't worked out or documented in detail a method for creating Chime presentations without using RasMol to save the scripts. Scripts can already be saved from Chime, of course, and run in Protein Explorer from its Project Folder (set in the Preferences). I'm working out the complete details for a future release. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: <37F8243E.B103315F@accefyn.org.co> X-Accept-Language: ca ++++------+------+------+------+------+------+------+------+------+------+ From: Antoni Parra Subject: Re: inquiry Date: Tue, 05 Oct 1999 19:00:02 +0200 To: rasmol@dhcp-srv2.oit.umass.edu I use Chime for that purpose, instead of Rasmol, and control it from a Delphi Pascal program through windows messages. Antonio Alex Garcia ha escrit: > I am trying to call ramol 2.6 from visual basic, so I can use rasmol > thru friendly menus, but rasmol 2.6 does not accept this topic (remote > control) , however raswin (ver ver 2.5) does allow it but does not load > any script, how can I get a 2.5 rasmol ver that may open and run script > files (.top) , or where can I get a 2.6 ras ml ver that may be handled > with VB? please if my english is not clear enought for explaining this > problem just ask I will be more than happy to ask again, cheers References: <37F8243E.B103315F@accefyn.org.co> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: inquiry Date: Tue, 05 Oct 1999 14:14:30 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Because Chime responds to scripts sent via the javascript executeScript() function, this is another way to build user-friendly menus. That is exactly what I'm doing in the Protein Explorer (url below), and I have plans to do much more along these lines. Visual Basic only works in Windows, I believe. Chime works in Windows and Macintosh but not unix. RasMol works on all 3 platform families. At 10/5/99, you wrote: >I use Chime for that purpose, instead of Rasmol, and control it from a >Delphi Pascal program through windows messages. > >Antonio > >Alex Garcia ha escrit: > >> I am trying to call ramol 2.6 from visual basic, so I can use rasmol >> thru friendly menus, but rasmol 2.6 does not accept this topic (remote >> control) , however raswin (ver ver 2.5) does allow it but does not load >> any script, how can I get a 2.5 rasmol ver that may open and run script >> files (.top) , or where can I get a 2.6 ras ml ver that may be handled >> with VB? please if my english is not clear enought for explaining this >> problem just ask I will be more than happy to ask again, cheers > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Lesson plans, ease of use, sharing Chime tutorials Date: Tue, 05 Oct 1999 15:25:12 -0400 To: kowitj@emmanuel.edu (Joel Kowit) Cc: rasmol@dhcp-srv2.oit.umass.edu Joel, I am delighted to hear of the successes you are having with molecular structure visualization in your classes, and I appreciate your sharing your pedagogic strategies. At 10/5/99, Joel Kowit wrote: >1) In the introductory biology class for majors ("Cell & Molecular >Biology"), one of the labs is a RasMol lab held in an IBM classroom. Each >student has their own computer and the instructor computer is projected on >a screen for demonstration. Students have RasMol loaded and a set of pdb >files can be accessed from the server. I introduce mouse and menu >commmands and a few commands to show the use of the command line. They >can access RasMol & pdb files in the student computer lab for practice. A >second lab introduces CHIME using your hemoglobin tutorial. I have a set >of questions I wrote up for this tutorial. I may have sent them to you >last year, but in case I didn't, will send a set in another email. I'd like to see your hemoglobin questions -- they could be posted on the Hb tutorial site with credit to you. I've found that handing out a set of questions on paper (such as those I've included in the antibody and MHC tutorials) makes a good focus for use of these tutorials by students in a computer lab class. I wish someone would contribute such questions for the DNA tutorial. >2) I currently teach the intro biol class in a multimedia class that >includes a P.C. projected on screen, with RasMol & CHIME loaded, and pdb >files available thru our server. It's very convenient, when relevant >questions arise, to be able to bring up a molecule in seconds. For >example, we were discussing cystic fibrosis and I decided on the spot to >bring up the cftr protein (already loaded), select and color phe508 and >show how a change in only a amino acid can cause CF. I'm glad to have learned of this great example from you! What are the PDB ID Codes for the wild type and mutant structures? >3) I have several freshman involved in a RasMol project. The ultimate >goal is to design a tutorial for our intro biol course. The steps include >(1) learning the basics of using RasMol; (2) learning to use CHIME and >going thru some tutorials; (3) sketching out the basic tutorial (goals, >design, etc); (4) Saving RasMol views as scripts; (5) converting to CHIME >(this part I haven't tried yet). Instructions for installing RasMol-saved scripts into a Chime presentation template are at http://www.umass.edu/microbio/chime/prsswc/template.htm Its not very hard and the instructions are very thorough (tested in my workshops) and include troubleshooting for common problems. >I have a couple of questions for you: > >1) Though I have dipped my toes in Protein Explorer, I haven't yet >immersed myself. At first view, Prot Ex doesn't seem as pretty as RasMol. > It seems to take longer, the window with the image can't be resized at >will, the texture of the structure seems courser, and the command line >only allows one to view a single line at a time [I think]. On the other >hand, I've read the reasons you like it better. My question is, in >teaching students the tools of molecular visualization, should one now >start with Protein Explorer, or is it better to begin with RasMol and >switch to Prot Ex when they become more proficient? 1A. Yes, the Protein Explorer, having added thousands of lines of interpreted javascript to Chime, takes a bit longer to load initially. But once loaded, the images move as fast or slightly faster than in RasMol (rotation or zooming). 1B. On Windows computers, the vertical frame boundary can be dragged to change the size of the Chime image, and so can the whole window size be changed, and Chime resizes itself automatically. Unfortunately, this doesn't work as well on Macs. 1C. I'm surprised to hear you say the images don't seem as 'pretty' or have a coarser texture than RasMol. The rendering is identical and as far as I know, the images are identical. I think if you put RasMol next to Chime/Protein Explorer at the same image size you won't see any differences at all. 1D. The command line in Protein Explorer allows you to see 7-12 message lines at once (it autosizes according to the size of your window or screen) and of course you can scroll to older ones. The input slot for the commands is only one line because after you hit Enter, the command appears in the message stream and the command slot is cleared. It would be possible to make a longer message box and I could make the number of lines in it a preference setting if there is demand. I don't find the present size of the message box to be a problem in practice. 1E. PE is easier to use, has more help, and more automation than RasMol. Therefore if anything, one should start students in PE and then when more advanced, go to RasMol. However, there are very few situations which need RasMol since PE can do 99% of what RasMol can do. Here's one example re: ease of use. In my RasMol workshops with college faculty, it took an hour of hands-on training to enable beginners to issue the correct commands in RasMol to find out (i) how many chains are present, (ii) whether any ligands/hetero atoms/water is present, (iii) whether disulfide bonds are present, and (iv) whether multiple (NMR) models are present. Even then, sometimes mistakes were made with new molecules, or people forgot, so this fundamental information was often not completed. In PE, the initial image shows the answers to all of these questions automatically. Add to this: menu for reloading the 10 most recently loaded molecules, explanations of atom identifications, ease of setting up side by side comparisons (Comparator mode) without getting confused about which command window goes with which graphics window, preferences remembered between sessions, command aliases to save typing ('r n w' = 'restrict not water'), convenience buttons for spin off/on, zoom, hide/show hetero atoms/water, changing background color, and the incredibly powerful Select Menu built into Chime, plus the ability to show solvent accessible surfaces. It is now easy to make a page of custom hyperlinks on your class web page, each of which will bring up a prespecified molecule (or pair of molecules) (demonstration page http://www.umass.edu/microbio/chime/explorer/links2pe.htm). Although downloaded molecules work fine, there is no need to download any if you have a fast Internet connection to the Protein Data Bank. >2) Other than your website with CHIME tutorials, is there a single site >where profs can post tutorials they have developed so as to share & to >obtain feedback? Is that a good idea? I think its an excellent idea, and long overdue, and here's one solution we hope to offer soon. We have begun work, at long last, on programming a CGI 'Visitor-Maintained Index' to replace the sadly out of date 'World Index of Animated Tutorials in Chime' at my site (http://www.umass.edu/microbio/rasmol/tutbymol.htm). When implemented sometime later this year, it will allow anyone to submit, via web form, the URL of a tutorial, title and cross-indexing terms, and a description. The HTML indexes (author, subject, site) will be automatically realphabetized after each such contribution. Later on, we hope to provide a mechanism to submit comments and critiques, or ratings, of the indexed Chime resources. For the moment, we have a Guestbook mechanism http://molvis.sdsc.edu/guestbk/guestbkc.htm which allows people to submit URL's and descriptions (but they appear in the order submitted, not in the main index to resources). The advantage of submitting to the guestbook (aside from the liklihood that others will use it!) is that when the VMI is available, we'll email invitations to submit entries to all who have contributed to the guestbook. Thanks for your thoughtful contributions, Joel! -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: <37F8243E.B103315F@accefyn.org.co> <199910051805.OAA13144@marlin.bio.umass.edu> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: AGC Subject: Re: inquiry Date: Tue, 05 Oct 1999 15:14:51 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Eric Martz wrote: > Because Chime responds to scripts sent via the javascript executeScript() > function, this is another way to build user-friendly menus. That is exactly > what I'm doing in the Protein Explorer (url below), and I have plans to do > much more along these lines. > > Visual Basic only works in Windows, I believe. Chime works in Windows and > Macintosh but not unix. RasMol works on all 3 platform families. > > At 10/5/99, you wrote: > >I use Chime for that purpose, instead of Rasmol, and control it from a > >Delphi Pascal program through windows messages. > > > >Antonio > > > >Alex Garcia ha escrit: > > > >> I am trying to call ramol 2.6 from visual basic, so I can use rasmol > >> thru friendly menus, but rasmol 2.6 does not accept this topic (remote > >> control) , however raswin (ver ver 2.5) does allow it but does not load > >> any script, how can I get a 2.5 rasmol ver that may open and run script > >> files (.top) , or where can I get a 2.6 ras ml ver that may be handled > >> with VB? please if my english is not clear enought for explaining this > >> problem just ask I will be more than happy to ask again, cheers > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > The Protein Explorer: www.umass.edu/microbio/chime/explorer > > Eric Martz, Professor (Immunology), Dept Microbiology > Morrill IVN 203, U Mass, Amherst MA US 01003-5720 > 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ thanks a lot for your replys, sure chime alows the definition uf friendly menus, I know that allready, however Chime is a web tool mainly, and the problem and the real situation in Colombia is that the conection to the internet are to slow, of course most of you may say sure but so what just load it from your hard disk....and to this point I must ask and who is gonna develop the menus in chime... so every one may downlooad them..... and one more thing besides the development of menus who is gonna keep developing for special needs?? that this vb menu works only on MS OS is right, and that more than the 90% of all OS installed arround the word are MS products is true as well, well hope that leaves clear all dobuts about what I am trying to do, cheers, and again thanks a lot for your kind replys, cheers ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Molecular Visualization Lessons Date: Wed, 06 Oct 1999 16:20:26 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Comment inserted by Eric: Charles, this is great! A lesson plan already worked out starting from nucleotide sequence thru to 3d structure, complete with detailed instructions for students to use BLAST and PDB. You could change the PDB url to www.rcsb.org, and in a week or two the PDB will make Protein Explorer a viewing option on their View Structure page (initially on a new beta test site). At that point, the old Chime viewer will be called 'FirstGlance in Chime'. Please email me the 'solution' information for your exercise. -Eric >From Charles Sackerson: Eric, I don't know if this is the kind of thing you are looking for, but I put together an exercise for my Molecular Biology class last spring to help them break the ice on web resources for DNA sequence and protein analysis -- it's posted in my folder at (http://www.iona.edu/faculty/csackerson/sequence.htm). The kids had fun with it, and others are welcome to use it. I'd like to expand it to include several classes of proteins -- transcription factors, kinases, tubulin maybe. Comments are welcome, particularly advice! best, Charles Charles Sackerson Department of Biology Iona College New Rochelle, NY 10801 email: csackerson@iona.edu phone: 914-633-2303 FAX: 914-633-2240 rasmol@dhcp-srv2.oit.umass.edu Content-Disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: Will McClure Subject: Re: Molecular Visualization Lessons Date: Wed, 06 Oct 1999 17:54:33 -0400 To: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu, --On Mon, Oct 4, 1999 6:01 PM -0400 Eric Martz wrote: > I'm giving a workshop next week > (http://www.umass.edu/microbio/chime/workshop/mactlac.htm) and I wanted to > put together some ideas for lesson plans. > If anyone has other ideas to contribute, or specifics for a given lesson > which they would be willing to share (perhaps via email only to other > profs, not necessarily on the web) please contact me. I'll credit all > contributors. > >We used a Chime Tutorial for a Biochemistry course this fall that got ~65 students into protein structure: http://info.bio.cmu.edu/courses/03231//chime_tut/chime.html At the bottom of that page is a link to a two-page PDF document ("Chime 2.0 Viewer's Guide") that has terse summaries of the Chime menu items, especially the 2.0 "Select" menu choices. An example of a problem set question and the submitted work of the students can be seen at: http://info.bio.cmu.edu/Courses/03231/psetF99/pset3/PS3Pix/PS3Pix.htm -Will McClure References: ++++------+------+------+------+------+------+------+------+------+------+ From: Phillip Barak Subject: Rasmol/Chime at Educause meeting in Long Beach (Oct 26-29)? Date: Thu, 07 Oct 1999 09:54:02 -0500 To: rasmol@dhcp-srv2.oit.umass.edu As the Educause meeting in Long Beach (Oct 26-29) approaches, it occurs to me to ask this group if there are presentations at that meeting about the use of Rasmol/Chime that participants should be alerted to? Phillip Barak Assoc. Prof., Soil Science Dept of Soil Science University of Wisconsin-Madison 1525 Observatory Dr. Madison, WI 53706-1299 tel: 608-263-5450 fax: 608-265-2595 e-mail: pwbarak@facstaff.wisc.edu web: http://www.soils.wisc.edu/~barak/ ========================================= References: <199910042151.RAA22104@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Brian White" Subject: Re: Molecular Visualization Lessons Date: Thu, 07 Oct 1999 11:34:07 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Eric - I have my lecture presentaitons on hemoglobin & catalase - no lecture notes, just the chime presentaitons. If you are interested, I can e-mail the handouts that I use. The presentaitons are at: http://intro.bio.umb.edu/111-112/111F98Lect/hemoglobin1/hemolect.html http://intro.bio.umb.edu/111-112/111F98Lect/hemoglobin2/hemolect.html http://intro.bio.umb.edu/111-112/111F98Lect/catalase/catlect.html Brian Eric Martz wrote: > I'm giving a workshop next week > (http://www.umass.edu/microbio/chime/workshop/mactlac.htm) and I wanted to > put together some ideas for lesson plans. My efforts so far are at > > http://www.umass.edu/microbio/chime/workshop/lessons.htm > > If anyone has other ideas to contribute, or specifics for a given lesson > which they would be willing to share (perhaps via email only to other > profs, not necessarily on the web) please contact me. I'll credit all > contributors. > > For example, I've offered the sequence of the unknown protein which is used > in the Amino Acid Quizzer, by email to profs only > (http://www.umass.edu/microbio/chime/quizzer/index.htm). So far I've had > only one such request. > > Gary Harris: do you have lists of sequences with information about each > which you'd be willing to email to profs on request for the exercise you do > at Wellesley? > > Thanks, -Eric > > P.S. The 90 participants in the workshops I gave summer 1997-summer 1999 > may be interested to know that this will be the first workshop in which I > don't use RasMol at all, but instead only the Protein Explorer and Chime. > Advantages of the Protein Explorer vs. RasMol for interactive exploration > are listed at > http://www.umass.edu/microbio/chime/explorer/why_pe.htm#appendix The main > 'gap' in the no-RasMol approach is that I haven't worked out or documented > in detail a method for creating Chime presentations without using RasMol to > save the scripts. Scripts can already be saved from Chime, of course, and > run in Protein Explorer from its Project Folder (set in the Preferences). > I'm working out the complete details for a future release. > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > The Protein Explorer: www.umass.edu/microbio/chime/explorer > > Eric Martz, Professor (Immunology), Dept Microbiology > Morrill IVN 203, U Mass, Amherst MA US 01003-5720 > 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://omega.cc.umb.edu/~bwhite/ References: <3.0.2.32.19991007095402.008b2210@facstaff.wisc.edu> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Alex Garcia Subject: Re: Rasmol/Chime at Educause meeting in Long Beach (Oct 26-29)? Date: Thu, 07 Oct 1999 09:51:46 -0500 To: rasmol@dhcp-srv2.oit.umass.edu what is educase meeting? wich is the web for this event? Phillip Barak wrote: > As the Educause meeting in Long Beach (Oct 26-29) approaches, it occurs to me to ask this group if there are presentations at that meeting about the use of Rasmol/Chime that participants should be alerted to? > > Phillip Barak > Assoc. Prof., Soil Science > > Dept of Soil Science > University of Wisconsin-Madison > 1525 Observatory Dr. > Madison, WI 53706-1299 > > tel: 608-263-5450 > fax: 608-265-2595 > e-mail: pwbarak@facstaff.wisc.edu > web: http://www.soils.wisc.edu/~barak/ > > ========================================= References: <3.0.2.32.19991007095402.008b2210@facstaff.wisc.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Phillip Barak Subject: Re: Rasmol/Chime at Educause meeting in Long Beach (Oct 26-29)? Date: Thu, 07 Oct 1999 13:23:10 -0500 To: rasmol@dhcp-srv2.oit.umass.edu At 09:51 AM 10/7/1999 -0500, you wrote: >what is educase meeting? wich is the web for this event? EDUCAUSE (http://www.educause.edu) is an international, nonprofit association whose mission is to help shape and enable transformational change in higher education through the introduction, use, and management of information resources and technologies in teaching, learning, scholarship, research, and institutional management. Membership is open to institutions of higher education, corporations serving the higher education information technology market, and other related associations and organizations. Programs include professional development activities, print and electronic publications, strategic/policy initiatives, research and development, and a wealth of online information services. (Current membership includes more than 1,600 colleges, universities, and education organizations and more than 150 corporations.) About 3000 people are expected at the Educause '99 meeting this year, I'm told, so I'm curious about possible Rasmol/Chime-related presentations. BTW: on Oct 26 at that meeting, I'll be making a poster presentation that will include, among other items, some uses of Chime in my course "Plant Nutrient Management", a soil fertility/plant nutrition course. --PBarak >Phillip Barak wrote: > >> As the Educause meeting in Long Beach (Oct 26-29) approaches, it occurs to me to ask this group if there are presentations at that meeting about the use of Rasmol/Chime that participants should be alerted to? >> >> Phillip Barak >> Assoc. Prof., Soil Science >> >> Dept of Soil Science >> University of Wisconsin-Madison >> 1525 Observatory Dr. >> Madison, WI 53706-1299 >> >> tel: 608-263-5450 >> fax: 608-265-2595 >> e-mail: pwbarak@facstaff.wisc.edu >> web: http://www.soils.wisc.edu/~barak/ >> >> ========================================= > > pdb-l@rcsb.org ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Perils of explorer.exe (and fix) -- Windows only. Date: Fri, 08 Oct 1999 15:49:38 -0400 To: rasmol@dhcp-srv2.oit.umass.edu, edmolvis@dhcp-srv2.oit.umass.edu, If you have not downloaded the Protein Explorer (Chime) package, or if you did so for a Macintosh computer, this message does not apply to you -- please just delete. If you have downloaded the Protein Explorer for use on a Windows computer, read on. In the computer lab for my class, students were asked to download and install the Protein Explorer. One of the downloaded files was named explorer.exe. Some students inadvertantly left a copy of this file (a self-unzipping one) in C:\ (root of primary hard drive). It turns out that when this is done, the computer cannot boot Windows! Windows takes any file named c:\explorer.exe to be the Windows desktop explorer, and the GUI never appears. So if any of your computers became unable to boot after downloading the Protein Explorer files, here's how to fix them: Win95: Early during boot, press F8 several times. If the timing is right, you'll get a text menu titled "Microsoft Windows 95 Startup Menu". Win98: Hold down the control key and power on -- keep Ctrl down until you get the Startup menu. At the Startup menu -- select 'Command prompt only'. Boot will proceed to the C:\ prompt. Enter "del explorer.exe". Power off and reboot. Sorry! The downloadable file has been renamed to protexpl.exe. You don't need to do anything if your computer is happy. If you want to be extra careful, rename the chime\explorer\explorer.exe file (if you kept it) from Protein Explorer to protexpl.exe. But be very careful not to change the file c:\windows\explorer.exe which IS your desktop -- an essential part of windows! (It doesn't actually matter what is the name of the folder in which sit the files unpacked from protexpl.exe. It does matter that the shared files go in a folder named 'shared', and that both folders are at the same level, e.g. c:\chime\protexpl and c:\chime\shared.) -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: Re: Perils of explorer.exe (and fix) -- Windows only. Date: Fri, 08 Oct 1999 20:56:17 -0700 To: rasmol@dhcp-srv2.oit.umass.edu There's actually some fun things you can do with the explorer.exe file (the windows one) for instance you can make the start button say any 5 letter word, as well as have any icon on it. Details are at http://www.annoyances.org/win95/index.html Sorry if this is off subject........... - - - - _ _ _ _ _ "Written laws are like spiders' webs, and like them will only entangle and hold the poor and weak, while the rich and powerful easily break through them. " Anacharsis (Scythian Philosipher) 600 BCE ++++------+------+------+------+------+------+------+------+------+------+ From: "Brian W. Beck" Subject: Multi letter elements Date: Mon, 11 Oct 1999 14:19:55 -0500 (CDT) To: rasmol@dhcp-srv2.oit.umass.edu Greetings rasmolians: I'm using the new rasmol 2.7.1 and I just noticed that in various charmm and pdb files, none of the atoms whose element would have 2 charactes (Na,Cl,Fe...) can be selected with their name (eg."select sodium or chlorine or iron"). I can successfully say "select *.Na or *.Cl or *.Fe" and have the correct atoms selected. I then tried "select fluorine" and sure enough, the Fe was selected. I thought it had to be an issue of which column the atom names where in, but it occurs for me in both charmm and pdb formats (which have different columns and justification conventions for atom name). I tried sliding the atom name forward or backward a column and that didn't help either. Has anyone else run into this? I've skimmed through the code, but I didn't see anything obviously wrong. FYI, I'm running rasmol 2.7.1 on an alpha running Digital UNIX 4.0F. -Brian -- ============================================================== | Brian W. Beck |E-mail Address: beck@uh.edu | | Inst. Molec. Design| | | Univ. of Houston |URL: | | 220 Fleming |http://www.chem.uh.edu/pettitt/beck | | Houston, TX, USA |VOICE (713) 743-3264 | | 77204-5641 |FAX (713) 743-2709 | ============================================================== X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: AGC Subject: inquiry/atcg Date: Thu, 14 Oct 1999 17:25:31 -0500 To: "rasmol@lists.umass.edu" where can I find pdb files of ATG and C?? cheers X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: AGC Subject: chime error Date: Wed, 20 Oct 1999 16:56:44 -0500 To: "rasmol@lists.umass.edu" I am gettiong an error when I open (from my hd) some pages I developed, the error reports an error on npchime.dll do any of you know what does this error mean? cheers ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Model identification while movie is running in Chime Date: Wed, 20 Oct 1999 18:58:08 -0400 To: ben davis Cc: rasmol@dhcp-srv2.oit.umass.edu At 10/20/99, you wrote: > Dear Dr. Martz, > >My name is Ben Davis and I am a research associate at The University of >Iowa. I am trying to put together a web site using Chime. From all the >research I have done on Chime you seem to be an expert. I am having a >problem which I would appreciate if you could help me solve in any way. >I have made a movie in Chime by superimposing many real structures. >What I would like to do next is make a list, next to the movie, of the >names of these structures and when each structure is present in the >movie have its name in the list highlighted in some way. If you have >any suggestions, again, I would greatly appreciate them. Thanks for your >time. > >Sincerely, >Ben Davis > The movie will be a Chime command script, I assume (see example below). In the script you can use javascript commands to call functions which will highlight the desired browser text. For example, if you are using an NMR structured file (are you?) and you've defined a function highlight(n) where n is the text of the current model, restrict model=1 backbone 0.2 javascript highlight(1); delay 2.5 #seconds restrict model=2 backbone 0.2 javascript highlight(2); delay 2.5 #and so forth refresh loop 2.5 #optional, loops entire script (can't specify start of loop other than first command) ('javascript javascript-expression' is a legal script command to Chime) If you are using NMR PDB format, and you load your multi-model file into Protein Explorer, pushing the [Auto] button on the NMR page will run such a movie, displaying the model number of the current model. However I use a different method which is much more complicated. I think the above simpler method will work fine for what you want (I had other needs). BTW, the Combinatorial Alignment site of Shindyalov and Bourne is now 'Protein Explorer cognizant'. This means that you can align as many molecules as you want, display the alignment in PE, and view them as a movie if you wish. Go to PE at the url below and you'll see this option on the second page (below the link for Comparator). -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: www.umass.edu/microbio/chime/explorer Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ References: <199910240403.AAA18657@dhcp-srv2.oit.umass.edu> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Dean Waldow Subject: Chime Mouse Problem on Mac B/W G3? Date: Sun, 24 Oct 1999 00:36:11 -0700 To: rasmol@dhcp-srv2.oit.umass.edu Hi, I am curious if others have noticed strange behavior when using chime 2 on a B/W G3 Mac? I am unable to rotate a molecule properly with the mouse. I am able to rotate it when the mouse is moved left and right but up and down yields magnification and minimization. This only happens on that mac and no other macs I have even using a duplicate copy of chime 2. I have tried downloading it again. I have emailed MDL support and they responded promptly but only to say they don't see that behavior and maybe I am holding down the shift key... 8-). The mac is a blue/white 450MHz G3, 328MRam, OS 8.6, or OSX server with OS8.6 in the blue box. Thanks, Dean W. -- ----------------------------------------------------------------------------- Dean Waldow, Associate Professor (253) 535-7533 Department of Chemistry (253) 536-5055 (FAX) Pacific Lutheran University waldowda@plu.edu Tacoma, WA 98447 USA http://www.chem.plu.edu/waldow.html ----------------------------------------------------------------------------- ---> CIRRUS and the Chemistry homepage: http://www.chem.plu.edu/ <--- ----------------------------------------------------------------------------- References: <199910240403.AAA18657@dhcp-srv2.oit.umass.edu> <3812B6E9.71BD7897@rainier.chem.plu.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: Re: Chime Mouse Problem on Mac B/W G3? Date: Sun, 24 Oct 1999 11:58:18 -0400 To: rasmol@dhcp-srv2.oit.umass.edu >Hi, > >I am curious if others have noticed strange behavior when using chime 2 >on a B/W G3 Mac? I am unable to rotate a molecule properly with the >mouse. I am able to rotate it when the mouse is moved left and right >but up and down yields magnification and minimization. This only >happens on that mac and no other macs I have even using a duplicate copy >of chime 2. I have tried downloading it again. I have emailed MDL >support and they responded promptly but only to say they don't see that >behavior and maybe I am holding down the shift key... 8-). The mac is a >blue/white 450MHz G3, 328MRam, OS 8.6, or OSX server with OS8.6 in the >blue box. > >Thanks, > >Dean W. >-- I have a blue and white Mac G3, 400 mHz, OS 8.6, 64 MB RAM, and this does not happen for me. Rotation is fine in any direction. Have you tried swapping keyboards with a computer on which this does not happen? Frieda Frieda Reichsman Biochemistry and Molecular Biology UMass, Amherst USA X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Fernando Gabriel Ranea Subject: Linux and Rasmol Date: Tue, 26 Oct 1999 00:28:16 -0300 To: rasmol@dhcp-srv2.oit.umass.edu Dear Rasmolers; I want install Rasmol y a PC using Slackware Linux 4.0 but I can´t compile the program. I receive the following message: In file included from rasmol.c:15: rasmol.h:25: warning: `EIGHTBIT' redefined *Initialization*:1: warning: this is the location of the previous definition rasmol.c: In function `FetchCharacter': rasmol.c:497: `WaitSet' has an incomplete type rasmol.c:503: warning: passing arg 2 of `select' from incompatible pointer type rasmol.c:503: warning: passing arg 3 of `select' from incompatible pointer type rasmol.c:503: warning: passing arg 4 of `select' from incompatible pointer type rasmol.c: At top level: rasmol.c:112: storage size of `OrigWaitSet' isn't known rasmol.c:113: storage size of `WaitSet' isn't known make: *** [rasmol.o] Error 1 Where is the problem because the rasmol.h is ok for a "unix" enviroment? Is the new gcc compiler? Sincerely charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 ++++------+------+------+------+------+------+------+------+------+------+ From: "T mehmet" Subject: RE: Linux and Rasmol Date: Tue, 26 Oct 1999 17:57:06 +0200 To: didn't know you could get the source , where from??? > -----Original Message----- > From: owner-rasmol@lists.umass.edu > [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Fernando Gabriel Ranea > Sent: 26 October 1999 05:28 > To: rasmol@dhcp-srv2.oit.umass.edu > Subject: Linux and Rasmol > > > Dear Rasmolers; > > I want install Rasmol y a PC using Slackware Linux 4.0 but I can´t > compile the program. I receive the following message: > > In file included from rasmol.c:15: > rasmol.h:25: warning: `EIGHTBIT' redefined > *Initialization*:1: warning: this is the location of the previous > definition > rasmol.c: In function `FetchCharacter': > rasmol.c:497: `WaitSet' has an incomplete type > rasmol.c:503: warning: passing arg 2 of `select' from incompatible > pointer type > rasmol.c:503: warning: passing arg 3 of `select' from incompatible > pointer type > rasmol.c:503: warning: passing arg 4 of `select' from incompatible > pointer type > rasmol.c: At top level: rasmol.c:112: storage size of `OrigWaitSet' > isn't known > rasmol.c:113: storage size of `WaitSet' isn't known > make: *** [rasmol.o] Error 1 > > Where is the problem because the rasmol.h is ok for a "unix" enviroment? > Is the new gcc compiler? > Sincerely > > ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: RE: Linux and Rasmol Date: Tue, 26 Oct 1999 13:34:05 -0400 (EDT) To: T mehmet Cc: rasmol@dhcp-srv2.oit.umass.edu The question has been posed as the availability of source for RasMol 2.7.1. The complete package is available from mirror sites provided courtesy of the International Union of Crystallography: England: IUCr, Chester, England http://www.iucr.org/iucr-top/cif/software/rasmol/ France: Universite P. et M. Curie, Paris, France http://www.fr.iucr.org/iucr-top/cif/software/rasmol/ Israel: Weizmann Institute of Science, Rehovot, Israel http://www.il.iucr.org/iucr-top/cif/software/rasmol/ South Africa: University of the Witwatersrand, South Africa http://www.za.iucr.org/iucr-top/cifsoftware/rasmol/ Sweden: University of Stockholm, Stockholm, Sweden http://www.se.iucr.org/iucr-top/cif/software/rasmol/ Switzerland: University of Geneva, Geneva, Switzerland http://www.ch.iucr.org/iucr-top/cif/software/rasmol/ USA: SDSC, San Diego, California, USA http://www.us.iucr.org/iucr-top/cif/software/rasmol/ The current version and development version are available from the primary site: http://www.bernstein-plus-sons.com/software/rasmol/ ftp://ftp.bernstein-plus-sons.com/software/rasmol/ ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-516-286-1339 FAX: 1-516-286-1999 ===================================================== X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id PAA28623 ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: Re: Linux and Rasmol Date: Tue, 26 Oct 1999 12:56:29 -0800 To: rasmol@dhcp-srv2.oit.umass.edu At 12:28 AM 10/26/99 -0300, you wrote: >Dear Rasmolers; > >I want install Rasmol y a PC using Slackware Linux 4.0 but I can´t >compile the program. I receive the following message: > (deleted) There's a file of all the old rasmol lists posts on the rasmol site that you can search for "linux" - that's what I did when I had compilation problems...sorry, don't remember seeing this one.... - - - - _ _ _ _ _ "Written laws are like spiders' webs, and like them will only entangle and hold the poor and weak, while the rich and powerful easily break through them. " Anacharsis (Scythian Philosipher) 600 BCE References: <3.0.6.32.19991026125629.00797c00@asis.com> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Fernando Gabriel Ranea Subject: Linux and Rasmol again Date: Tue, 26 Oct 1999 21:21:54 -0300 To: rasmol@dhcp-srv2.oit.umass.edu Hi! Me again. I have downloaded the Rasmol 2.7.1 source file. I have generated the Makefile using the command xmkmf and I have definided rasmol.h for a Unix enviroment with 8 bit. The files compile OK and I have copied the rasmol file to /usr/local/bin directory. But when I want run the file using a terminal window I receive the following message: ... [8-bit version] No suitable display detected And the Rasmol prompt is available for enter the commands. Well, I think that the compilation don´t recognized my graphical interphase but why? Regards, References: <3.0.6.32.19991026125629.00797c00@asis.com> <381645A2.AB6AC10D@dinamica.com.ar> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Mark Brooks Subject: Re: Linux and Rasmol again Date: Tue, 26 Oct 1999 20:48:39 -0400 To: rasmol@dhcp-srv2.oit.umass.edu Hi there! I guess you must be using X-windows in either 16 bit or 32 mode. 8 bit mode is _horrible_ , so I expect you're not using this. Did you install Linux? If so, you would have chosen this yourself.... No matter. You could try pressing CTRL+ALT+F1 at the same time, and a line like: "(**) SVGA: Using 16 bpp, depth 16, color weight 565" should be printed on one of the lines of the console. (Press CTRL+ALT+F7 to get back to X-windows) This message will vary depending on which graphics card and bits per pixel (bpp) that you're using, so use this info to adjust your defines in rasmol.h accordingly. Good luck, Mark. I would try again, but define Fernando Gabriel Ranea wrote: > Hi! > > Me again. I have downloaded the Rasmol 2.7.1 source file. I have generated > the Makefile using the command xmkmf and I have definided rasmol.h for a Unix > enviroment with 8 bit. The files compile OK and I have copied the rasmol file > to /usr/local/bin directory. But when I want run the file using a terminal > window I receive the following message: > > ... > [8-bit version] > > No suitable display detected > > And the Rasmol prompt is available for enter the commands. > Well, I think that the compilation don´t recognized my graphical interphase > but why? > Regards, X-Envelope-To: rasmol@dhcp-srv2.oit.umass.edu X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by dhcp-srv2.oit.umass.edu id WAA29431 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Linux and Rasmol again Date: Tue, 26 Oct 1999 22:51:16 -0400 (EDT) To: Fernando Gabriel Ranea Cc: rasmol@dhcp-srv2.oit.umass.edu Since this is a common problem, I'll answer to the list. There are three flavors of RasMol and three flavors of display -- 8-bit, 16-bit and 24/32-bit. For the current version of RasMol you have to match the RasMol version to the capabilities of the display. If you do an X-windows style build and get "No suitable display detected", you need to redo the build to create a match. Since you have already done "xmkmf" you have a fairly good Makefile. You just have to edit it to put in the correct pixel bit depth. You will find three lines in the Makefile, partway down: # DEPTHDEF = -DTHIRTYTWOBIT # DEPTHDEF = -DSIXTEENBIT DEPTHDEF = -DEIGHTBIT Comment out the EIGHTBIT line and uncomment whichever of the other two matches your display, then make clean make rasmol and you should be home free. -- HJB ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-516-286-1339 FAX: 1-516-286-1999 ===================================================== On Tue, 26 Oct 1999, Fernando Gabriel Ranea wrote: > Hi! > > Me again. I have downloaded the Rasmol 2.7.1 source file. I have generated > the Makefile using the command xmkmf and I have definided rasmol.h for a Unix > enviroment with 8 bit. The files compile OK and I have copied the rasmol file > to /usr/local/bin directory. But when I want run the file using a terminal > window I receive the following message: > > ... > [8-bit version] > > No suitable display detected > > And the Rasmol prompt is available for enter the commands. > Well, I think that the compilation don´t recognized my graphical interphase > but why? > Regards, > > References: X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Fernando Gabriel Ranea Subject: =?iso-8859-1?Q?It=B4s?= working! Date: Wed, 27 Oct 1999 02:04:08 -0300 To: rasmol@dhcp-srv2.oit.umass.edu Hi! Thanks to Herbert, Steve Gill, Marks Brooks and Don Harden for your help. Now, Rasmol 2.7.1 is running in my old Pentium 133 with Slackware Linux 4.0. If you are interesting in microbiology, visit Microbiologia! (outside), my home page: http://www.microbiologia.com.ar Is written in spanish but it has many graphics, includes Chime and VRML. Other question: Is there available (or a project to make it) a chime plugin for Netscape Browser thats works under Linux? I have the Win plugin but Linux is very stable! Regards > Since this is a common problem, I'll answer to the list. There are three > flavors of RasMol and three flavors of display > -- 8-bit, 16-bit and > 24/32-bit. For the current version of RasMol you have to match the RasMol > version to the capabilities of the display. If you do an X-windows style > build and get "No suitable display detected", you need to redo the build > to create a match. Since you have already done "xmkmf" you have a fairly > good Makefile. You just have to edit it to put in the correct pixel bit > depth. > > You will find three lines in the Makefile, partway down: > > # DEPTHDEF = -DTHIRTYTWOBIT > # DEPTHDEF = -DSIXTEENBIT > DEPTHDEF = -DEIGHTBIT > > Comment out the EIGHTBIT line and uncomment whichever of the other two > matches your display, then > > make clean > make rasmol > > and you should be home free. > X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Fernando Gabriel Ranea Subject: =?iso-8859-1?Q?It=B4s?= working Date: Wed, 27 Oct 1999 02:07:10 -0300 To: "rasmol@lists.umass.edu" Hi! Thanks to Herbert, Steve Gill, Marks Brooks and Don Harden for your help. Now, Rasmol 2.7.1 is running in my old Pentium 133 with Slackware Linux 4.0. If you are interesting in microbiology, visit Microbiologia! (outside), my home page: http://www.microbiologia.com.ar Is written in spanish but it has many graphics, includes Chime and VRML. Other question: Is there available (or a project to make it) a chime plugin for Netscape Browser thats works under Linux? I have the Win plugin but Linux is very stable! Regards > Since this is a common problem, I'll answer to the list. There are three > flavors of RasMol and three flavors of display > -- 8-bit, 16-bit and > 24/32-bit. For the current version of RasMol you have to match the RasMol > version to the capabilities of the display. If you do an X-windows style > build and get "No suitable display detected", you need to redo the build > to create a match. Since you have already done "xmkmf" you have a fairly > good Makefile. You just have to edit it to put in the correct pixel bit > depth. > > You will find three lines in the Makefile, partway down: > > # DEPTHDEF = -DTHIRTYTWOBIT > # DEPTHDEF = -DSIXTEENBIT > DEPTHDEF = -DEIGHTBIT > > Comment out the EIGHTBIT line and uncomment whichever of the other two > matches your display, then > > make clean > make rasmol > > and you should be home free. References: <3.0.6.32.19991026125629.00797c00@asis.com> <381645A2.AB6AC10D@dinamica.com.ar> ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: Re: Linux and Rasmol again Date: Wed, 27 Oct 1999 10:11:53 -0800 To: rasmol@dhcp-srv2.oit.umass.edu > > >I would try again, but define > I think he was going to say make your rasmol 16 bit (much nicer). - - - - _ _ _ _ _ "Written laws are like spiders' webs, and like them will only entangle and hold the poor and weak, while the rich and powerful easily break through them. " Anacharsis (Scythian Philosipher) 600 BCE References: <3.0.6.32.19991026125629.00797c00@asis.com> <381645A2.AB6AC10D@dinamica.com.ar> <38164BE7.1CE70DDB@po.cwru.edu> X-Accept-Language: German/Germany, de-DE, en ++++------+------+------+------+------+------+------+------+------+------+ From: Karl Sarnow Subject: Re: Linux and Rasmol again Date: Wed, 27 Oct 1999 20:11:31 +0200 To: rasmol@dhcp-srv2.oit.umass.edu Mark Brooks wrote: > > Hi there! > I guess you must be using X-windows in either 16 bit or 32 mode. 8 bit > mode is _horrible_ , so I expect you're not using this. Did you install Linux? > If so, you would have chosen this yourself.... No matter. > > You could try pressing CTRL+ALT+F1 at the same time, and a line like: > "(**) SVGA: Using 16 bpp, depth 16, color weight 565" > should be printed on one of the lines of the console. (Press CTRL+ALT+F7 to > get back to X-windows) This message will vary depending on which graphics card > and bits per pixel (bpp) that you're using, so use this info to adjust your > defines in rasmol.h accordingly. > > Good luck, > > Mark. > > I would try again, but define > > Fernando Gabriel Ranea wrote: > > > Hi! > > > > Me again. I have downloaded the Rasmol 2.7.1 source file. I have generated > > the Makefile using the command xmkmf and I have definided rasmol.h for a Unix > > enviroment with 8 bit. The files compile OK and I have copied the rasmol file > > to /usr/local/bin directory. But when I want run the file using a terminal > > window I receive the following message: > > > > ... > > [8-bit version] > > > > No suitable display detected > > > > And the Rasmol prompt is available for enter the commands. > > Well, I think that the compilation don´t recognized my graphical interphase > > but why? > > Regards, If you compiled the source for 8 bit, it is necessary to set your X-Terminal to 8 bit as well. You must set the color depth at compilation time. Bad, but reality. Karl -- Dr. Karl Sarnow Teacher at Gymnasium Isernhagen German national co-ordinator of the European Schools Project e-Mail: karl@dadoka.h.ni.schule.de Attention: New URL: http://www.shuttle.schule.de/h/dadoka ++++------+------+------+------+------+------+------+------+------+------+ From: Nehal Patel Subject: Chime surfaces Date: Fri, 29 Oct 1999 09:27:48 -0400 To: rasmol@dhcp-srv2.oit.umass.edu hello, does anyone know if the surfaces Chime can generate for proteins and such can be saved into a file (of some particular format). (I hope it is appropriate to ask Chime questions here?) thanks, nehal __________________________________________________________ Nehal Patel 791 Tremont St., Apt W314 Boston, MA 02118 tel: +617 536-2882 email: nehal@alum.mit.edu http://members.bellatlantic.net/~patelne _________________________________________________ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer available at the PDB Date: Sun, 31 Oct 1999 11:00:07 -0500 To: edmolvis@dhcp-srv2.oit.umass.edu, rasmol@dhcp-srv2.oit.umass.edu Cc: badger@SDSC.EDU, helgew@SDSC.EDU, bourne@SDSC.EDU The Protein Data Bank has begun to offer Protein Explorer from their website. On October 6, they released a new beta test site, beta.rcsb.org. Structures found here through SearchLite or SearchFields offer the Protein Explorer as a viewing option on the View Structure page. Protein Explorer (PE) enables you to view and explore the three-dimensional (3D) structures of any macromolecule, such as proteins, DNA, RNA, carbohydrates, and complexes such as between transcriptional regulatory proteins and DNA, or enzymes and drugs. Protein Explorer is derived from RasMol, but is much easier to use and considerably more powerful (http://www.umass.edu/microbio/chime/explorer/why_pe.htm#appendix), e.g. rolling-probe surfaces colored by distance at contact interfaces, or by molecular electrostatic potential. It includes an extensive tutorial and context-sensitive help. Because it requires Chemscape Chime 2, it works only on Windows 95/98/NT and Macintosh PPC. An advantage for educators is that class websites can easily be constructed which offer prespecified molecules in the Protein Explorer. For example, the following url displays oxyhemoglobin in PE from the beta site: http://beta.rcsb.org/pdb/pe/explorer/pe.htm?id=1hho The first time you go to the above URL, it will take awhile to load all the components of Protein Explorer. The second time, then only delay will be for the structure file itself, as PE will then be in your local cache. For example, after loading the above, take a look at the membrane channel gramicidin (5 NMR structures). http://beta.rcsb.org/pdb/pe/explorer/pe.htm?id=1grm To play these 5 structures as a movie (simulation of thermal motion) click on Explore 1GRM, NMR, Auto. Excerpts from the PDB file header: RESIDUES LEU 4, VAL 6, VAL 8, LEU 10, LEU 12, AND LEU 14 IN EACH CHAIN EXHIBIT THE D CONFIGURATION OF THE AMINO ACID. DIMER FORMED BY TWO RIGHT-HANDED SINGLE-STRANDED BETA-HELIXES WITH 6.3 RESIDUES PER TURN. The beta test site is served only from San Diego. After a month or so to allow reporting of any problems from the beta site, its contents will be moved to the main server (www.rcsb.org), which is mirrored at 3 locations in the USA plus Japan and Singapore. Additional mirror sites are being completed and are expected soon. After Protein Explorer becomes available on the main PDB site later this fall, change the 'beta' in the above URL's to 'www'. Or change 'www.rcsb.org' to any mirror URL, e.g. 'pdb.protein.osaka-u.ac.jp'. The version of PE at the PDB will typically lag slightly behind development at the primary site, www.umass.edu/microbio/chime/explorer. Here you'll find links to EBI's Probably Quaternary Structure site, and the alignment server of Shindyalov and Bourne. For example, you can view the full tetramer constructed from the dimer in 1hho, or the alpha and beta chains of 1hho aligned. Note: Because Microsoft has chosen not to provide full support for Plugins (such as Chemscape Chime), only Netscape, but not Internet Explorer, works correctly with Protein Explorer. This is beyond our control. -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 To unsubscribe from the RasMol Email List, change your address, etc., see ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Re: Protein Explorer available at the PDB Date: Sun, 31 Oct 1999 11:13:16 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Congratulations, Eric! I am sure I echo the feelings of all RasMolluscs and Chimeleons on this list, when I say thanks for all the help you provide to all us molecular modelers and teachers. Cheers! ***************************** "Some people place favorite quotations at the end of their e-mails, but I don't." Anonymous, Greece, 3rd century BC. Gale Rhodes mailto:rhodes@usm.maine.edu http://www.usm.maine.edu/~rhodes/GRHomePage.html Professor of Chemistry Chemistry Department University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 Phone: (207)780-4734 Fax: (207) 228-8288 X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id RAA04840 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Chime problem Date: Fri, 05 Nov 1999 17:12:13 -0500 To: Janos Angyan Cc: rasmol@dhcp-srv2.oit.umass.edu I have never seen the message "Sorry, no elemnet tables are available". Does this appear on Chime's menu?? Or in a Netscape box? I am copying this to the email list (see URL below) in case someone else has an answer. At 11/5/99, you wrote: >Hello, > >I have some problems with chime: I have installed CHIMEHOW, and >when I open the main menu the following message appears: >"Sorry, no elemnet tables are available" (3 times). >Similarly in http://www.umass.edu/microbio/chime/atp.pdb >the same message appears, and nothing is deisplayed. >In the mean time some other chime applications (display of >molecules in a web page) work correctly. >Could you help me? > >Thanks > Janos >-- >--------------------------------------------------------------- >János Ángyán e-mail: Janos.Angyan@lctn.u-nancy.fr >Lab. Chimie théorique Université Henri Poincaré >B.P. 239 54506 Vandoeuvre-lès-Nancy FRANCE >tel: +33-(0)3.83.91.25.29 fax: +33-(0)3.83.91.25.30 >--------------------------------------------------------------- > - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE OR UNSUBSCRIBE, GO TO THE ABOVE ADDRESS. charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2120.0 ++++------+------+------+------+------+------+------+------+------+------+ From: "Michael Bruist, PhD" Subject: RE: Chime problem Date: Sun, 7 Nov 1999 11:08:20 -0500 To: Guillermo, I have a conflict on Moday. I am the speaker at the Sigma Xi discussion group. I annot make it to the meeting. My talk should be over by 4:45. Mike -----Original Message----- Behalf Of Eric Martz Sent: Friday, November 05, 1999 5:12 PM From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu] On Subject: Re: Chime problem To: Janos Angyan Cc: rasmol@dhcp-srv2.oit.umass.edu I have never seen the message "Sorry, no elemnet tables are available". Does this appear on Chime's menu?? Or in a Netscape box? I am copying this to the email list (see URL below) in case someone else has an answer. At 11/5/99, you wrote: >Hello, > >I have some problems with chime: I have installed CHIMEHOW, and >when I open the main menu the following message appears: >"Sorry, no elemnet tables are available" (3 times). >Similarly in http://www.umass.edu/microbio/chime/atp.pdb >the same message appears, and nothing is deisplayed. >In the mean time some other chime applications (display of >molecules in a web page) work correctly. >Could you help me? > >Thanks > Janos >-- >--------------------------------------------------------------- >János Ángyán e-mail: Janos.Angyan@lctn.u-nancy.fr >Lab. Chimie théorique Université Henri Poincaré >B.P. 239 54506 Vandoeuvre-lès-Nancy FRANCE >tel: +33-(0)3.83.91.25.29 fax: +33-(0)3.83.91.25.30 >--------------------------------------------------------------- > - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE OR UNSUBSCRIBE, GO TO THE ABOVE ADDRESS. ++++------+------+------+------+------+------+------+------+------+------+ From: john nixon Subject: Problems running Chime from a remote server Date: Tue, 9 Nov 1999 11:36:04 +0000 To: rasmol@dhcp-srv2.oit.umass.edu Can anyone help? I have sent some chime based web pages to a remote server. My local copy works without trouble, and I don't have any problems running Chime based material from anywhere else on the Net. From the remote server, here I have used the embed command I just get a 'plug-in request icon', and where I have used text files given the file extension .spt to request .pdb files from the same folder all that appears in the window is a copy of the text of the file - Chime is not called up by .spt (nor does the script call up the .pdb file.) Links to Chime material on other servers from these same pages work without problem. I don't know if the problem lies in the way I've written and assembled the material, or in the way I transmitted it to the server (as a zip file with my MIME box ticked), or with the configurations on the server. If the problem lies within my material (or the configuration of my PC) I am clearly embarrassed to cause aggro to folk trying to help at the remote server: if the problem lies with the server configurations I don't want to cause them embarrassment, but have no personal experience to call on (the remote server, a UNIX system I believe, does not routinely use Chime - I don't even know if they have access to it on their machines.) If anyone has run into similar problems I'd be glad to benefit from their experience. Many thanks, John Nixon -- john nixon Content-Disposition: inline X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id HAA15704 ++++------+------+------+------+------+------+------+------+------+------+ From: "Peter Birch" Subject: Problems running Chime from a remote server -Reply Date: Tue, 09 Nov 1999 12:05:11 +0000 To: rasmol@dhcp-srv2.oit.umass.edu John Nixon asked about problems with Chime files not being recognised properly when sent from a remote server. It sounds to me as if the remote server doesn't have the Chime file types (PDB, SPT etc.) set up in its Mime type database. If that's the case it would send them to the browser as its default Mime type (usually text/plain) and that would have the effect of the browser displaying the files as text as you've described. If you look under Help/About Plugins in Netscape you should see a list of all the file types that Chime can interpret and the associated Mime types. I don't imagine the Webmaster at the remote server would object to your asking them to be added. Peter Birch ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Problems running Chime from a remote server Date: Tue, 09 Nov 1999 12:54:41 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Dear John Nixon: Your problem is probably the most frequently asked question at this list. Please see the answer to FAQ #1 in the Martz FAQ list www.umass.edu/microbio/rasmol/faq.htm -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE OR UNSUBSCRIBE, GO TO THE ABOVE ADDRESS. ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RasMol/UMass website stats for past year Date: Tue, 09 Nov 1999 13:18:26 -0500 To: rasmol@dhcp-srv2.oit.umass.edu During the past academic year (Sept 1998 through Aug 1999), 191,000 "people" (distinct IP addresses) from over 100 countries visited the RasMol Home Page/Molecular Visualization Freeware/UMass Chime Resources website (www.umass.edu/microbio/rasmol or www.umass.edu/microbio/chime), requesting 5,000,000 file fetches. Roger Sayle's RasMol 2.6b2a program was downloaded 94,000 times. The RasMol downloads were 15% for Macintosh and 85% for Windows; the Mac percentage has been declining steadily from a high of 36% in 1995-6. (I have no count for unix since binaries are not offered at the site; the source code was downloaded 1,500 times.) Educational "movie" scripts for RasMol were downloaded 6,300 times, and Chime tutorial packages 12,000 times, for a total of over 18,000 downloads of Martz-authored educational packages. When last checked (about a year ago) the majority of downloaders were educators. Of the newer resources on the Chime page, the most popular was the Noncovalent Bond Finder. Its main page (index.htm) was visited 22,000 times by 4,800 people. Most probably didn't have Chime installed, or weren't using Netscape: only about 1,000 people used it (for about 5,000 sessions). The Protein Explorer was available for beta test only, not publically linked, for most of the year. Its main page was visited by 1,900 people, about 400 of whom used it. This email list increased by 100 subscribers, from 380 to 480. Traffic increased from 7 to 12 messages/week. The columns in this table line up if you display it in a fixed-pitch font (Courier). RASMOL HOME PAGE STATISTICS -------------------------------------------------------------- 95-6 96-7 97-8 98-9 Total -------------------------------------------------------------- Filed fetched, millions: 0.6M 1.9M 3.4M 5.0M 11M People*, thousands: 30K 90K 127K 191K 438K RasMol Downloads: 5K 41K 67K 94K 207K % Macintosh: 36% 20% 18% 15% "Movie" script downloads: 1.5K 4.5K 5.2K 6.3K 17.5K Chime tutorial downloads: 0 2.4K 6.8K 12K 21K People*/week 3.1- 4.0- 4.3K 6.4K Email Subscribers, August 200 290 380 480 ------------------------------------------------------------- * "People" defined as distinct IP addresses. During October and November 1999, the site has been visited by 7,700 people/week. -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE OR UNSUBSCRIBE, GO TO THE ABOVE ADDRESS. ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: RasMol/UMass website stats for past year Date: Tue, 9 Nov 1999 16:03:10 -0500 (EST) To: rasmol@dhcp-srv2.oit.umass.edu Cc: rasmol@dhcp-srv2.oit.umass.edu On the basis of checking the most recent week for one of the multiple RasMol 2.7.1 (the current release) sites: If we consider Unix, Windows and Mac downloads, of more than 500 downloads from this one 2.7.1 site, the splits are approximately 38% Unix, 38% Windows and 24% Mac. The current "hot" download for Unix is the Linux binary (3/4 of the Unix downloads). If we consider only the Windows and Mac downloads of RasMol 2.7.1, the Windows version downloads are about 62% of the subtotal and the Mac version downloads are about 38% of the subtotal. We will post more detailed statistics after the end of the calendar year. -- H. J. Bernstein ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== ++++------+------+------+------+------+------+------+------+------+------+ From: john nixon Subject: Rubisco mechanism feedback request Date: Sun, 14 Nov 1999 17:59:16 +0000 To: rasmol@dhcp-srv2.oit.umass.edu Hi folks, I have just completed the first draft of a Chime based project which explores the mechanism of the enzyme Rubisco. Designed as an introduction and tutorial, the site is described as 'an experiment in molecular visualisation'. I would value informed constructive criticism from any experienced chime users with the time and interest. The project is at: http://pps99.cryst.bbk.ac.uk/projects/jnixon/Title_Page.html Many thanks -- john nixon ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: We're 500 strong Date: Mon, 15 Nov 1999 13:36:49 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Today the subscribers to this list reached 500 for the first time. -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE OR UNSUBSCRIBE, GO TO THE ABOVE ADDRESS. References: <199911151825.NAA22689@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: Re: We're 500 strong Date: Mon, 15 Nov 1999 12:53:55 -0800 To: rasmol@dhcp-srv2.oit.umass.edu On Mon, 15 Nov 1999, you wrote: > Today the subscribers to this list reached 500 for the first time. And the repository of back issues on the rasmol home page is an incredible resource.....often I've found solutions to problems by loading the pages & using the search page function of netscape. Thanks again everyone...... rendering in 3d studio max, electric image, Content-Disposition: inline X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id UAA07611 ++++------+------+------+------+------+------+------+------+------+------+ From: "Jill Blue LIN" Subject: is rasmol capable of exporting 3d mesh files for use in Date: Wed, 17 Nov 1999 17:10:59 -0800 To: is rasmol capable of exporting 3d mesh files for use in rendering in 3d studio max, electric image, etc.? i would like to use the models created for rasmol, and render them in a more sophisticated rendering program. Jill Blue Lin phone: 415-536-2212 fax: 415-536-2323 References: ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: Re: is rasmol capable of exporting 3d mesh files for use in rendering in 3d studio max, electric image, Date: Thu, 18 Nov 1999 09:45:06 -0800 To: rasmol@dhcp-srv2.oit.umass.edu On Wed, 17 Nov 1999, you wrote: > is rasmol capable of exporting 3d mesh files for use in rendering in 3d studio max, electric image, etc.? i would like to use the models created for rasmol, and render them in a more sophisticated rendering program. > No, bit it does export povray pov files which (if I'm not mistaken) can be converted into 3d files........... References: <99111809455300.00624@localhost.localdomain> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: David Fahrney Subject: Chime tutorials and WebCT Date: Thu, 18 Nov 1999 11:52:01 -0700 To: rasmol@dhcp-srv2.oit.umass.edu Hello, Has anyone tried to use Chime as direct application in WebCT? Dave Fahrney Professor of Biochemistry Colorado State University charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 ++++------+------+------+------+------+------+------+------+------+------+ From: "Henry Brzeski" Subject: RE: Chime tutorials and WebCT Date: Fri, 19 Nov 1999 08:27:32 -0000 To: Dave >Has anyone tried to use Chime as direct application in WebCT? If you mean direct feedback by picking up Chime messages and then relaying these back to users as constructive comments then I have *started* to do this ie I have shown it is possible. See http://www.herts.ac.uk/natsci/Bio/cube99/pst.htm It *is* possible but just takes a lot of writing. I have volunteered to develop this idea for somebody after Christmas so watch this space. h Henry Brzeski Department of Biosciences University of Hertfordshire College Lane Hatfield AL10 9AB Phone +44 (0)1707 284554 Fax +44 (0)1707 285046 References: <000001bf3267$ecef76c0$19c7c593@HenryBrzeski.herts.ac.uk> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: David Fahrney Subject: Re: Chime tutorials and WebCT Date: Fri, 19 Nov 1999 11:31:35 -0700 To: rasmol@dhcp-srv2.oit.umass.edu Henry, Your URL very much appreciated. Your work is very nice, indeed. Now that I know that it *is* possible, I may try to develop something less elaborate than what you have done. Many thanks, Dave Henry Brzeski wrote: > > Dave > > >Has anyone tried to use Chime as direct application in WebCT? > > If you mean direct feedback by picking up Chime messages and then relaying > these back to users as constructive comments then I have *started* to do > this ie I have shown it is possible. See > http://www.herts.ac.uk/natsci/Bio/cube99/pst.htm > > It *is* possible but just takes a lot of writing. I have volunteered to > develop this idea for somebody after Christmas so watch this space. > > h > > Henry Brzeski > Department of Biosciences > University of Hertfordshire > College Lane > Hatfield > AL10 9AB > > Phone +44 (0)1707 284554 > Fax +44 (0)1707 285046 ++++------+------+------+------+------+------+------+------+------+------+ From: "Craig T. Martin" Subject: RasMac_PPC_32BIT - slow? Date: Mon, 22 Nov 1999 10:14:45 -0500 To: rasmol@dhcp-srv2.oit.umass.edu I have recently downloaded Rasmol 2.7.1 for the Mac (RasMac_PPC_32BIT) from Bernstein and Sons. I have a fairly big molecule that I play with it, and this version of Rasmol seems much slower in simple cursor-drag rotation than earlier versions (2.6.4, which says it's an 8 bit version). Interestingly, a large script seems to run faster with the new version, while manual rotation is slower. I'm running a 400 Mhz G3. Has anyone else seen this? Is this a compilation issue (I downloaded pre-compiled versions, so it's not me). (If this message appears twice, my apologies. Trouble with the listserver...). Craig T. Martin Associate Professor Department of Chemistry University of Massachusetts Lederle Graduate Research Tower, Box 34510 Amherst, MA 01003-4510 413-545-3299 Voice 413-545-4490 FAX CMartin@Chem.UMass.edu http://www.chem.umass.edu/~cmartin/ ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: RasMac_PPC_32BIT - slow? Date: Mon, 22 Nov 1999 10:53:41 -0500 (EST) To: "Craig T. Martin" Cc: rasmol@dhcp-srv2.oit.umass.edu Yes, the 32-bit version is slower than the 8 bit version. The 8-bit version is still available, but the 32 bit version makes prettier pictures. It should also be noted that the mac versions of RasMol choke on large memory demands more often than the Unix versions. There are special large memory versions available which are not suitable for small memory macs, but which run faster on mac with lots of real memory. See: ftp://ftp.bernstein-plus-sons.com/software/RasMol_2.7.1.MAC_BIG -- H.J. Bernstein ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Mon, 22 Nov 1999, Craig T. Martin wrote: > I have recently downloaded Rasmol 2.7.1 for the Mac > (RasMac_PPC_32BIT) from Bernstein and Sons. I have a fairly big > molecule that I play with it, and this version of Rasmol seems much > slower in simple cursor-drag rotation than earlier versions (2.6.4, > which says it's an 8 bit version). Interestingly, a large script > seems to run faster with the new version, while manual rotation is > slower. > > I'm running a 400 Mhz G3. Has anyone else seen this? Is this a > compilation issue (I downloaded pre-compiled versions, so it's not > me). > > (If this message appears twice, my apologies. Trouble with the listserver...). > > Craig T. Martin > Associate Professor > Department of Chemistry > University of Massachusetts > Lederle Graduate Research Tower, Box 34510 > Amherst, MA 01003-4510 > > 413-545-3299 Voice > 413-545-4490 FAX > > CMartin@Chem.UMass.edu > http://www.chem.umass.edu/~cmartin/ > ++++------+------+------+------+------+------+------+------+------+------+ From: dank@hq.lindsayelec.com (Dan Kolis) Subject: Rasmol and Ray tracing output Date: Mon, 22 Nov 1999 13:26:09 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Cc: a.mueller@icrf.icnet.uk, JILL_BLUE_LIN@bararch.com Jill LIN asked: >is rasmol capable of exporting 3d mesh files for use in rendering >in 3d studio max, electric image, etc.? I would like to use the >models created for rasmol, and render them in a more >sophisticated rendering program. >Jill Blue Lin >phone: 415-536-2212 >fax: 415-536-2323 Dan Kolis says: There is a version of Rasmol (Not an "official" version, but official is an old fashioned idea anyway), which exports to Povray. Povray overview at: http://www.povray.org/ a.mueller@icrf.icnet.uk did the port to it. He is CCed in as above. Others might be able to give you ideas so I emailed to the reflector too. Povray is free and makes better images than 3D studio. Its uses real Ray tracing, not Z-Buffering. I haven't kept track of the state of the art from Autodesk, but Povray is usually the tool of choice, no kidding around with surfaces that look waxy. Povray is NOT easy to work. When you first run it, results will be dissappointing. Everything is defaulted to crummy to get it to work once so you can grasp how it works at all. However, 4 hours later, you will be making startling rendered images, just amazing! When you say 'mesh' right away I think usually biomolecular images are full of sphere's. Any mesh.ex Bezier, etc won't look as perfect as exporting and rendering spheres. I wouldn't mind helping with the Pov-ray OP. You could perhaps email me the script and I'll do a test image(s) returned as lovely Tiff's or JPG's. Id rather not be drawn into a big porgramme, but if its only a few images, I'll help for sure if I can. Cool Dan K Dan Kolis - Lindsay Electronics Ltd dank@hq.lindsayelec.com 50 Mary Street West, Lindsay Ontario Canada K9V 2S7 (705) 324-2196 Phone (705) 324-5474 Fax Ext: 272 (888) 326-5654 Pager Anywhere (888) DANKOLIS {Same as above} An ISO 9001 Company; Certificate 950-97-0136 T.U.V. America SCTE Member ISM-127194 Some Email for professional correspondence is reflected automatically to mail reflectors via Blind carbon copy. If this is not suitable for your correspondence, please instead email danknocopies@hq.lindsayelec.com /Document end X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Boshoff Subject: Radii Date: Tue, 23 Nov 1999 13:38:35 -0500 To: Rasmol List Hi Is there a way to edit the radius that Rasmol uses for the atoms that it reads in? I have a united atom model of a polymer and would like to know how I can create pdb files where Rasmol shows the VdW radius of the united atoms. Is there a way one can modify the database that Rasmol gets the radii from so that you can create new atom names, for example? Thanks Jan Boshoff ++++------+------+------+------+------+------+------+------+------+------+ From: "Brian W. Beck" Subject: Re: Radii Date: Tue, 23 Nov 1999 13:48:23 -0600 (CST) To: rasmol@dhcp-srv2.oit.umass.edu Jan Boshoff wrote: > > Hi > > Is there a way to edit the radius that Rasmol uses for the atoms that it > reads in? I have a united atom model of a polymer and would like to > know how I can create pdb files where Rasmol shows the VdW radius of the > united atoms. > > Is there a way one can modify the database that Rasmol gets the radii > from so that you can create new atom names, for example? > > Thanks > Jan Boshoff > Jan: The atom radii are in structure "ElemStruct" in the file abstree.h. I've edited mine to use values derived from the CHARMM22 forcefield. Herbert/Roger/Rasmol Community: This is a common problem. Wouldn't a method of changing the radii (or other properties) without recompiling be beneficial? -Brian -- ============================================================== | Brian W. Beck |E-mail Address: beck@uh.edu | | Inst. Molec. Design| | | Univ. of Houston |URL: | | 220 Fleming |http://www.chem.uh.edu/pettitt/beck | | Houston, TX, USA |VOICE (713) 743-3264 | | 77204-5641 |FAX (713) 743-2709 | ============================================================== ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Radii Date: Tue, 23 Nov 1999 16:53:21 -0500 To: rasmol@dhcp-srv2.oit.umass.edu At 11/23/99, Jan Boshoff wrote: >Is there a way to edit the radius that Rasmol uses for the atoms that it >reads in? I have a united atom model of a polymer and would like to >know how I can create pdb files where Rasmol shows the VdW radius of the >united atoms. One method is to create a script with the radii you prefer, then run it on any molecule (instead of using the menu's Display, Spacefill). For example (using meaningless numbers just for an example): select carbon spacefill 2.0 select nitrogen spacefill 2.2 select hydrogen spacefill 0.8 select oxygen spacefill 1.0 Provided your united atoms are selectable in appropriate categories (and if not, modify the PDB file to make them selectable), this will work in your case. To specify the radii in Angstroms, you MUST INCLUDE A DECIMAL POINT. Without one (e.g. "2") RasMol interprets the value in different units. The same method works in Chime. -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 RasMol Email List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Date: Tue, 23 Nov 1999 13:48:15 -0800 To: rasmol@dhcp-srv2.oit.umass.edu > Jan: > > The atom radii are in structure "ElemStruct" in > the file abstree.h. I've edited mine to use values > derived from the CHARMM22 forcefield. > > Herbert/Roger/Rasmol Community: > This is a common problem. Wouldn't a method of > changing the radii (or other properties) without > recompiling be beneficial? > Well, you can do it on a per molecule basis by using the spacefill command, and creating a script that sets the spacefill for each element.....I've done this when I wanted to animate certain atoms expanding or contracting. You can set spacefill to any value (eg spacefill 0.1 or spacefill 9.5) and the selected atoms will become the size indicated.................Cheers! ++++------+------+------+------+------+------+------+------+------+------+ From: Seth Harris Subject: PovRay orientation matrix on Mac Date: Tue, 23 Nov 1999 16:47:47 -0800 To: rasmol@dhcp-srv2.oit.umass.edu Dear all, With recent mailings of POVray output from Rasmol I thought I'd give it a go. This resulted in a few questions, the main one being that while Arne Mueller reported that Windows uses a different coordinate system than unix it sounded to me that the Mac output should match the orientation seen in the RasMol window from which it is derived. This does not seem to be the case. It seems to be rotated close to 180 and also skewed at some angle as near as I can tell, so the centering is different as well. Before I got too involved and confused myself more I thought I might check if this was a known problem? I'm using a recent download of RasMol 2.7.1 with the command "write povray3 outfile" and POVRay 3.1, though if I set PovRay to read earlier versions the results are the same. Also, I notice that the order of items in the "camera" command output by RasMol are not consistent with what is recommended by POVRay, specifically that the "up" and "right" commands come after the "look_at" command, but switching the order to the recommended one, while producing a different orientation of the final image, did not produce the correct one. The problem is of course complicated by the fact that the position of the perceived image can be affected by both the camera position and the matrix command in the POVRAY file produced by RasMol, so I'm not sure which (or both?!) is right or wrong, and hence this request to someone with more than one day of experience with povray and its interface with Rasmol...Arne??? I'd also like to thank all of you who have worked on RasMol and its derivatives and supplements for a truly useful tool, and in direct relation to this message thanks to Arne Mueller for the povray output stuff. I also read in the archives that while the ribbons and cartoons were not yet supported there were some plans for it pending changes to how these objects were generated in RasMol...any breaking news on that if it's not too pestering to ask? Also, Arne, one of your messages mentions that different representations of a molecule can be combined under a single orienting matrix citing for example a translucent molecular surface over a ball and stick model. This piqued my curiosity as to what other common crystallography graphics applications (e.g. ones that create molecular surfaces) also generate povray output seeing as RasMol doesn't have extensive surface modelling features (and while Chime does it doesn't allow such output...?) In closing, sorry for the verbose nature of my mail, but thought it would help to thoroughly describe the situation and if it turns out to be something simple that I've missed I apologize in advance...I tried to be thorough in checking README files and archives! Cheers and thanks, seth ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Seth Harris Botchan Lab UC Berkeley (510)642-5932 Beauty is truth (unpublished results), truth beauty (data not shown). That is all ye know on earth and all ye need to know. References: X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Arne Mueller Subject: Re: PovRay orientation matrix on Mac Date: Wed, 24 Nov 1999 21:36:40 +0000 To: rasmol@dhcp-srv2.oit.umass.edu, sharris@uclink4.berkeley.edu Seth Harris wrote: > > Dear all, > With recent mailings of POVray output from Rasmol I thought I'd give it a > go. This resulted in a few questions, the main one being that while Arne > Mueller reported that Windows uses a different coordinate system than unix > it sounded to me that the Mac output should match the orientation seen in > the RasMol window from which it is derived. This does not seem to be the > case. It seems to be rotated close to 180 and also skewed at some angle as > near as I can tell, so the centering is different as well. Before I got > too involved and confused myself more I thought I might check if this was a > known problem? I'm using a recent download of RasMol 2.7.1 with the > command "write povray3 outfile" and POVRay 3.1, though if I set PovRay to > read earlier versions the results are the same. Also, I notice that the > order of items in the "camera" command output by RasMol are not consistent > with what is recommended by POVRay, specifically that the "up" and "right" > commands come after the "look_at" command, but switching the order to the > recommended one, while producing a different orientation of the final > image, did not produce the correct one. The problem is of course > complicated by the fact that the position of the perceived image can be > affected by both the camera position and the matrix command in the POVRAY > file produced by RasMol, so I'm not sure which (or both?!) is right or > wrong, and hence this request to someone with more than one day of > experience with povray and its interface with Rasmol...Arne??? Hi All, When i've developed the code for povray version 3 in rasmol I've only tested it on unix (where I've done all the developement work) and on winNT&95 and the tests failed on the windows. The molecule in in the povray output under window has is in the wrong transformation. Obvioulsy this also affects the Mac :-( (which I haven't tested). One has to adjust the generation of the transformation matrix in scrit.c (POVWriteHeader). Probally one has to insert some #ifdef INVERT prepocessor directives to cope with windows, mac and unix (like in function WritePOVRayFile for povray version 2.2 output). Anyway the different graphics systems seem to have different coordinate systems :-( . I'm afraid I cannot fix the problem in the near future so the povray 3 stuff will be a privilege of the unix/linux users. I remember it was an awful pain to implement the correct rotation matrix in combination with camera and 'look_at' and it took me a long time to get it working under unix. And now it turned out to be exclusively working under unix. I'm sorry for this! > I'd also like to thank all of you who have worked on RasMol and its > derivatives and supplements for a truly useful tool, and in direct relation > to this message thanks to Arne Mueller for the povray output stuff. I > also read in the archives that while the ribbons and cartoons were not yet > supported there were some plans for it pending changes to how these objects > were generated in RasMol...any breaking news on that if it's not too > pestering to ask? Also, Arne, one of your messages mentions that different > representations of a molecule can be combined under a single orienting > matrix citing for example a translucent molecular surface over a ball and > stick model. This piqued my curiosity as to what other common > crystallography graphics applications (e.g. ones that create molecular > surfaces) also generate povray output seeing as RasMol doesn't have > extensive surface modelling features (and while Chime does it doesn't allow > such output...?) The stroy is that I was working together with Roger Sayle for a while. Roger had a program to display surfaces generated by the Grasp programm. That programm was an incredibly fast viewer without using OpenGL! To get realy nice surfaces I implemented povray output for that program. Those days I've used a completey different system to generate povray output in rasmol (the display coordinates without using an explicit transformation matrix). Because we wanted to combine the povray files from the surfaces with output comming from rasmol (e.g. stricks) I've implemented the rasmol povray filter in a way that it uses the 'world coordinates' (the original coordinates from the pdb file) in combination with a transformation matrix that resembles the current transformation of the molecule in rasmol. We were able to combine both povray files showing a stick model from rasmol under a glassy surface. The advantage of using the original pdb coordinates and then apply an explicit transformation to the coordinates is that you can combine a pobvray representation of a molecule using rasmol (or another program that saves povray output with the original coordinates) with another one of e.g. the same pdb-file irrespective of the rotation, zoom etc . You simply add an 'include' line with the second file to the '.pov' file of the first file. Both representations will then have the same rotation, magnification and translation. In fact using the rasmol spacefill presentation of a molecule and generate a slightly transparent surface looks ugly. This is because the complete atom is rendered not only it's surface. In the end I'm not happy anymore with the current implementation of the povray code in rasmol because of the trouble with windwos (and now mac) and with an implementation of 'slab mode'. The problem with slabbing is the combination of a slab-plane to clip the parts of the molecuel in combination with the transformation matrix (I guess my mathematics is not good enough ;-( ). Anyway nowerdays I think it's more clever to use transformed coordinates instead of the matrix since obviously nobody uses the facility to combine different representation of one pdb-file. Alas, I don't have the time to go deeply in that povray/rasmol stuff - so so it'll stay buggy :-( unless someone else ... The reason why there's no support for the smoothed presentations like cartoons and trace in rasmol is that there's no direct access to the elements building these representations. In other programs the triangels building the cartoons are stored in a bifg array - rasmol calculates these somehow 'on the fly' and so it's difficult to write output filters because you cannot access the relevant data. I don't think there's someone spending work at the moment to change that. I've thought about a way of 'emulating' the cartoons in povray by giving the povray program the job of interpolating between the backbone atoms of the molecule but I haven't done any work on that and I don't think that's a long term solution since the output will be different from that of rasmol. > In closing, sorry for the verbose nature of my mail, but thought it would > help to thoroughly describe the situation and if it turns out to be > something simple that I've missed I apologize in advance...I tried to be > thorough in checking README files and archives! Obviously you've read the archives carefully and I'm afraid it's nothing simple :-( thanks for your interest, Arne -- Arne Mueller Biomolecular Modelling Laboratory Imperial Cancer Research Fund 44 Lincoln's Inn Fields London WC2A 3PX, U.K. phone : +44-(0)171 2693405 | fax :+44-(0)171-269-3534 email : a.mueller@icrf.icnet.uk | http://www.icnet.uk/bmm/ References: <383C5A68.17257B61@icrf.icnet.uk> X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Soerge Kelm Subject: Re: PovRay orientation matrix on Mac Date: Thu, 25 Nov 1999 05:33:11 +0100 To: rasmol@dhcp-srv2.oit.umass.edu Dear All interested in PovRay presentations, I have followed the discussion on this topic. I have never tried to generate PovRay files with RasMol or chime which I am basically using for teaching. To generate nice pictures of proteins in PovRay, I am using the PDB-viewer from GlaxoWellcome (v3.5b4). http://www.expasy.ch/spdbv/mainpage.html This offers a save as Pov file. After playing around with the "illumunation and camera" settings, this works fine even for me not knowing a anything about programming. It works for space filled and for cartoon models. Soerge Both programs run without problems under Windows NT 4.0 (SP 5 installed). -- Soerge Kelm Biochemisches Institut Universitaet Kiel Olshausenstrasse 40 D-24098 Kiel Germany Phone: x49-431-8802215 FAX: x49-431-8802238 email: skelm@biochem.uni-kiel.de home page: http://www.uni-kiel.de/Biochemie/kelm/ ++++------+------+------+------+------+------+------+------+------+------+ From: Seth Harris Subject: PovRay orientation on Windows not broken? Date: Sun, 28 Nov 1999 11:00:40 -0800 To: rasmol list Just an update on my earlier Povray question and problem: Perhaps Arne has achieved more than he claims...I was trying the RasMol 2.7.1 povray3 output mode on Windows98 with PovRay3.1 and it seems to produce almost the correct orientation. The camera statement in the output generally looks like this (number values will vary of course): camera { orthographic location <0.5, -0.6, -7> look_at <0.5, -0.6, 0.697691> up <0, -1.4, 0> right <1.4, 0, 0> } The image I got seemed to be off by a simple transformation (i.e. it looked basically right just upside down), so changing the sign of the "up" definition (e.g. from -1.4 to 1.4 in the above example) produced the correct orientation that matched the original RasMol window, at least in the few test cases I tried. I was en route to switching to the Linux system, but thought I'd send that update to the list in case anyone had been scared off from trying out this RasMol/PovRay combo. Thanks again to Arne and to others for their tips and info on PovRay. Cheers, Seth ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Seth Harris Botchan Lab UC Berkeley (510)642-5932 Beauty is truth (unpublished results), truth beauty (data not shown). That is all ye know on earth and all ye need to know. Content-Disposition: inline X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id TAA17893 ++++------+------+------+------+------+------+------+------+------+------+ From: "Brendan O'Malley" Subject: Povray Image Size Date: Mon, 29 Nov 1999 11:55:35 +1100 To: I've used Rasmol 2.71 with Povray 3.1 as Seth has and find one particular problem. The Povray image appears streched in the horizontal direction. As Rasmol generates square gif images eg. 500X500 pixels I think it may be something to do with a square image size assumed by the Povray file produced by Rasmol. Povray appears to allow only standard image formats e.g. 640X480 resulting in stetching. Is there any way around this problem? Brendan O'Malley (brendan.omalley@rmit.edu.au) Applied Physics RMIT References: ++++------+------+------+------+------+------+------+------+------+------+ From: Steve Gill Subject: Re: Povray Image Size Date: Sun, 28 Nov 1999 19:42:24 -0800 To: rasmol@dhcp-srv2.oit.umass.edu On Sun, 28 Nov 1999, you wrote: > I've used Rasmol 2.71 with Povray 3.1 as Seth has and find one particular problem. > The Povray image appears streched in the horizontal direction. As Rasmol generates > square gif images eg. 500X500 pixels I think it may be something to do with a square > image size assumed by the Povray file produced by Rasmol. Povray appears to allow > only standard image formats e.g. 640X480 resulting in stetching. Is there any way around this problem? > Yes - in povray you can apply scaling corrections. Call your image as an object, and rescale it in whichever direction you need to (see the povray help files for more info). ++++------+------+------+------+------+------+------+------+------+------+ From: Seth Harris Subject: Re: Povray Image Size Date: Mon, 29 Nov 1999 10:23:08 -0800 To: rasmol@dhcp-srv2.oit.umass.edu Also, you can edit PovRay's output size. On the Mac there's a pull-down menu under Edit-->Render Settings where you can enter the size you desire. On a PC I poked around a found you can edit the QuickRes.ini file or some other ini file to enter the sizes you'd like available in that version's pull down menu (square sizes weren't initially presented so I had to do the mentioned editing). Haven't used the unix version yet, but I thought I saw something about defining Width and Height (W,H) in the command line or something...hope that helps. Cheers, Seth ps above is assuming the "up" and "right" commands are properly set as there was some section in povray's documentation about adjusting these for a rare system that has non-square pixels, but I don't remember the details...I'd look in the documentation directory of PovRay at povray.doc for more info on that... >I've used Rasmol 2.71 with Povray 3.1 as Seth has and find one particular >problem. >The Povray image appears streched in the horizontal direction. As Rasmol >generates >square gif images eg. 500X500 pixels I think it may be something to do >with a square >image size assumed by the Povray file produced by Rasmol. Povray appears >to allow >only standard image formats e.g. 640X480 resulting in stetching. Is there >any way around this problem? > >Brendan O'Malley >(brendan.omalley@rmit.edu.au) >Applied Physics >RMIT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Seth Harris Botchan Lab UC Berkeley (510)642-5932 Beauty is truth (unpublished results), truth beauty (data not shown). That is all ye know on earth and all ye need to know. X-Accept-Language: en,pdf ++++------+------+------+------+------+------+------+------+------+------+ From: Joseph Fioretti Subject: options3d Date: Fri, 03 Dec 1999 08:12:58 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Hello, everyone. I have just a simple question about setting the "options3d" enbed tag for Chime. One of the options available in the popup menu activated when clicking on pdb file in a web browser is "Optons->Display Hydrogen Bonds." Is there any way to control this feature's on/off state via an embed tag? One of the tags available for use with the "options3d" is "hydrogen," but this did not have the desired effect, but rather, I believe, just simply displayed hydrogen atoms. Any help any of you can provide would be greatly appreciated! Thank you all very much!! -Joseph Fioretti fioretti@panther.middlebury.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Ian Macara Date: Tue, 7 Dec 1999 13:33:19 -0500 To: rasmol@dhcp-srv2.oit.umass.edu Is a patch available to enable Rasmol to run on the new Mac OS9?? Ian G. Macara, Ph.D. Professor of Pharmacology Markey Center for Cell Signaling Box 800577, HSC University of Virginia Charlottesville VA 22908-0577 voice: 804-982-0074 (lab: 804-982-0083) fax: 804-924-1236 email: imacara@virginia.edu http://hsc.virginia.edu/signals X-Accept-Language: en,pdf ++++------+------+------+------+------+------+------+------+------+------+ From: Jeff Cohlberg Subject: select a single (average?) NMR structure? Date: Wed, 08 Dec 1999 14:26:38 -0800 To: rasmol@dhcp-srv2.oit.umass.edu Dear RasMoleans, A question about viewing structures in files with NMR data-- A student writing a term paper was trying to view the structure 1BNB (beta-defensin), which contains 20 NMR structures. Using RasMol version 2.7 or First Glance or Protein Explorer gave a superposition of all the NMR structures. Then we discovered that RasMol version 2.6 gave a single structure. (Cn3D and MAGE also gave a single structure.) Of course the superposition is a more accurate representation of the data, but the single structure in RasMol 2.6 was much easier to visualize and much more useful to the student. So I have two questions: 1) What is the single structure displayed in RasMol version 2.6 (and Cn3D and MAGE) -- an average of the 20 NMR structures? 2) Is there any way to force RasMol version 2.7 or Chime or Protein Explorer to display a single structure? Jeff Cohlberg P. S. I have tried to develop an undergraduate student-friendly web site which includes links for molecular modeling. Some of you might find it useful. It's at http://www.csulb.edu/~cohlberg/biochemlinks.html#Molecular -- Jeffrey A. Cohlberg, Professor Department of Chemistry and Biochemistry California State University, Long Beach 1250 Bellflower Blvd. Long Beach, CA 90840 phone (562) 985-4944 fax (209) 821-4471 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime 2 bug: stereo rotation centering Date: Tue, 28 Dec 1999 12:20:54 -0500 To: chime-feedback@mdli.com Cc: rasmol@dhcp-srv2.oit.umass.edu Dear MDL Chime team: Please add this to the bug log. (RasMol 2.7 team please take note.) Chime 2 fails to maintain the correct center of rotation, with respect to the vertical axis, when stereo is on, provided the center is not the original default center of the entire structure. To see this, 'set picking center' and pick an atom near the edge. 'center selected'. Zoom to put the center of rotation in the center of the screen. Notice that when rotating, the center works properly. Now turn stereo on. Notice that when rotating about the X axis, the center behaves properly, but when rotating about the Y axis, the center drifts left and right. The above was observed on Windows and has not been tested on Macintosh nor in RasMol. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - UMass Chime Resources: www.umass.edu/microbio/chime Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime 2 bug: stereo centering error after a surface Date: Tue, 28 Dec 1999 12:20:58 -0500 To: chime-feedback@mdli.com Cc: rasmol@dhcp-srv2.oit.umass.edu Dear MDL Chime team: Please add this to the bug log. Chime 2 has a bug which causes surfaces to be off center when stereo is invoked. This bug does not affect images which include only non-surface renderings (such as backbone, spacefill, etc.) until after a surface has been generated. Once a surface has been generated, even if it is deleted before stereo is invoked, and even if the rendering at the time stereo is invoked contains only non-surface renderings, the stereo images are rendered off-center to the left. A workaround is to follow 'stereo' with 'translate x 0'. However, zooming (in default mode 'set zoom center true') causes the stereo images to go off-center again. The above was observed on Windows and has not been verified on Macintosh. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - UMass Chime Resources: www.umass.edu/microbio/chime Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.edu - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Re: Chime 2 bug: stereo rotation centering Date: Tue, 28 Dec 1999 12:19:42 -0500 To: rasmol@dhcp-srv2.oit.umass.edu This bug has always been present in the Mac versions of RasMol (back to v 2.5) and Chime. Cheers! ***************************** "Some people place favorite quotations at the end of their e-mails, but I don't." Anonymous, Greece, 3rd century BC. Gale Rhodes mailto:rhodes@usm.maine.edu WWW Home Page: http://www.usm.maine.edu/~rhodes/GRHomePage.html Professor of Chemistry Chemistry Department University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 Phone: (207)780-4734 Fax: (207) 228-8288 X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Ignacio Valdes Subject: Psychiatric Medication PDB files? Date: Wed, 29 Dec 1999 21:32:47 -0600 To: rasmol@dhcp-srv2.oit.umass.edu Hello all, I am involved in teaching an advanced Psychopharmacology course at the University of Texas Houston. I've got Chime running on my machine and want to be able to display 2-D and 3-D molecular models of common Psychiatric medications. I've searched the net and several databases without success. My list is basically the commonly used antipsychotics and benzodiazepines such as: Haloperidol Droperidol Thiothixene Pimozide Chlorpromazine Trifluoperazine Fluphenazine Thioridazine Risperdal Diazepam Lorazepam Clonazepam, etc. I would be greatly appreciative of any leads/advice anyone could give in obtaining definition files of these for use with Chime. Thanks, -- IV charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 ++++------+------+------+------+------+------+------+------+------+------+ From: "DALE SAMPSON" Subject: RE: Psychiatric Medication PDB files? Date: Wed, 29 Dec 1999 23:56:16 -0500 To: "Rasmol List (E-mail)" HI Ignacio, This site has some of the meds you're looking for in chime format: http://triton.ps.toyaku.ac.jp/~dobashi/database/in dexe.html Hope this helps, Dale Sampson -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Ignacio Valdes Sent: Wednesday, December 29, 1999 10:33 PM From: owner-rasmol@lists.umass.edu Subject: Psychiatric Medication PDB files? To: rasmol@dhcp-srv2.oit.umass.edu Hello all, I am involved in teaching an advanced Psychopharmacology course at the University of Texas Houston. I've got Chime running on my machine and want to be able to display 2-D and 3-D molecular models of common Psychiatric medications. I've searched the net and several databases without success. My list is basically the commonly used antipsychotics and benzodiazepines such as: Haloperidol Droperidol Thiothixene Pimozide Chlorpromazine Trifluoperazine Fluphenazine Thioridazine Risperdal Diazepam Lorazepam Clonazepam, etc. I would be greatly appreciative of any leads/advice anyone could give in obtaining definition files of these for use with Chime. Thanks, -- IV charset=ISO-8859-1 Content-Disposition: inline X-MIME-Autoconverted: from quoted-printable to 8bit by dhcp-srv2.oit.umass.edu id BAA19582 ++++------+------+------+------+------+------+------+------+------+------+ From: Jean Debord Subject: Re: Psychiatric Medication PDB files? Date: Thu, 30 Dec 1999 01:56:04 -0500 To: "INTERNET:rasmol@lists.umass.edu" Texte du message écrit par INTERNET:rasmol@lists.umass.edu >I've got Chime running on my machine and want to be able to display 2-D and 3-D molecular models of common Psychiatric medications.< Hello, You will find a set of phenothiazine molecules (PDB files) at my web site: http://ourworld.compuserve.com/homepages/JDebord/models.htm Best regards, and happy new year! Jean Debord Laboratoire de Pharmacologie, Faculte de Medecine 2 Rue du Dr Marcland, F-87025 Limoges, France References: <386AD25F.54153A5D@csi.com> X-Accept-Language: en,pdf ++++------+------+------+------+------+------+------+------+------+------+ From: Jeff Cohlberg Subject: Re: Psychiatric Medication PDB files? Date: Thu, 30 Dec 1999 09:55:39 -0800 To: rasmol@dhcp-srv2.oit.umass.edu Try http://triton.ps.toyaku.ac.jp/~dobashi/database/structure/index_t.html. It looks like everything in your list except thiothixene and risperdal can be found there. Note: This site is listed on the page "Where to Get Molecules for Rasmol" at http://www.umass.edu/microbio/rasmol/whereget.htm. Jeff Cohlberg -- Jeffrey A. Cohlberg, Professor Department of Chemistry and Biochemistry California State University, Long Beach 1250 Bellflower Blvd. Long Beach, CA 90840 phone (562) 985-4944 fax (209) 821-4471 Ignacio Valdes wrote: > Hello all, > > I am involved in teaching an advanced Psychopharmacology course at the > University of Texas Houston. I've got Chime running on my machine and > want to be able to display 2-D and 3-D molecular models of common > Psychiatric medications. I've searched the net and several databases > without success. My list is basically the commonly used antipsychotics > and benzodiazepines such as: > > Haloperidol > Droperidol > Thiothixene > Pimozide > Chlorpromazine > Trifluoperazine > Fluphenazine > Thioridazine > Risperdal > > Diazepam > Lorazepam > Clonazepam, etc. > > I would be greatly appreciative of any leads/advice anyone could give in > obtaining definition files of these for use with Chime. > > Thanks, > > -- IV References: <386AD25F.54153A5D@csi.com> charset="iso-8859-1" X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 ++++------+------+------+------+------+------+------+------+------+------+ From: "Roy Fultun" Subject: Re: Psychiatric Medication PDB files? Date: Thu, 30 Dec 1999 23:19:04 -0800 To: One dumb, if obvious solution, is to use any of the several commercial molecular modeling programs which offer free and functional demos to enter the molecules by hand. Then use the included molecular modeling packages such as MM3 (mechanical) or GAUSS (quantum) to clean the molecule up. While you run the risk of getting some of the finer points wrong, such as aromatic rings and double bonds, you can probably enter the molecules accurately by hand. And, after all, you're the Psychopharmacology expert, so you'll have a leg up on most of us. My favorite is CAChe by Oxford Molecular, available at: http://www.oxmol.com/software/cache/ My next favorite is WebLab from MSI at: http://www.msi.com/life/index.html I believe that Hyper 5D also supports a GUI editor, available at: http://www.hyper.com/products/evaluation/hyper5/eval5download.htm Let me know if this is of any use. ----- Original Message ----- Sent: Wednesday, December 29, 1999 7:32 PM From: Ignacio Valdes Subject: Psychiatric Medication PDB files? To: > Hello all, > > I am involved in teaching an advanced Psychopharmacology course at the > University of Texas Houston. I've got Chime running on my machine and > want to be able to display 2-D and 3-D molecular models of common > Psychiatric medications. I've searched the net and several databases > without success. My list is basically the commonly used antipsychotics > and benzodiazepines such as: > > Haloperidol > Droperidol > Thiothixene > Pimozide > Chlorpromazine > Trifluoperazine > Fluphenazine > Thioridazine > Risperdal > > Diazepam > Lorazepam > Clonazepam, etc. > > I would be greatly appreciative of any leads/advice anyone could give in > obtaining definition files of these for use with Chime. > > Thanks, > > -- IV > ++++------+------+------+------+------+------+------+------+------+------+