Beginning Jan 1, 2004: ++++------+------+------+------+------+------+------+------+------+------+ From: Mike Garbett Subject: Cell Membrane Modelling Date: Sun, 04 Jan 2004 18:12:14 +0000 To: rasmol@lists.umass.edu This may be a little 'off topic' so I apologise in advance. I have been using Rasmol, Chime and Protein explorer with my A-level (pre-university) students for some time and have found the teaching resources produced by Eric and others of great value. Recently my current 'star student' came up with the idea of writing a programme which could be used to build 'on-screen' a functional (if rather simplistic) model of the cell membrane. The aim would be to see the effects of dropping intrinsic proteins with specific ion channels into the basic bilayer structure. The idea came out of our studies relating to the generation and propagation of nerve impulses via ion-pumping and facilitated diffusion. The project is probably beyond my rather limited programming skills but I would be interested to know if anyone has come across a similar resource. Mike Garbett Science College Director The Aldridge School Tynings Lane Aldridge WS9 0BG United Kingdom Tel. 01922 743988 extn. 277 e-mail: mike@mikegarbett.demon.co.uk ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: Darrell Brooks Subject: Re: Cell Membrane Modelling Date: Mon, 05 Jan 2004 17:47:37 +0000 To: rasmol Hi Mike I was at conference over the summer 2003 (last year!) and there was a group from Middlebury College, VT, USA who had used a program called Lightwave. This is an old program that is used in the media industry to produce 3D virtual objects. This package was demonstrated by a short animation that the group had produced showing the sodium/potassium pump in cell membranes. The real advantage of this program however is that it is possible to import 3D files of molecules (PDB files) without having to build them de novo. The disadvantage is that is does not allow any interactivity. It will only produce sequences for animation. Nevertheless during discussion it became clear that it was possible to export the 'objects' to Shockwave and then QuickTime to produce interactivity that was otherwise missing. Don't know if this help regards Darrell Brooks >>> rasmol@mikegarbett.demon.co.uk 01/04/04 06:12pm >>> This may be a little 'off topic' so I apologise in advance. I have been using Rasmol, Chime and Protein explorer with my A-level (pre-university) students for some time and have found the teaching resources produced by Eric and others of great value. Recently my current 'star student' came up with the idea of writing a programme which could be used to build 'on-screen' a functional (if rather simplistic) model of the cell membrane. The aim would be to see the effects of dropping intrinsic proteins with specific ion channels into the basic bilayer structure. The idea came out of our studies relating to the generation and propagation of nerve impulses via ion-pumping and facilitated diffusion. The project is probably beyond my rather limited programming skills but I would be interested to know if anyone has come across a similar resource. Mike Garbett Science College Director The Aldridge School Tynings Lane Aldridge WS9 0BG United Kingdom Tel. 01922 743988 extn. 277 e-mail: mike@mikegarbett.demon.co.uk ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <9ej+drA+dF+$EwDx@mikegarbett.demon.co.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Dave Hurley Subject: Re: Cell Membrane Modelling Date: Mon, 05 Jan 2004 16:50:02 -0800 To: rasmol@lists.umass.edu How detailed do you want this representation to be? It wouldn't be hard, I think, to create a somewhat schematized interactive animation in Flash (for instance) that would demonstrate the effects of arbitrary numbers of channels and pumps on transmembrane potentials. Dave Hurley Senior Computer Specialist Department of Biology University of Washington On Jan 4, 2004, at 10:12 AM, Mike Garbett wrote: > > This may be a little 'off topic' so I apologise in advance. > > I have been using Rasmol, Chime and Protein explorer with my A-level > (pre-university) students for some time and have found the teaching > resources produced by Eric and others of great value. > Recently my current 'star student' came up with the idea of writing a > programme which could be used to build 'on-screen' a functional (if > rather simplistic) model of the cell membrane. > The aim would be to see the effects of dropping intrinsic proteins with > specific ion channels into the basic bilayer structure. The idea came > out of our studies relating to the generation and propagation of nerve > impulses via ion-pumping and facilitated diffusion. > The project is probably beyond my rather limited programming skills but > I would be interested to know if anyone has come across a similar > resource. > > Mike Garbett > Science College Director > The Aldridge School > Tynings Lane > Aldridge > WS9 0BG > United Kingdom > Tel. 01922 743988 extn. 277 > e-mail: mike@mikegarbett.demon.co.uk > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: lpotapov@pceg2.weizmann.ac.il X-Authentication-warning: pceg2.weizmann.ac.il: lpotapov owned process doing -bs ++++------+------+------+------+------+------+------+------+------+------+ From: Vladimir Potapov Subject: Molscript and Molecular Surfaces Date: Wed, 07 Jan 2004 14:11:19 +0200 (IST) To: rasmol@lists.umass.edu Hello, I am preparing illustrations in Molscript. Additionally, I need to visualize molecular surfaces for a whole protein or just a small region. As far as I understand, Molscript cannot generate molecular surfaces and uses for this purpose external files. Could anyone share his/her experience on this subject? What is "the standart program" to generate surfaces? How to plug it into Molscript? Is it worth to deal with Molscript for such task? Regards, Vladimir Potapov ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Ilan Samish Subject: Re: Molscript and Molecular Surfaces Date: Wed, 07 Jan 2004 14:21:36 +0200 To: rasmol@lists.umass.edu Hi, The best software I know for this is DINO (combined with msms). For example: http://cobra.mih.unibas.ch/dino/gallery.php?cat=2 Best Regards, Ilan Vladimir Potapov wrote: >Hello, > >I am preparing illustrations in Molscript. Additionally, I need to >visualize molecular surfaces for a whole protein or just a small region. >As far as I understand, Molscript cannot generate molecular surfaces and >uses for this purpose external files. > >Could anyone share his/her experience on this subject? What is "the >standart program" to generate surfaces? How to plug it into Molscript? Is >it worth to deal with Molscript for such task? > >Regards, >Vladimir Potapov > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: MODEL...TER Date: Thu, 08 Jan 2004 16:48:53 +0000 (GMT) To: rasmol@lists.umass.edu Hi Multi model pdb files (such as 1htq) give rasmol problems as it tries to draw bonds between all atoms, making these files slow to load / manipulate. How do I select individual models in rasmol? Could rasmol be made to only connect atoms within models and not between? I know I should just read the manual, but how do I select individual nucleotides with rasmol? Cheers, Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <45889.193.60.81.207.1073580533.squirrel@www.mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: MODEL...TER Date: Thu, 08 Jan 2004 20:28:51 +0100 (CET) To: rasmol@lists.umass.edu I don't have much direct experience as an actual rasmol user, but I'll take a crack at it ... > Multi model pdb files (such as 1htq) give rasmol problems as it tries to > draw bonds between all atoms, making these files slow to load / > manipulate. > > How do I select individual models in rasmol? In RasMol 2.6 you can say select model=2 or select *::2 // select :: The RasMol 2.7 doc says select model=2 or select */2 > Could rasmol be made to only connect atoms within models and not > between? Surely you are not seeing this behavior. If so then I would call it a bug. (If it is *not* a bug, then someone please explain :-) > I know I should just read the manual, but how do I select individual > nucleotides with rasmol? ummm ... not sure exactly what you mean by 'individual nucleotides' try select 1 or select a Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: MODEL...TER Date: Thu, 08 Jan 2004 14:59:41 -0500 To: rasmol@lists.umass.edu Miguel Howard already answered some of Dan's questions. At 1/8/04, you wrote: >Could rasmol be made to only connect atoms within models and not between? In all RasMol discussions it will be helpful to specify 2.6 or 2.7. Although bonds should not be drawn between models, there is a bug in RasMol 2.6 and Chime: SS bonds (only disulfide bonds) ARE drawn between models. If you have a lot of disulfides, this can be somewhat problematic. If you don't need multiple models, use Olderado to choose the most representative model (in Protein Explorer, when an NMR file is loaded, the External Resources / Mol Info menu lists a link to Olderado). http://neon.chem.le.ac.uk/olderado/ >I know I should just read the manual, but how do I select individual >nucleotides >with rasmol? The guide to selection is at http://www.umass.edu/microbio/rasmol/seleccmd.htm The "reference manual" really doesn't give you a good overview of how to select, which is why I wrote the above. Of course you can "and" model selection with other criteria, e.g. select model=1 and G and 32 and :A (Guanosine 32 in chain A in model 1) /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <5.2.0.9.2.20040108145242.02422b10@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: MODEL...TER Date: Fri, 09 Jan 2004 10:15:44 +0000 (GMT) To: rasmol@lists.umass.edu Cc: emartz@microbio.umass.edu ++ Eric Martz-- > Miguel Howard already answered some of Dan's questions. Thanks to him for that! > At 1/8/04, you wrote: >>Could rasmol be made to only connect atoms within models and not between? > > In all RasMol discussions it will be helpful to specify 2.6 or 2.7. I am using Version 2.7.2.1 April 2001 > Although bonds should not be drawn between models, there is a bug in RasMol 2.6 > and Chime: SS bonds (only disulfide bonds) ARE drawn between models. If you have > a lot of disulfides, this can be somewhat problematic. I am seeing bonds everywhere! For example in the structure 1gtv... restrict 39-41a, 39-41b center selected However, I cant find MODEL lines in this structure (only TER). Which is probably why... RasMol> select *::0 3700 atoms selected! RasMol> select *::1 No atoms selected! Hence the whole problem. > If you don't need multiple models, use Olderado to choose the most representative > model (in Protein Explorer, when an NMR file is loaded, the External Resources / > Mol Info menu lists a link to Olderado). > http://neon.chem.le.ac.uk/olderado/ Olderado is very nice, but it is only (currently?) applicable to multi-model NMR structures, and does not keep records for multi-model X-Ray structures. In this class I find (the hard way)... 1gtv - 2 models (no MODEL lines, chain A/B) 1cm4 - 4 models (no MODEL lines, chain A+B/C+D/E+F/G+H) 1cwq - 2 models (no MODEL lines, chain A/B) 1e0p - 2 models (no MODEL lines, chain A/B) 1gu8 - 2 models (MODEL lines! - hey this one works fine!) Again I am too ignorant of the PDB format specification to know if these PDB files are correctly formatted. >>I know I should just read the manual, but how do I select individual nucleotides >>with rasmol? > > > The guide to selection is at > http://www.umass.edu/microbio/rasmol/seleccmd.htm Bookmarked! Cheers, Dan. > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - > Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of > Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor Emeritus, Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <5.2.0.9.2.20040108145242.02422b10@marlin.bio.umass.edu> <58243.193.60.81.207.1073643344.squirrel@www.mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: MODEL...TER Date: Fri, 09 Jan 2004 12:05:50 +0100 (CET) To: rasmol@lists.umass.edu > However, I cant find MODEL lines in this structure (only TER). > > Which is probably why... > 1gtv - 2 models (no MODEL lines, chain A/B) > 1cm4 - 4 models (no MODEL lines, chain A+B/C+D/E+F/G+H) > 1cwq - 2 models (no MODEL lines, chain A/B) > 1e0p - 2 models (no MODEL lines, chain A/B) > 1gu8 - 2 models (MODEL lines! - hey this one works fine!) > > Again I am too ignorant of the PDB format specification to know if these > PDB files are correctly formatted. Models should be started with MODEL and ended with ENDMDL I have seen evidence that TER records are completely ignored in RasMol 2.6/Chime. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <5.2.0.9.2.20040108145242.02422b10@marlin.bio.umass.edu> <58243.193.60.81.207.1073643344.squirrel@www.mrc-dunn.cam.ac.uk> <34865.212.128.142.25.1073646350.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: MODEL...TER Date: Fri, 09 Jan 2004 11:03:02 +0000 (GMT) To: rasmol@lists.umass.edu Cc: mth@mth.com ++ Miguel Howard-- >> However, I cant find MODEL lines in this structure (only TER). >> >> Which is probably why... > > > Models should be started with MODEL and ended with ENDMDL > > I have seen evidence that TER records are completely ignored in RasMol 2.6/Chime. Sorry, now I know better... Overview The TER record indicates the end of a list of ATOM/HETATM records for a chain. Details * Every chain of ATOM/HETATM records presented on SEQRES records is terminated with a TER record. > > > Miguel > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <0HRB000IM783KI@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Robert M. Horton, PhD" Subject: Re: Cell Membrane Modelling Date: Sun, 11 Jan 2004 14:31:49 -0800 To: rasmol@lists.umass.edu Cc: rasmol@mikegarbett.demon.co.uk > Recently my current 'star student' came up with the idea of writing a > programme which could be used to build 'on-screen' a functional (if > rather simplistic) model of the cell membrane. > The aim would be to see the effects of dropping intrinsic proteins with > specific ion channels into the basic bilayer structure. The idea came > out of our studies relating to the generation and propagation of nerve > impulses via ion-pumping and facilitated diffusion. You can do this sort of thing in VRML. It is not as nice for molecular viewing as a real molecule viewer, but it lets you put non-molecular things (like planes representing membrane surfaces) into the molecular "world". See: http://gaia.ecs.csus.edu/~cs296n/assignments/w9/1PRHmemb.html (Shout3D version, if you have Java) or http://gaia.ecs.csus.edu/~cs296n/assignments/w9/1PRHmemb.wrl (straight VRML; requires a VRML plugin that can view extrusions). This example uses a simple extrusion to trace the alpha carbons. You can get much nicer VRML models of your favorite protein from PDB, though they take a lot more hardware resources to view and examine. __ Robert M. Horton, Ph.D. 0 [] ~ ~ ~ http://www.cybertory.com ~ ~ ~ ~[] 0 |-/_| rmhorton@attotron.com |_\-| -\_|| He travels swiftest who telecommutes. ||_/- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed boundary="Boundary_(ID_98/07KW2781tE/Mo0tYFwA)" ++++------+------+------+------+------+------+------+------+------+------+ From: "Conrad, Steven" Subject: RE: Cell Membrane Modelling Date: Mon, 12 Jan 2004 10:16:32 -0600 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. --Boundary_(ID_98/07KW2781tE/Mo0tYFwA) This type of interface (or something very similar) for cellular process modeling has been developed by a group at the University of Texas Health Science Center-Houston and Rice University. Contact Akhil Bidani, MD PhD in the Department of Medicine at UTHSC-H. -----Original Message----- Sent: Sunday, January 11, 2004 4:32 PM From: Robert M. Horton, PhD [mailto:rmhorton@attotron.com] Subject: Re: Cell Membrane Modelling To: rasmol@lists.umass.edu Cc: rasmol@mikegarbett.demon.co.uk > Recently my current 'star student' came up with the idea of writing a > programme which could be used to build 'on-screen' a functional (if > rather simplistic) model of the cell membrane. > The aim would be to see the effects of dropping intrinsic proteins > with specific ion channels into the basic bilayer structure. The idea > came out of our studies relating to the generation and propagation of > nerve impulses via ion-pumping and facilitated diffusion. You can do this sort of thing in VRML. It is not as nice for molecular viewing as a real molecule viewer, but it lets you put non-molecular things (like planes representing membrane surfaces) into the molecular "world". See: http://gaia.ecs.csus.edu/~cs296n/assignments/w9/1PRHmemb.html (Shout3D version, if you have Java) or http://gaia.ecs.csus.edu/~cs296n/assignments/w9/1PRHmemb.wrl (straight VRML; requires a VRML plugin that can view extrusions). This example uses a simple extrusion to trace the alpha carbons. You can get much nicer VRML models of your favorite protein from PDB, though they take a lot more hardware resources to view and examine. __ Robert M. Horton, Ph.D. 0 [] ~ ~ ~ http://www.cybertory.com ~ ~ ~ ~[] 0 |-/_| rmhorton@attotron.com |_\-| -\_|| He travels swiftest who telecommutes. ||_/- --Boundary_(ID_98/07KW2781tE/Mo0tYFwA) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_98/07KW2781tE/Mo0tYFwA)-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: "IKEHATA, Akihisa" Subject: I need your help Date: Wed, 14 Jan 2004 19:32:58 +0900 To: rasmol@lists.umass.edu Dear all I need your help. I installed the rasmol ver. 2.7.2.1. I opened the some pdb files, but unfortunately, the structures did not show up and the commandline said the file not found!. I previously installed other viewer and uninstallled it. The kind of file showed pdb. I do not know how to do that. Please help me! Akihisa from Yokohama, Japan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: fink rasmol (panther) Date: Fri, 16 Jan 2004 13:30:54 -0500 To: LIST rasmol hello, still trying to 'install' RasMol via fink. I have installed Apple's X11 and X11 SDK packages, based on XFree86-4.3. however, running fink install rasmol from a bash shell crunches along merrily for about an hour before failing with this message: Unpacking xfree86 (from .../xfree86_4.3.99.16-2_darwin-powerpc.deb) ... WARNING: if you compile X11 applications against this XFree86 release, you will *not* be able to run them if you decide to revert to Apple's X11 provided with Panther. You have an existing X11 installation in /usr/X11R6 and/or /etc/X11. This package refuses to overwrite these. Remove them, then tell Fink to install xfree86 again. (The package won't be recompiled.) If you want to keep your X11 installation, install system-xfree86 resp. system-xtools instead to make this known to Fink's package system. I don't want to remove my existing X11. so can anyone give me a hint - how do I install system-xfree86 resp. system-xtools, and then make it known to fink? thanks for any help, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: helgew@gollum.grajagan.net ++++------+------+------+------+------+------+------+------+------+------+ From: Helge Weissig Subject: Re: fink rasmol (panther) Date: Fri, 16 Jan 2004 11:21:54 -0800 (PST) To: LIST rasmol Hi Tim, you should be able to install them with 'fink install system-xfree86 system-xtools'. AFAIK, both are just flags to let fink know that X11 is installed already. hth, h. On Fri, 16 Jan 2004 at 13:30 -0500, owner-rasmol@lists.umass.edu wrote: td> hello, td> td> still trying to 'install' RasMol via fink. I have installed Apple's X11 and td> X11 SDK packages, based on XFree86-4.3. however, running td> td> fink install rasmol td> td> from a bash shell crunches along merrily for about an hour before failing td> with this message: td> td> td> Unpacking xfree86 (from .../xfree86_4.3.99.16-2_darwin-powerpc.deb) ... td> WARNING: if you compile X11 applications against this XFree86 release, td> you will *not* be able to run them if you decide to revert to Apple's td> X11 provided with Panther. td> td> You have an existing X11 installation in /usr/X11R6 and/or /etc/X11. td> This package refuses to overwrite these. Remove them, then tell Fink to td> install xfree86 again. (The package won't be recompiled.) If you want td> to keep your X11 installation, install system-xfree86 resp. system-xtools td> instead to make this known to Fink's package system. td> td> td> I don't want to remove my existing X11. so can anyone give me a hint - how td> do I install system-xfree86 resp. system-xtools, and then make it known to td> fink? td> td> td> thanks for any help, td> td> :tim td> td> ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en ++++------+------+------+------+------+------+------+------+------+------+ From: Ilan Samish Subject: 3D SIG: 1st Structural Bioinformatics ISMB/ECCB Satellite meeting Date: Mon, 19 Jan 2004 08:08:25 +0200 To: rasmol@lists.umass.edu Dear Friends, We are happy to announce a 2-day Satellite Meeting called "3D SIG" that is dedicated exclusively to STRUCTURAL BIOINFORMATICS. 3D SIG will be held on 29-30 July 2004, at Glasgow, Scotland, UK., immediately preceding ISMB/ECCB 2004. The 3D SIG web site is http://3dsig.weizmann.ac.il/ 3D SIG will go on for 2 full days (don't plan anything for the evenings!) and will include a balanced mix of main talks, short presentations (selected from laptop-session submissions - see below) and panel discussions. TOPICS will include: =============== * 3D data-mining * 3D programming modules * Docking and protein-protein/ligand interaction prediction * Membrane protein assembly prediction * Secondary structure and domain assignment * Structure-based function prediction * Structural databases * Structural genomics * Structure prediction * Structure representation * The role of geometry and energetics in protein structure and function LAPTOP SESSION =============== A novel Laptop Session will take place following lunch each day where authors will be at their numbered stations with their laptops describing their work. The idea is to offer a semi-formal, yet intimate, channel during the meeting to facilitate the discussion of individual research. 3D SIG participants are encouraged to submit an abstract and representative figure/table that will be placed online. 20 short talks will be selected by the Scientific Committee for inclusion in the program based on the submitted abstracts. The number of Laptop Session stations is limited, so reserve a place in advance. For details see http://3dsig.weizmann.ac.il/laptop.html SCIENTIFIC COMMITTEE: ===================== John Moult (chair) - Center for Advanced Research in Biotech., U. Maryland, USA Phil Bourne - University of California San Diego, USA Luis Serrano - European Molecular Biology Laboratory, Heidelberg, Germany Michael Sternberg - Dept. Biological Sciences, Imperial College, London, UK Ron Unger - Faculty of Life Science, Bar-Ilan University, Israel David Gilbert (honorary) - Dept. Computing Science, U. Glasgow, Scotland, UK Janet Thornton (honorary) - European Bioinformatics Institute, Hingston, UK ORGANIZING COMMITTEE: ====================== Ilan Samish and Marvin Edelman - Weizmann Institute of Science, Rehovot, Israel John Moult - Center for Advanced Research in Biotech., U. Maryland, USA Looking forward to seeing you at 3D SIG, --------------------------------- 3D SIG Organizing Committee 3Dsig@weizmann.ac.il http://3dsig.weizmann.ac.il/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal X-Spam-Level: ++++------+------+------+------+------+------+------+------+------+------+ From: Raanan Subject: No compren marca NIKE - DO NOT BUY NIKE ANYMORE Date: Thu, 29 Jan 2004 12:43:36 +0200 To: Raanan Dunowicz This is a multi-part message in MIME format. --Boundary_(ID_4dR7YsRpvaPSrGxeWz5Ehw) > >Subject: Fw: No compren marca NIKE - DO NOT BUY NIKE ANYMORE Dear people I am sending this email to all the people I was once in contact, or I am still (Hope it wont change...). Sorry for the inconvenient. It is my first time I have decided to send an email to every one, since Enough is enough! Please forward it around the entire world! Raanan Dunowicz --Boundary_(ID_4dR7YsRpvaPSrGxeWz5Ehw) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_4dR7YsRpvaPSrGxeWz5Ehw)-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 boundary="Boundary_(ID_BrzDWXSWPp3/Z24C8cTknA)" X-MSMail-priority: High X-Spam-Level: ++++------+------+------+------+------+------+------+------+------+------+ From: Raanan Subject: Date: Thu, 29 Jan 2004 13:10:40 +0200 To: !000 This is a multi-part message in MIME format. --Boundary_(ID_BrzDWXSWPp3/Z24C8cTknA) =E8=F2=E5=FA =E8=E5=F2=E9=ED =E8=F2=E9=F0=E5, =EE=FA=E9=E7=E4 = =EE=E2=F2=E9=EC=E4.... http://info.org.il/irrelevant/item.php/107479305878947129 Soory it was a fake This is an answer from Nike Nike is committed to being a good corporate citizen including = understanding and appreciating the values of all communities. We would like you to know this e-mail is not related to the Nike = Corporation in any way. Nike's trademark Swoosh is among the most widely recognized = in the world and unfortunately is sometimes misappropriated for = unauthorized uses. We do our best to protect our trademark and prevent its = association with inappropriate subject matter, such as in this case, which = trivializes human suffering. To help us stop the spread of this e-mail, we ask that you refrain from forwarding it. We are currently investigating the source of this e-mail. Thank you for bringing this to our attention and we hope you continue to think of Nike as a name that represents quality. Sincerely, Kim Nike Raanan --Boundary_(ID_BrzDWXSWPp3/Z24C8cTknA) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_BrzDWXSWPp3/Z24C8cTknA)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Oops, "pbd" registry typo not fixed in SP5 Date: Tue, 10 Feb 2004 18:18:39 -0500 To: bdickey@mdli.com, chime-team@mdli.com, johno@mdli.com Cc: rasmol@lists.umass.edu To: Bob Dickey at MDL & MDL Chime Team Dear Bob and Chime Team: I just noticed that unfortunately the typographical error in the Chime installer that puts "pbd" in the Windows registry instead of "pdb" did not get fixed in SP5. Please put it at the top of the list for SP6. I reported this bug to you in May, 2003. Search for chimeshim "pbd" [including double quotes] at to review the full details. The bug was introduced in SP4. This bug breaks the central Chime troubleshooting tool I have offered for years on my websites, clicking on http://www.umass.edu/microbio/chime/atp.pdb to display the ATP molecule in Internet Explorer! (It does not seem to affect Netscape 4.8.) As with the earlier bug in the installer, the only fix for this that I know is to edit the Windows registry -- not what someone having trouble getting Chime to work should be trying! Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Robert Dickey , chime-team@mdli.com, John Olson ++++------+------+------+------+------+------+------+------+------+------+ From: Robert Dickey Subject: RE: Oops, "pbd" registry typo not fixed in SP5 Date: Tue, 10 Feb 2004 15:45:57 -0800 To: "'Eric Martz'" , Cc: rasmol@lists.umass.edu Eric, I apologize for this oversight. I will make sure that this problem is corrected in the next Chime service pack. Regards, Bob Dickey -----Original Message----- Sent: Tuesday, February 10, 2004 3:19 PM From: Eric Martz [mailto:emartz@microbio.umass.edu] Subject: Oops, "pbd" registry typo not fixed in SP5 To: bdickey@mdli.com; chime-team@mdli.com; johno@mdli.com Cc: rasmol@lists.umass.edu To: Bob Dickey at MDL & MDL Chime Team Dear Bob and Chime Team: I just noticed that unfortunately the typographical error in the Chime installer that puts "pbd" in the Windows registry instead of "pdb" did not get fixed in SP5. Please put it at the top of the list for SP6. I reported this bug to you in May, 2003. Search for chimeshim "pbd" [including double quotes] at to review the full details. The bug was introduced in SP4. This bug breaks the central Chime troubleshooting tool I have offered for years on my websites, clicking on http://www.umass.edu/microbio/chime/atp.pdb to display the ATP molecule in Internet Explorer! (It does not seem to affect Netscape 4.8.) As with the earlier bug in the installer, the only fix for this that I know is to edit the Windows registry -- not what someone having trouble getting Chime to work should be trying! Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: en-us, en X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Richard Harrington Subject: secondary structure for small pdb segments Date: Fri, 13 Feb 2004 17:34:50 +0000 To: rasmol list Dear all, I'm using Rasmol to select sections of a pdb file (portions of the surface of the pdb structure), and then save them as a smaller, surface pdb file. Most of the files are between 20-80 residues in length, and usually comprise 2 or more sequence fragments. As far as I understand, Rasmol uses some implementation of DSSP to determine the secondary structre of the pdb file it is showing. Thus, when I save the small surface file as a pdb, although it may include every atom that was selected in the original rasmol rendering of the pdb molecule (which is easy to check by eye by viewing in spacefill), it still doesn't allocate all the same secondary structure elements. This is presumably because the secondary structure elements in the original pdb are designated by a combination of the non-highlighted (non-selected) regions of the pdb aswell as the highlighted regions. Does anyone know if there is a way that I could explicitly get the secondary structure calculation from the original pdb file, say by using the rasmol 'structure' command, and then use this saved secondary structure by applying it to the small surface file? Many thanks for any help, Richie _______________________________________________ Richard Harrington, Men's Boat Club Captain, Homerton College. PhD student, ATP Synthase Group, MRC-Dunn Human Nutrition Unit, Cambridge University. e-mail: rah@mrc-dunn.cam.ac.uk telephone: +44 (0) 1223 252861 mobile: 07817 927175 _______________________________________________ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: secondary structure for small pdb segments Date: Fri, 13 Feb 2004 17:00:42 -0500 To: rasmol@lists.umass.edu At 2/13/04, Richard Harrington wrote: >Does anyone know if there is a way that I could explicitly get the >secondary structure calculation from the original pdb file, say by using >the rasmol 'structure' command, and then use this saved secondary >structure by applying it to the small surface file? Well, you can designate any residues you wish as helix, sheet, or turn, with HELIX, SHEET, and TURN records in the PDB file header. By default, RasMol & Chime use this information. Only if such records are missing, or if you enter the command "structure" is the internal algorithm run (superceding the header records, if any). -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: compatible *restrict* behavior Date: Sat, 14 Feb 2004 20:55:31 +0100 (CET) To: jmol-developers@lists.sourceforge.net, rasmol@lists.umass.edu This question refers to the 'restrict' scripting command. I have received several complaints that the Jmol implementation of 'restrict' is not correct. The RasMol doc says: This command is very similar to the RasMol 'select' command, except 'restrict' disables the 'wireframe', 'spacefill' and 'backbone' representations in the non-selected region. Q: Is it the case that 'restrict' applies to *all* graphic shapes ... cartoons, strands, etc? Q: Are there any special cases or anomolies that I should be aware of? Thanks, Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: compatible *restrict* behavior Date: Sat, 14 Feb 2004 12:43:19 -0700 (MST) To: rasmol@lists.umass.edu Cc: jmol-developers@lists.sourceforge.net Hi Miguel, On Sat, 14 Feb 2004, Miguel Howard wrote: > Q: Is it the case that 'restrict' applies to *all* graphic shapes ... > cartoons, strands, etc? The intention is that RasMol's restrict command applies to all graphics representations. The documentation was written when there were only a handful of representations used by RasMol, and (of course) it was rarely updated as new representations were subsequently added. > Q: Are there any special cases or anomolies that I should be aware of? There may be exceptions in existing RasMol/Chime implementations; perhaps dot surfaces, Chime's solid surfaces, distance monitors, hydrogen bonds, disulphide bridges, atom labels, etc... However these should be considered bugs (perhaps quirks or features) of a particular RasMol script interpreter. Script writers shouldn't rely on "restrict none" leaving anything behind, and future versions may "fix" any anomalies that currently exist. If JMol supports more representations than RasMol and/or Chime, these should ideally also be turned off by the restrict command. In theory, "restrict none" should be a portable way for a RasMol/Chime/JMol script to reset the "display list" independent of any additional functionality that may be added in future. I hope this explains the intend or prescribed behaviour of "restrict" if not any particular implementation. Roger -- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: compatible *restrict* behavior Date: Sat, 14 Feb 2004 16:29:03 -0500 To: jmol-developers@lists.sourceforge.net, rasmol@lists.umass.edu I would love to see Jmol's "restrict" command turn off all renderings. The fact that neither RasMol nor Chime do this is problematic. Typically, when trying to hide everything ("restrict none"), one ends up with stray disulfide bonds, hydrogen bonds, or surfaces. I vote for "restrict" in Jmol to hide *all* renderings. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <40656.80.58.16.235.1076788531.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: compatible *restrict* behavior Date: Sun, 15 Feb 2004 00:02:17 +0100 (CET) To: rasmol@lists.umass.edu Cc: roger@eyesopen.com, jmol-developers@lists.sourceforge.net >> Q: Is it the case that 'restrict' applies to *all* graphic shapes ... >> cartoons, strands, etc? > > The intention is that RasMol's restrict command applies to all graphics > representations. The documentation was written when there were only a > handful of representations used by RasMol, and (of course) it was rarely > updated as new representations were subsequently added. Very good. Thanks! Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-pair-Authenticated: 209.197.6.81 References: <5.2.0.9.2.20040214162154.0213f918@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: compatible *restrict* behavior Date: Sat, 14 Feb 2004 23:15:49 -0500 To: rasmol@lists.umass.edu, jmol-developers@lists.sourceforge.net I am agreeable to cleaning up this problem to the extent it exists in RasMol 2.7. Please forward sample scripts for which "restrict none" leaves around artifacts and I'll fix as many as possible in the 2.7.3 test release that will be coming up shortly after the 2.7.2.1.1 release is finished. -- HJB At 4:29 PM -0500 2/14/04, Eric Martz wrote: >I would love to see Jmol's "restrict" command turn off all >renderings. The fact that neither RasMol nor Chime do this is >problematic. Typically, when trying to hide everything ("restrict >none"), one ends up with stray disulfide bonds, hydrogen bonds, or >surfaces. > >I vote for "restrict" in Jmol to hide *all* renderings. > > > >/* - - - - - - - - - - - - - - - - - - - - - - - - - - - >Protein Explorer - 3D Visualization: http://proteinexplorer.org >Workshops: http://www.umass.edu/molvis/workshop >World Index of Molecular Visualization Resources: http://molvisindex.org >ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il >Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm >PDB Lite Macromolecule Finder: http://pdblite.org >Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > >Eric Martz, Professor Emeritus, Dept Microbiology >U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz >- - - - - - - - - - - - - - - - - - - - - - - - - - - */ > -- ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com References: <47243.80.58.16.235.1076895342.squirrel@www.howards.org> <4030A29D.60209@imb-jena.de> <33383.212.128.142.26.1076930485.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 09:38:44 -0500 (EST) To: Miguel Howard Cc: jmol-users@lists.sourceforge.net, jr@imb-jena.de, rasmol@lists.umass.edu To help get us all on the same page, I have prepared a draft positioning test at: http://arcib.dowling.edu/~BernsteH/postest/ I will run rasmol for a variety of platforms (including sgi, mac and windows )through this test later today and see if we have gotten turned around on any of them. In any case it is the intention, as stated in the manual for y to be increasing going down and x to be increasing going to the right. Regards, Herbert ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 16 Feb 2004, Miguel Howard wrote: > >>So, RasMol/Chime is right-handed, but it has the +Y axis pointing > >> *down*. > >> > >> > > no, only the Windows version, > > I do not believe that it is only the Windows version. > RasMol 2.6b2 also has the +Y axis pointed down. > Since RasMol had it in this orientation, so does Chime. > > > on Irix RasMol2.7.2.1 shows up with true right-handed annotated axis > > system, but > > By 'true right-handed' I assume that you mean that +Y goes up. > > Someone else also told me that this changed in RasMol 2.7 > > At the present time I am not in a position where I can verify that with > RasMol 2.7. > > >>(Note that we are going to try to keep this relatively simple by not > >> yet introducing the issue of rotations about the axes) > >> > >> > > that is a problem, > > though rotation on x and z are as expected, y rotation is not on Irix > > (but it is in agreement with with the wrong axis annotation in RasWin) > > this should be corrected in RasMol and RasWin, too. > > We will discuss the rotation issues very soon. > > First I want to get everyone to understand the current status of Chime and > the various versions of RasMol regarding axis orientation. > > The rotation issue will be more difficult for people to understand and > will have a much larger impact on existing scripts. > > > >>What do people think we should do about it? > >> > >> 1. Maintain RasMol/Chime compatibility ... +Y points down > >> - RasMol/Chime users are used to seeing their molecules > >> in this orientation > >> - won't break existing scripts > >> - nobody really cares, just leave it alone > >> > >> > >> 2. Break RasMol/Chime compatibility ... +Y points up > >> - this is the way it should have been done in the > >> first place, we have an opportunity to fix it, > >> let's not propogate errors > >> - if someone *really* needs to see their molecules > >> in the RasMol/Chime orientation they can just do a > >> 'rotate x 180' > >> > >> > > I vote for 2 don't pollute the Jmol code with bugs. > > OK > > >> 3. Support both > >> - just add a switch/script command to Jmol > >> - it is easy to do ... Jmol already does both > >> - Q: What should the *default* orientation be? > >> - Q: What do you call this switch in a menu? > >> - Q: Any proposal for what the script command should be? > >> > > > Miguel > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- jr@imb-jena.de Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 16:35:13 +0100 (CET) To: rasmol@lists.umass.edu Cc: yaya@bernstein-plus-sons.com, jmol-users@lists.sourceforge.net, Herbert said: > To help get us all on the same page, I have prepared a draft > positioning test at: > > http://arcib.dowling.edu/~BernsteH/postest/ > > I will run rasmol for a variety of platforms (including sgi, mac and > windows )through this test later today and see if we have gotten > turned around on any of them. Thanks for posting this. It is helpful. There were several follow-up messages about this on jmol-users, and you may not have been copied on some critical ones. I believe that the general concensus is that the confusion is caused by a labelling error in RasWin (and possibly some older versions of RasMol). Jan says that RasWin puts the Y label at the *top* of the axis, which is actually the negative end. Nevertheless, the coordinate system *is* right-handed ... it was only a labelling issue. Jan also says that this problem does not exist in RasMol 2.7 > In any case it is the intention, > as stated in the manual for y to be increasing going down and x > to be increasing going to the right. This was actually the genesis of the discussion on jmol-users ... the fact that the +Y axis goes down. The axis orientation discussion was a prelude to the *real* discussion that we need to have about the rotations in RasMol. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; de-AT; rv:1.6) Gecko/20040113 X-Accept-Language: de, en-us, en References: <47243.80.58.16.235.1076895342.squirrel@www.howards.org> <4030A29D.60209@imb-jena.de> <33383.212.128.142.26.1076930485.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 16:37:36 +0100 To: rasmol@lists.umass.edu Cc: jmol-users@lists.sourceforge.net Herbert J. Bernstein schrieb: >To help get us all on the same page, I have prepared a draft positioning >test at: > > http://arcib.dowling.edu/~BernsteH/postest/ > >I will run rasmol for a variety of platforms (including sgi, mac >and windows )through this test later today and see if we have gotten >turned around on any of them. In any case it is the intention, >as stated in the manual for y to be increasing going down and x >to be increasing going to the right. > > I would suggest to change the manual to get a right handed system timothy driscoll schrieb: >>Q: Given that there *are* existing applications and tutorials, what do you >>think we should do about this issue? >> >> >> >a right-handed orientation "seems" more natural to me, though I am >hard-pressed to explain why (I'm left-handed). > > > > >>Q: Do other molecular visualization applications have the +Y axis pointing >>upwards or downwards? >> >> >> >I can take a look... > > RasMol2.7 Irix (starts with rotate x 180) translation Y down, X right, Z to front (rotation after a rotate x 180 command! x+ y+ z- ) InsightII (starts as expected) translation: Y up, X right, Z to front (rotation x+, y+, z-) MolMol (as expected) Y up, X right, Z ? (rotation x+, y+, z+) MolScript (as expected) Y up, X right, Z ? according documentation, to the front (rotation x+, y+, z+) +rotation means right handed (as the fingers around the thumb pointing to positive values) I suggest, lets make it like MolMol and MolScript. Regards, Jan ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com References: <33609.212.128.142.26.1076945713.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 10:47:04 -0500 (EST) To: rasmol@lists.umass.edu Cc: jmol-users@lists.sourceforge.net, jr@imb-jena.de RasMol 2.6 is not the current version, and it is not very productive to work from that as a base, nor does it make sense to drop back and fix problems in such an old version. The best current release is RasMol 2.7.2.1. I am working on a final clean up to 2.7.2 that will be released shortly as 2.7.2.1.1. Then I will incorporate the next round of improvements into 2.7.3. If there is a problem with axis labelling, I will be happy to fix it in 2.7.3, but first we need to know for sure what we want to do. I believe most users are used to the coordinate system in the manual in which the Y axis goes down and the X axis run to the right. Is there some disagreement about that? -- Herbert ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 16 Feb 2004, Miguel Howard wrote: > Herbert said: > > > To help get us all on the same page, I have prepared a draft > > positioning test at: > > > > http://arcib.dowling.edu/~BernsteH/postest/ > > > > I will run rasmol for a variety of platforms (including sgi, mac and > > windows )through this test later today and see if we have gotten > > turned around on any of them. > > Thanks for posting this. It is helpful. > > There were several follow-up messages about this on jmol-users, and you may > not have been copied on some critical ones. > > I believe that the general concensus is that the confusion is caused by > a labelling error in RasWin (and possibly some older versions of RasMol). > > Jan says that RasWin puts the Y label at the *top* of the axis, which > is actually the negative end. > > Nevertheless, the coordinate system *is* right-handed ... it was only a > labelling issue. > > Jan also says that this problem does not exist in RasMol 2.7 > > > > In any case it is the intention, > > as stated in the manual for y to be increasing going down and x > > to be increasing going to the right. > > This was actually the genesis of the discussion on jmol-users ... the fact > that the +Y axis goes down. > > The axis orientation discussion was a prelude to the *real* discussion > that we need to have about the rotations in RasMol. > > > Miguel > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- jr@imb-jena.de Importance: Normal References: <33609.212.128.142.26.1076945713.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 17:45:32 +0100 (CET) To: rasmol@lists.umass.edu Cc: yaya@bernstein-plus-sons.com, jmol-users@lists.sourceforge.net, Herbert, > RasMol 2.6 is not the current version, and it is not very productive to > work from that as a base, In general I agree that people should use the current version of OpenRasMol. However, in my particular case I have two special reasons for running 2.6: 1. My primary motivation for working on Jmol is to build a Chime replacement. Since 2.6 was the basis for Chime, I think it makes sense for me to use it. 2. I have recently had the need to look at the source code in order to understand the rules for hydrogen bonding. Since the 2.6 source code is in the public domain, I can read the source code without infringing upon any licensing issues. I am not doing any real *work* with RasMol :-) > nor does it make sense to drop back > and fix problems in such an old version. I agree. > The best current release is > RasMol 2.7.2.1. I am working on a final clean up to 2.7.2 that will be > released shortly as 2.7.2.1.1. Then I will incorporate > the next round of improvements into 2.7.3. If there is a problem > with axis labelling, I will be happy to fix it in 2.7.3, but first we > need to know for sure what we want to do. Jan indicated that the labelling was *not* an issue in 2.7.? on Irix. He indicated that the Y axes labelling was a problem with RasWin. He did not say which version. (For my part, I don't understand the RasMol lineage/progeny well enough to know where RasWin fits in relative to RasMol 2.6 or 2.7 :-) > I believe most users are used > to the coordinate system in the manual in which the Y > axis goes down and the X axis run to the right. Is there some > disagreement about that? I will address this in a separate email. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com References: <33609.212.128.142.26.1076945713.squirrel@www.howards.org> <33624.212.128.142.26.1076949932.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 12:08:53 -0500 (EST) To: Miguel Howard Cc: rasmol@lists.umass.edu, jmol-users@lists.sourceforge.net, jr@imb-jena.de The only possible license conflict in using RasMol 2.7 as a base would be if you were planning to make a non-open-source derivative. Is jmol changing from being open source? If you are concerned about the different license wording used for RasMol, we will be able to move over to the GPL once we have excised the GIF code. Richard Stallman has agreed that the CIF code does not create a conflict. Your real problem arises if you download and use Chime. The MDL license forbids reverse engineering. Use of 2.6 as a base will just create yet another slightly different variant of RasMol and propogate some rather arcane bugs for a few more years. Regards, Herbert P.S. I have corrected a couple of typos on the postest page. As part of a right-handed system, the Z axis should run from the front to the back, not the back to the front. ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 16 Feb 2004, Miguel Howard wrote: > Herbert, > > > RasMol 2.6 is not the current version, and it is not very productive to > > work from that as a base, > > In general I agree that people should use the current version of OpenRasMol. > > However, in my particular case I have two special reasons for running 2.6: > 1. My primary motivation for working on Jmol is to build > a Chime replacement. Since 2.6 was the basis for Chime, > I think it makes sense for me to use it. > 2. I have recently had the need to look at the source code > in order to understand the rules for hydrogen bonding. > Since the 2.6 source code is in the public domain, I > can read the source code without infringing upon any > licensing issues. > > I am not doing any real *work* with RasMol :-) > > > > nor does it make sense to drop back > > and fix problems in such an old version. > > I agree. > > > The best current release is > > RasMol 2.7.2.1. I am working on a final clean up to 2.7.2 that will be > > released shortly as 2.7.2.1.1. Then I will incorporate > > the next round of improvements into 2.7.3. If there is a problem > > with axis labelling, I will be happy to fix it in 2.7.3, but first we > > need to know for sure what we want to do. > > Jan indicated that the labelling was *not* an issue in 2.7.? on Irix. > > He indicated that the Y axes labelling was a problem with RasWin. He did > not say which version. > > (For my part, I don't understand the RasMol lineage/progeny well enough to > know where RasWin fits in relative to RasMol 2.6 or 2.7 :-) > > > > I believe most users are used > > to the coordinate system in the manual in which the Y > > axis goes down and the X axis run to the right. Is there some > > disagreement about that? > > I will address this in a separate email. > > > > Miguel > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com References: <33609.212.128.142.26.1076945713.squirrel@www.howards.org> <33624.212.128.142.26.1076949932.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 12:13:39 -0500 (EST) To: rasmol@lists.umass.edu Cc: jmol-users@lists.sourceforge.net, jr@imb-jena.de RasWin is just the name of the Winodws executable of RasMol. Most of the code for the Windows, Mac and X-Windows versions of RasMol is identical. So there is a RasWin for each version of RasMol. ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 16 Feb 2004, Miguel Howard wrote: > > (For my part, I don't understand the RasMol lineage/progeny well enough to > know where RasWin fits in relative to RasMol 2.6 or 2.7 :-) > > Miguel > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <33609.212.128.142.26.1076945713.squirrel@www.howards.org> <33624.212.128.142.26.1076949932.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 18:49:32 +0100 (CET) To: yaya@bernstein-plus-sons.com Cc: rasmol@lists.umass.edu, jmol-users@lists.sourceforge.net, jr@imb-jena.de Herbert said: > The only possible license conflict in using RasMol 2.7 as a base would > be if you were planning to make a non-open-source derivative. Is jmol > changing from being open source? We've had this discussion before ... There are no plans to change Jmol from being open source. > If you are concerned about the > different license wording used for RasMol, we will be able to move over > to the GPL once we have excised the GIF code. Richard Stallman has > agreed that the CIF code does not create a conflict. Per our email exchanges last year, I am not comfortable using the 2.7 code until it is available under a GPL license. This is especially the case because of the history of the RasMol licensing terms. And because you indicated that the GIF code was a particular problem with the GPL terms. I believe that you previously indicated that you were hoping that your students could get most of the work done during the Fall of 2003. Once OpenRasMol is available under GPL I will be eager to use it. > Your real problem arises if you download and use Chime. The MDL > license forbids reverse engineering. Thank you. I am aware of the MDL licensing terms. > Use of 2.6 as a base will just create yet another slightly different > variant of RasMol and propogate some rather arcane bugs for a few > more years. I appreciate your concern. I am comfortable that I am using 2.6 as a reference, not as a base. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- jr@imb-jena.de Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: +Y axis orientation Date: Mon, 16 Feb 2004 19:13:11 +0100 (CET) To: rasmol@lists.umass.edu Cc: yaya@bernstein-plus-sons.com, jmol-users@lists.sourceforge.net, Herbert said: > I believe most users are used > to the coordinate system in the manual in which the Y > axis goes down and the X axis run to the right. Is there some > disagreement about that? I wouldn't say that there is *disagreement* ... but I would say that the fact that the +Y axis points down was an unfortunate choice. We have been discussing this on the jmol-users mailing list as a smaller group prior to bringing it to the broader rasmol list. I believe that an outsider or newcomer taking a look at this would naturally assume that the +Y axis points up: - effectively all 2D graphs have +Y pointing upwards - 3D graphs in math textbooks have the +Y axis pointing upwards and the +Z axis coming out of the page - OpenGL has the +Y axis pointing up - VRML has the +Y axis pointing up It is true that most computer windowing systems have the increasing Y axis going down the page. But in my opinion we should insulate the end-users from this technical artifact. Our discussion has been whether Jmol should: 1. maintain RasMol/Chime compatibility and keep +Y going down 2. drop compatibility and make +Y point up 3. offer a backward-compatibility switch/setting in order to support both axis orientations. In general, those who have voiced opinions on jmol-users have advocated options 2 or 3. I was more comfortable having the initial discussion on jmol-users with a smaller group of people. But, we got 'sidetracked' because of confusion caused by erroneous Y axis labelling in some version of RasWin ... Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com References: <47243.80.58.16.235.1076895342.squirrel@www.howards.org> <4030A29D.60209@imb-jena.de> <33383.212.128.142.26.1076930485.squirrel@www.howards.org> <4030E3C0.3090309@imb-jena.de> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 13:30:34 -0500 (EST) To: rasmol@lists.umass.edu Cc: jmol-users@lists.sourceforge.net > RasMol2.7 Irix (starts with rotate x 180) translation Y down, X right, > Z to front (rotation after a rotate x 180 command! x+ y+ z- ) I have just done a clean recompile and install of the SGI version of release 2.7.2.1.1. I get a right-handled system with Z running into the screen, Y running down the screen and X running from left to right. Is there a Z-inversion happening somewhere to produce the left-handed "RasMol2.7 Irix" display? -- Herbert ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 16 Feb 2004, Jan Reichert wrote: > Herbert J. Bernstein schrieb: > > >To help get us all on the same page, I have prepared a draft positioning > >test at: > > > > http://arcib.dowling.edu/~BernsteH/postest/ > > > >I will run rasmol for a variety of platforms (including sgi, mac > >and windows )through this test later today and see if we have gotten > >turned around on any of them. In any case it is the intention, > >as stated in the manual for y to be increasing going down and x > >to be increasing going to the right. > > > > > I would suggest to change the manual to get a right handed system > > timothy driscoll schrieb: > > >>Q: Given that there *are* existing applications and tutorials, what do you > >>think we should do about this issue? > >> > >> > >> > >a right-handed orientation "seems" more natural to me, though I am > >hard-pressed to explain why (I'm left-handed). > > > > > > > > > >>Q: Do other molecular visualization applications have the +Y axis pointing > >>upwards or downwards? > >> > >> > >> > >I can take a look... > > > > > RasMol2.7 Irix (starts with rotate x 180) translation Y down, X right, > Z to front (rotation after a rotate x 180 command! x+ y+ z- ) > InsightII (starts as expected) translation: Y up, X right, Z to front > (rotation x+, y+, z-) > MolMol (as expected) Y up, X right, Z ? (rotation x+, y+, z+) > MolScript (as expected) Y up, X right, Z ? according documentation, to > the front (rotation x+, y+, z+) > > +rotation means right handed (as the fingers around the thumb pointing > to positive values) > > I suggest, lets make it like MolMol and MolScript. > Regards, Jan > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 20:13:50 +0100 (CET) To: yaya@bernstein-plus-sons.com Cc: rasmol@lists.umass.edu > I have just done a clean recompile and install of the SGI version of > release 2.7.2.1.1. I get a right-handled system with Z running into > the screen, Y running down the screen and X running from left to > right. > > Is there a Z-inversion happening somewhere to produce the left-handed > "RasMol2.7 Irix" display? Herbert, I did not interpret Jan's message as saying that he saw a left-handed RasMol 2.7 Irix display. On the contrary, Jan was quite clear that the system was always right-handed, and that this RasWin issue was just a labelling problem. He did not say which version of RasWin. What may have caused some of the confusion is that I believe that that Jan is advocating a change to make the default +Y axis orientation point upwards. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com References: <60349.80.58.16.235.1076958830.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 14:32:22 -0500 (EST) To: rasmol@lists.umass.edu > RasMol2.7 Irix (starts with rotate x 180) translation Y down, X right, > Z to front (rotation after a rotate x 180 command! x+ y+ z- ) is a left-handed system. You have to put Z into the screen (to the back) to get a right-handed system. That is what RasMol produces. All you need to do if you like to have Y up and Z out is the rotate around X by 180, which can be done trivially at startup. ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 16 Feb 2004, Miguel Howard wrote: > > I have just done a clean recompile and install of the SGI version of > > release 2.7.2.1.1. I get a right-handled system with Z running into > > the screen, Y running down the screen and X running from left to > > right. > > > > Is there a Z-inversion happening somewhere to produce the left-handed > > "RasMol2.7 Irix" display? > > Herbert, > > I did not interpret Jan's message as saying that he saw a left-handed > RasMol 2.7 Irix display. > > On the contrary, Jan was quite clear that the system was always > right-handed, and that this RasWin issue was just a labelling problem. He > did not say which version of RasWin. > > What may have caused some of the confusion is that I believe that that Jan > is advocating a change to make the default +Y axis > orientation point upwards. > > > Miguel > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: de,en References: <47243.80.58.16.235.1076895342.squirrel@www.howards.org> <4030A29D.60209@imb-jena.de> <33383.212.128.142.26.1076930485.squirrel@www.howards.org> <4030E3C0.3090309@imb-jena.de> ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 20:37:10 +0100 To: rasmol@lists.umass.edu Herbert J. Bernstein wrote: >>RasMol2.7 Irix (starts with rotate x 180) translation Y down, X right, >>Z to front (rotation after a rotate x 180 command! x+ y+ z- ) >> >> Y down, X right, Z to front is right handed, but the rotation around the Z-axis is not. > >I have just done a clean recompile and install of the SGI version of >release 2.7.2.1.1. I get a right-handled system with Z running into >the screen, Y running down the screen and X running from left to right. > > yes, this is the start orientation in RasMol2.7.2.1, too ("rotate x 180" different from the orientation I expect a PDB file to show up in a molecular graphics program) look at published images from molecules, e.g. in the discussion of the poplar plastocyanin 1plc they call the flat surface with [His]87 near the copper the northern surface, but in RasMol2.7 it is "rotate x 180" and the acidic patch around [TYR]83 is shown on nearly every published plastocyanin image on the right side. So a RasMol user starts up with an unexpected view, when he has read a paper and starts RasMol to compare. I agree with Miguel, that it is better to change the RasMol documentation and start with Y up and X right Z out of the plain because the authors of the PDB files often deposited them with this orientation in mind. >Is there a Z-inversion happening somewhere to produce the left-handed >"RasMol2.7 Irix" display? > > no, not on Irix, only in RasWin2.7.2.1 the label of the Y axis is on the opposite side, which looks like left-handed, but translation indicates the right right-handed internal orientation. Regards, Jan >-- Herbert >===================================================== > Herbert J. Bernstein, Professor of Computer Science > Dowling College, Kramer Science Center, KSC 121 > Idle Hour Blvd, Oakdale, NY, 11769 > > +1-631-244-3035 > yaya@dowling.edu >===================================================== > >On Mon, 16 Feb 2004, Jan Reichert wrote: > > > >>Herbert J. Bernstein schrieb: >> >> >> >>>To help get us all on the same page, I have prepared a draft positioning >>>test at: >>> >>> http://arcib.dowling.edu/~BernsteH/postest/ >>> >>>I will run rasmol for a variety of platforms (including sgi, mac >>>and windows )through this test later today and see if we have gotten >>>turned around on any of them. In any case it is the intention, >>>as stated in the manual for y to be increasing going down and x >>>to be increasing going to the right. >>> >>> >>> >>> >>I would suggest to change the manual to get a right handed system >> >>timothy driscoll schrieb: >> >> >> >>>>Q: Given that there *are* existing applications and tutorials, what do you >>>>think we should do about this issue? >>>> >>>> >>>> >>>> >>>> >>>a right-handed orientation "seems" more natural to me, though I am >>>hard-pressed to explain why (I'm left-handed). >>> >>> >>> >>> >>> >>> >>>>Q: Do other molecular visualization applications have the +Y axis pointing >>>>upwards or downwards? >>>> >>>> >>>> >>>> >>>> >>>I can take a look... >>> >>> >>> >>> >>RasMol2.7 Irix (starts with rotate x 180) translation Y down, X right, >>Z to front (rotation after a rotate x 180 command! x+ y+ z- ) >>InsightII (starts as expected) translation: Y up, X right, Z to front >> (rotation x+, y+, z-) >>MolMol (as expected) Y up, X right, Z ? (rotation x+, y+, z+) >>MolScript (as expected) Y up, X right, Z ? according documentation, to >>the front (rotation x+, y+, z+) >> >>+rotation means right handed (as the fingers around the thumb pointing >>to positive values) >> >>I suggest, lets make it like MolMol and MolScript. >>Regards, Jan >> >> >> >> >> >-----------------------------------------------------ra > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com References: <47243.80.58.16.235.1076895342.squirrel@www.howards.org> <4030A29D.60209@imb-jena.de> <33383.212.128.142.26.1076930485.squirrel@www.howards.org> <4030E3C0.3090309@imb-jena.de> <40311BE6.7040206@imb-jena.de> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 15:28:32 -0500 (EST) To: rasmol@lists.umass.edu The initial orientation, Y down, X right, Z into the screen (not Z to the front) is right-handed, so the rotation around the Z-axis is right-handed as well. Unless someone has an example of an image coming up differently on some platform using RasMol 2.7, I don't think we should change the current default code. However, if there is a significant demand, I will be happy to include a command-line option to specify a initial screen orientation. I would appreciate suggestion on the way to interact with, say, the reset command to provide the best interaction with existing scripts. With so many users already working with the current initial orientation (X to the right, Y down, Z into the screen) it would be unwise to make a different orientation the default. -- HJB ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 16 Feb 2004, Jan Reichert wrote: > Herbert J. Bernstein wrote: > > >>RasMol2.7 Irix (starts with rotate x 180) translation Y down, X right, > >>Z to front (rotation after a rotate x 180 command! x+ y+ z- ) > >> > >> > Y down, X right, Z to front is right handed, but the rotation around the > Z-axis is not. > > > > >I have just done a clean recompile and install of the SGI version of > >release 2.7.2.1.1. I get a right-handled system with Z running into > >the screen, Y running down the screen and X running from left to right. > > > > > yes, this is the start orientation in RasMol2.7.2.1, too ("rotate x 180" > different from the orientation I expect a PDB file to show up in a > molecular graphics program) > look at published images from molecules, e.g. in the discussion of the > poplar plastocyanin 1plc they call the flat surface with [His]87 near > the copper the northern surface, but in RasMol2.7 it is "rotate x 180" > and the acidic patch around [TYR]83 is shown on nearly every published > plastocyanin image on the right side. So a RasMol user starts up with an > unexpected view, when he has read a paper and starts RasMol to compare. > I agree with Miguel, that it is better to change the RasMol > documentation and start with Y up and X right Z out of the plain because > the authors of the PDB files often deposited them with this orientation > in mind. > > >Is there a Z-inversion happening somewhere to produce the left-handed > >"RasMol2.7 Irix" display? > > > > > no, not on Irix, only in RasWin2.7.2.1 the label of the Y axis is on the > opposite side, which looks like left-handed, but translation indicates > the right right-handed internal orientation. > Regards, Jan > > >-- Herbert > >===================================================== > > Herbert J. Bernstein, Professor of Computer Science > > Dowling College, Kramer Science Center, KSC 121 > > Idle Hour Blvd, Oakdale, NY, 11769 > > > > +1-631-244-3035 > > yaya@dowling.edu > >===================================================== > > > >On Mon, 16 Feb 2004, Jan Reichert wrote: > > > > > > > >>Herbert J. Bernstein schrieb: > >> > >> > >> > >>>To help get us all on the same page, I have prepared a draft positioning > >>>test at: > >>> > >>> http://arcib.dowling.edu/~BernsteH/postest/ > >>> > >>>I will run rasmol for a variety of platforms (including sgi, mac > >>>and windows )through this test later today and see if we have gotten > >>>turned around on any of them. In any case it is the intention, > >>>as stated in the manual for y to be increasing going down and x > >>>to be increasing going to the right. > >>> > >>> > >>> > >>> > >>I would suggest to change the manual to get a right handed system > >> > >>timothy driscoll schrieb: > >> > >> > >> > >>>>Q: Given that there *are* existing applications and tutorials, what do you > >>>>think we should do about this issue? > >>>> > >>>> > >>>> > >>>> > >>>> > >>>a right-handed orientation "seems" more natural to me, though I am > >>>hard-pressed to explain why (I'm left-handed). > >>> > >>> > >>> > >>> > >>> > >>> > >>>>Q: Do other molecular visualization applications have the +Y axis pointing > >>>>upwards or downwards? > >>>> > >>>> > >>>> > >>>> > >>>> > >>>I can take a look... > >>> > >>> > >>> > >>> > >>RasMol2.7 Irix (starts with rotate x 180) translation Y down, X right, > >>Z to front (rotation after a rotate x 180 command! x+ y+ z- ) > >>InsightII (starts as expected) translation: Y up, X right, Z to front > >> (rotation x+, y+, z-) > >>MolMol (as expected) Y up, X right, Z ? (rotation x+, y+, z+) > >>MolScript (as expected) Y up, X right, Z ? according documentation, to > >>the front (rotation x+, y+, z+) > >> > >>+rotation means right handed (as the fingers around the thumb pointing > >>to positive values) > >> > >>I suggest, lets make it like MolMol and MolScript. > >>Regards, Jan > >> > >> > >> > >> > >> > >-----------------------------------------------------ra > > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <47243.80.58.16.235.1076895342.squirrel@www.howards.org> <4030A29D.60209@imb-jena.de> <33383.212.128.142.26.1076930485.squirrel@www.howards.org> <4030E3C0.3090309@imb-jena.de> <40311BE6.7040206@imb-jena.de> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 21:34:42 +0100 (CET) To: rasmol@lists.umass.edu >>>RasMol2.7 Irix (starts with rotate x 180) translation Y down, X >>> right, Z to front (rotation after a rotate x 180 command! x+ y+ z- >>> ) >>> >>> > Y down, X right, Z to front is right handed, Jan, what you have just described is a left-handed system. thumb -> +X index -> +Y middle -> +Z > but the rotation around the Z-axis is not. I believe that the rotations in RasMol are not consistently right-handed. > I agree with Miguel, that it is better to change the RasMol > documentation and Just to clarify ... I have not advocated making *any* changes to RasMol documention or RasMol. It would not be my place to do so. I *did* ask the question in the context of *Jmol* because: - the default orientation of +Y going down seems unnatural to me - the rotations are not consistently right-handed So, in the context of Jmol, I have raised the question of whether it is appropriate to propogate these characteristics. And, if we want to make changes, whether or not we should have a switch to maintain backward-compatibility. >>Is there a Z-inversion happening somewhere to produce the left-handed >> "RasMol2.7 Irix" display? >> >> > no, not on Irix, only in RasWin2.7.2.1 the label of the Y axis is on the > opposite side, which looks like left-handed, but translation indicates > the right right-handed internal orientation. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: RasMol rotations about axes Date: Tue, 17 Feb 2004 01:37:23 +0100 (CET) To: jmol-users@lists.sourceforge.net, rasmol@lists.umass.edu Summary ======= I may be wrong on this, so I need people to check my work ... It looks to me like the RasMol rotations about axes are not consistently right-handed. We need to discuss this and try to figure out what to do about it ... if anything ... whether or not it is something we need to *fix* in Jmol. The bad news is that changing the rotation behavior would break every script that uses the 'rotate y ' command or the Chime 'move' command. The good news is that the repair is quite easy. Should Jmol be 100% RasMol/Chime compatible? Should Jmol only support a fully right-handed system? Can't we have both? Detail ====== I think we have the general understanding that the axis orientation in RasMol is right-handed. With the default orientation of having - +X to the right - +Y going down - +Z into the screen The general feeling from the jmol-users seems to be that we should offer the option of having +Y go up and +Z come out of the screen. Many think that this is a more natural orientation that is adopted by math textbooks, OpenGL, VRML, etc. Now, we need to talk about the rotations. As I understand it, a right-handed rotation should be counter-clockwise when the viewer is positioned on the + axis and is looking towards the origin. To visualize it with your hand ... - with your right hand - extend your thumb - curl your fingers - point your thumb at your nose - you are looking at the origin from the + end of the axis - your fingers are pointing in the direction of the rotation I believe that this is consistent with Anthony Stone's previous email to jmol-users. Let's look at the axis rotations in RasMol ... load someMolecule set axes on rotate x 10 You then need to take the mouse and wiggle it a little. I observe that the +Z axis (which is in the back) comes up. Point your thumb to the right with your fingers curled. The fingers are curling up from the back. This means that RasMol did a right-handed rotation around the X axis. Good. Let's skip to the Z axis reset rotate z 10 I observe that the +X drops on the right. The +Z axis goes into the screen. Point your right thumb into the screen. Your fingers are curling down on the right. RasMol is doing a right-hand rotation around the Z axis. Good. Finally, let's look at the Y axis reset rotate y 10 I observe that the +Z axis at the back moves to the left. The +Y axis points down, so point your right thumb down. Fingers are curling around back to the *right* ... but +Z moved to the *left*. Huh? Try it with your left hand. Thumb down, fingers curl to the left, +Z moved to the left ... it sure looks like to me that RasMol is doing a left-hand rotation around the Y axis. I have looked at this several dozen times over the past 6 months. At first I wasn't confident of my observations, but now I have convinced myself. But I may be wrong ... I certainly have struggled with this 'handedness' stuff :-) Q: Please post some independent confirmations telling me that you concur ... or explaining my error :-) Q: I have not tried this in Chime ... can someone check it out and confirm that it behaves the same way? Q: Can someone also confirm that the chime 'move' command about the y axis is also left-handed? Unfortunately, this has pretty big implications for someone who has a large investment in existing scripts (Eric?). It means that all moves and rotates around the Y axis need to be negated. At least it isn't difficult. My goal for Jmol has been to get as close as possible to 100% RasMol/Chime script compatibility, to ease the migration path for people who have existing scripts. But this might be a pretty big change for people who have an investment in tutorials/courseware. As I see it, the options are pretty similar to the Axis Orientation question: 1. Jmol should only support RasMol/Chime rotations - people have made an investment in existing RasMol/Chime scripts - it works fine, leave it alone - people are used to seeing it behave this way - it doesn't really matter, no one has looked at it for years so nobody really cares 2. Jmol should be completely right-handed - the system should be consistently right-handed - the fact that y rotates backwards is a design flaw that should be corrected, not propogated - people have been confused by this for years - noone is going to use existing scripts anyway - OR, those who have scripts can easily change them - OR, just write a script converter that will fix existing scripts ... just negate the parameter to 'rotate y ' and 'move x z ...' commands 3. Jmol should offer both - it is easy to support both Q: What should the default orientation be in Jmol? Q: What should the script command be to change the setting? Q: Is this *exactly* the same switch that controls the Y axis orientation? I am interested in your thoughts and feedback. Thanks, Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline User-Agent: Mutt/1.5.1i References: <50647.80.58.16.235.1076978243.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Wayne M Barnes Subject: Re: RasMol rotations about axes Date: Mon, 16 Feb 2004 19:14:12 -0600 To: rasmol@lists.umass.edu Thank you Miguel; that was fun. On my Rasmol 2.6, the command set axes on puts X and Z at their positive ends, but Y at the top, which you say is negative. [Why does the Y axis point down, anyway. If it pointed up, the rotations would be fine.] If you want Y to point down, this axis label Y should be down there, too. - Wayne On Tue, Feb 17, 2004 at 01:37:23AM +0100, Miguel Howard wrote: > Summary > ======= > I may be wrong on this, so I need people to check my work ... > > It looks to me like the RasMol rotations about axes are not consistently > right-handed. [message cut here] -- Wayne M. Barnes, Ph.D. wayne@barnes1.wustl.edu Biochemistry Dept. 8231 fax: 314.754.9556 Washington Univ. Medical School ph: 314.362.3351 660 South Euclid Ave., St. Louis, MO 63110 http://barnes1.wustl.edu Just plain Taq is old tech anymore. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com References: <50647.80.58.16.235.1076978243.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: RasMol rotations about axes Date: Mon, 16 Feb 2004 20:15:41 -0500 (EST) To: rasmol@lists.umass.edu Cc: jmol-users@lists.sourceforge.net Dear Miguel, I think you are right. Once again, the best fix would be a command line switch. Changing the default would break lots of scripts. Clearly Jmol is an independent program and its developers can do whatever they think best, but with over a million existing rasmol users worldwide, providing them with a program that works in a similar fashion when they are using a browser might be a good idea. Regards, Herbert ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Tue, 17 Feb 2004, Miguel Howard wrote: > Summary > ======= > I may be wrong on this, so I need people to check my work ... > > It looks to me like the RasMol rotations about axes are not consistently > right-handed. > > We need to discuss this and try to figure out what to do about it ... if > anything ... whether or not it is something we need to *fix* in Jmol. > > The bad news is that changing the rotation behavior would break every > script that uses the 'rotate y ' command or the Chime 'move' > command. The good news is that the repair is quite easy. > > Should Jmol be 100% RasMol/Chime compatible? > Should Jmol only support a fully right-handed system? > Can't we have both? > > > Detail > ====== > I think we have the general understanding that the axis orientation in > RasMol is right-handed. With the default orientation of having > - +X to the right > - +Y going down > - +Z into the screen > > The general feeling from the jmol-users seems to be that we should offer > the option of having +Y go up and +Z come out of the screen. Many think > that this is a more natural orientation that is adopted by math > textbooks, OpenGL, VRML, etc. > > > > Now, we need to talk about the rotations. > > As I understand it, a right-handed rotation should be counter-clockwise > when the viewer is positioned on the + axis and is looking towards the > origin. > > To visualize it with your hand ... > - with your right hand > - extend your thumb > - curl your fingers > - point your thumb at your nose > - you are looking at the origin from the + end of the axis > - your fingers are pointing in the direction of the rotation > > I believe that this is consistent with Anthony Stone's previous email to > jmol-users. > > Let's look at the axis rotations in RasMol ... > > load someMolecule > set axes on > rotate x 10 > > You then need to take the mouse and wiggle it a little. I observe that > the +Z axis (which is in the back) comes up. > > Point your thumb to the right with your fingers curled. The fingers are > curling up from the back. This means that RasMol did a right-handed > rotation around the X axis. Good. > > Let's skip to the Z axis > > reset > rotate z 10 > > I observe that the +X drops on the right. The +Z axis goes into the > screen. Point your right thumb into the screen. Your fingers are curling > down on the right. RasMol is doing a right-hand rotation around the Z > axis. Good. > > Finally, let's look at the Y axis > > reset > rotate y 10 > > I observe that the +Z axis at the back moves to the left. The +Y axis > points down, so point your right thumb down. Fingers are curling around > back to the *right* ... but +Z moved to the *left*. Huh? > > Try it with your left hand. Thumb down, fingers curl to the left, +Z > moved to the left ... it sure looks like to me that RasMol is doing a > left-hand rotation around the Y axis. > > > > I have looked at this several dozen times over the past 6 months. At > first I wasn't confident of my observations, but now I have convinced > myself. But I may be wrong ... I certainly have struggled with this > 'handedness' stuff :-) > > Q: Please post some independent confirmations telling me that you concur ... > or explaining my error :-) > > Q: I have not tried this in Chime ... can someone check it out and > confirm that it behaves the same way? > > Q: Can someone also confirm that the chime 'move' command about the y > axis is also left-handed? > > > Unfortunately, this has pretty big implications for someone who has a > large investment in existing scripts (Eric?). It means that all moves and > rotates around the Y axis need to be negated. At least it isn't difficult. > > My goal for Jmol has been to get as close as possible to 100% RasMol/Chime > script compatibility, to ease the migration path for people who have > existing scripts. But this might be a pretty big change for people who > have an investment in tutorials/courseware. > > As I see it, the options are pretty similar to the Axis Orientation > question: > > 1. Jmol should only support RasMol/Chime rotations > - people have made an investment in existing > RasMol/Chime scripts > - it works fine, leave it alone > - people are used to seeing it behave this way > - it doesn't really matter, no one has looked > at it for years so nobody really cares > > 2. Jmol should be completely right-handed > - the system should be consistently right-handed > - the fact that y rotates backwards is a design > flaw that should be corrected, not propogated > - people have been confused by this for years > - noone is going to use existing scripts anyway > - OR, those who have scripts can easily change them > - OR, just write a script converter that will > fix existing scripts ... just negate the parameter > to 'rotate y ' and 'move x z ...' > commands > > 3. Jmol should offer both > - it is easy to support both > Q: What should the default orientation be in Jmol? > Q: What should the script command be to change > the setting? > Q: Is this *exactly* the same switch that controls > the Y axis orientation? > > > > I am interested in your thoughts and feedback. > > > Thanks, > Miguel > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; fr-FR; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: fr-fr, fr References: <50647.80.58.16.235.1076978243.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Jean-Philippe Demers Subject: Re: RasMol rotations about axes Date: Tue, 17 Feb 2004 00:16:27 -0500 To: rasmol@lists.umass.edu --Boundary_(ID_726NahPBNJd/sVmUAG8zDw) Hello! This has been my first appearance in the list for months; I've begun my B.Sc an it takes a lot of time/work... Since the beginning of Jmol development, it's not the first time that there's a struggle between changing the current Rasmol scripting language and keeping it as it is. First, there was the insertion code, and then it's the axis orientation and who knows what will be next. In fact, as the Jmol code gets written, it is normal that some features seem (to the development team at least) to be better designed in another way than they were in Chime/Rasmol. There are advantages to keep the current scripting format (backward compatibility with previous material so no need to modify this material, people are used to it...) as well as to change it (more logical/intuitive approach, more similar to what is used elsewhere in science and computing, better implementation of a feature, and not carrying a flaw that was in a previous software). There is the third option for Jmol to be able to interpret two scripting languages that has not been discussed a lot. It's certain that there are some disadvantages to that: need for a more complex interpreter, need for a mechanism to distinguish the two scripting language, more hassle for the script developer. However, in my mind, two facts stand clear. First, there is too much stuff out there that already uses the Chime/Rasmol scripting language so that we can say, "no one is going to use existing scripts anyway". Of course, it would be easy to modify the current scripts - I guess there will code to change anyway when we will definitely move to Jmol - but how time and labour-consuming this will be! Second fact, there will be a demand for the addition of new features to Jmol and, along with each new feature, there will be a new command added to the scripting language (and the new command will generate a syntax error if run in Chime/Rasmol). Here I discuss some ways this option could be implemented in Jmol. First, a script has an effect either on the molecule display or on the "state" of the molecule in the software memory. If two languages are supported, they can have a direct effect on the molecule; this choice would require two interpreters. Alternatively, one language could be translated into the other and the latter will affect the loaded molecule. (Interestingly, it is stated in the Chime documentation that CSML (a mere scripting language) is supported by Chime, in addition to Rasmol scripts. A CSML script is just translated into a Rasmol script and then sent to be executed). This choice would require only a script interpreter, but also a translator. It is also now a good time to think about the evolution of Jmol. I take as an asset that the development of Jmol will be rapid and continuous: addition of several features but nothing can be done perfectly at first, so there will be adjustments made to the implemented features. How can the scripting language used by Jmol cope with that? Should a script specify the version of the language in which it is written? Nevertheless, HTML has the !DOCTYPE tag to identify the version of the language used. However, it would be cumbersome to have an interpreter or a translation if there are dozens of versions of different languages. This brings us to the second problem: how to tell which language or which version a script uses. This reminds me that Mr. Bernstein had suggested to implement a command switch, a compromise that IMO does not solve the problems involved: It would add a new command (for sure not recognized by Chime, which could even less interpret the other scripting language) and would allow the sudden switching of language into a script, a situation that could introduce some confusion in the coding and interpretation of scripts. For the two facts stated below, it would not be a good idea to make a compromise language that would mix new and old, apples and oranges :-) . A solution could be to include the script specifications as comments at the beginning of the script. Another solution could be to handle each format differently. Each format could have its own file extension and MIME type. I don't know yet how scripts are handled in Jmol but there could be a way of telling the script specifications to the applet, with a PARAM tag for instance. This was my two cents; I hope it will help the development of Jmol or that it will create more debates among us, Rasmolers, Chimeleons and Jmolers. Jean-Philippe Demers Herbert J. Bernstein a écrit: >Dear Miguel, > > I think you are right. Once again, the best fix would be a >command line switch. Changing the default would break lots >of scripts. > > Clearly Jmol is an independent program and its developers >can do whatever they think best, but with over a million >existing rasmol users worldwide, providing them with >a program that works in a similar fashion when they are >using a browser might be a good idea. > > Regards, > Herbert > > --Boundary_(ID_726NahPBNJd/sVmUAG8zDw)-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; de-AT; rv:1.6) Gecko/20040113 X-Accept-Language: de, en-us, en References: <47243.80.58.16.235.1076895342.squirrel@www.howards.org> <4030A29D.60209@imb-jena.de> <33383.212.128.142.26.1076930485.squirrel@www.howards.org> <4030E3C0.3090309@imb-jena.de> <40311BE6.7040206@imb-jena.de> <41808.80.58.16.235.1076963682.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Tue, 17 Feb 2004 08:14:26 +0100 To: rasmol@lists.umass.edu Miguel Howard schrieb: >>>>RasMol2.7 Irix (starts with rotate x 180) translation Y down, X >>>>right, Z to front (rotation after a rotate x 180 command! x+ y+ z- >>>>) >>>> >>>> >>>> >>>> >>Y down, X right, Z to front is right handed, >> >> > >Jan, what you have just described is a left-handed system. > > thumb -> +X > index -> +Y > middle -> +Z > > you are right, but I think I get confused myself because the slab method to detect z movements is difficult to interpret (I think there are bugs with this function (I noticed that only translate z -50, which I used first, but neither -40 nor -60 results in something which may be interpreted), I tried again on RasWin2.7.2.1 and Irix RasMol2.7.2.1 loading a second molecule into the scene and then try relative translate z motions, and it looks really right-handed. > > > >>but the rotation around the Z-axis is not. >> >> > >I believe that the rotations in RasMol are not consistently right-handed. > > > > >>I agree with Miguel, that it is better to change the RasMol >>documentation and >> >> > >Just to clarify ... I have not advocated making *any* changes to RasMol >documention or RasMol. It would not be my place to do so. > > that is true >I *did* ask the question in the context of *Jmol* because: > - the default orientation of +Y going down seems unnatural to me > - the rotations are not consistently right-handed > >So, in the context of Jmol, I have raised the question of whether it is >appropriate to propogate these characteristics. And, if we want to make >changes, whether or not we should have a switch to maintain >backward-compatibility. > > > > and I suggest, to alter this in future RasMol versions and hence, change the documentation. Regards, Jan > > >>>Is there a Z-inversion happening somewhere to produce the left-handed >>>"RasMol2.7 Irix" display? >>> >>> >>> >>> >>no, not on Irix, only in RasWin2.7.2.1 the label of the Y axis is on the >> opposite side, which looks like left-handed, but translation indicates >>the right right-handed internal orientation. >> >> > > >Miguel > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; de-AT; rv:1.6) Gecko/20040113 X-Accept-Language: de, en-us, en References: <50647.80.58.16.235.1076978243.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: RasMol rotations about axes Date: Tue, 17 Feb 2004 09:08:15 +0100 To: rasmol@lists.umass.edu Herbert J. Bernstein schrieb: >Dear Miguel, > > I think you are right. Once again, the best fix would be a >command line switch. Changing the default would break lots >of scripts. > > Clearly Jmol is an independent program and its developers >can do whatever they think best, but with over a million >existing rasmol users worldwide, providing them with >a program that works in a similar fashion when they are >using a browser might be a good idea. > > I agree, although I had loved the idea to get both programs totally right-handed and upside up. There is an other problem with the RasMol translate, it only translates in % of the view, especially since RasMol is able to load and manipulate up to 5 different molecules, it would be very useful to allow translation in A units e.g. translate x 50.0 would translate the selected molecule 50 A to the right side, not half out of the viewing area. > Regards, > Herbert >===================================================== > Herbert J. Bernstein, Professor of Computer Science > Dowling College, Kramer Science Center, KSC 121 > Idle Hour Blvd, Oakdale, NY, 11769 > > +1-631-244-3035 > yaya@dowling.edu >===================================================== > >On Tue, 17 Feb 2004, Miguel Howard wrote: > > > >>Summary >>======= >>I may be wrong on this, so I need people to check my work ... >> >>It looks to me like the RasMol rotations about axes are not consistently >>right-handed. >> >>We need to discuss this and try to figure out what to do about it ... if >>anything ... whether or not it is something we need to *fix* in Jmol. >> >>The bad news is that changing the rotation behavior would break every >>script that uses the 'rotate y ' command or the Chime 'move' >>command. The good news is that the repair is quite easy. >> >>Should Jmol be 100% RasMol/Chime compatible? >> >> grr, yes >>Should Jmol only support a fully right-handed system? >>Can't we have both? >> >> interpreter switches like #!RasMol -version 2.7 in contrast to #!Jmol -version 10 >> >>Detail >>====== >>I think we have the general understanding that the axis orientation in >>RasMol is right-handed. With the default orientation of having >> - +X to the right >> - +Y going down >> - +Z into the screen >> >>The general feeling from the jmol-users seems to be that we should offer >>the option of having +Y go up and +Z come out of the screen. Many think >>that this is a more natural orientation that is adopted by math >>textbooks, OpenGL, VRML, etc. >> >> >> >>Now, we need to talk about the rotations. >> >>As I understand it, a right-handed rotation should be counter-clockwise >>when the viewer is positioned on the + axis and is looking towards the >>origin. >> >>To visualize it with your hand ... >> - with your right hand >> - extend your thumb >> - curl your fingers >> - point your thumb at your nose >> - you are looking at the origin from the + end of the axis >> - your fingers are pointing in the direction of the rotation >> >>I believe that this is consistent with Anthony Stone's previous email to >>jmol-users. >> >>Let's look at the axis rotations in RasMol ... >> >> load someMolecule >> set axes on >> rotate x 10 >> >>You then need to take the mouse and wiggle it a little. I observe that >>the +Z axis (which is in the back) comes up. >> >>Point your thumb to the right with your fingers curled. The fingers are >>curling up from the back. This means that RasMol did a right-handed >>rotation around the X axis. Good. >> >>Let's skip to the Z axis >> >> reset >> rotate z 10 >> >>I observe that the +X drops on the right. The +Z axis goes into the >>screen. Point your right thumb into the screen. Your fingers are curling >>down on the right. RasMol is doing a right-hand rotation around the Z >>axis. Good. >> >>Finally, let's look at the Y axis >> >> reset >> rotate y 10 >> >>I observe that the +Z axis at the back moves to the left. The +Y axis >>points down, so point your right thumb down. Fingers are curling around >>back to the *right* ... but +Z moved to the *left*. Huh? >> >>Try it with your left hand. Thumb down, fingers curl to the left, +Z >>moved to the left ... it sure looks like to me that RasMol is doing a >>left-hand rotation around the Y axis. >> >> you are right I had got mad on xyz here as with the translation, it is x+ y- z+ for rotation, too, using Irix RasMol2.7.2.1. >> >> >>I have looked at this several dozen times over the past 6 months. At >>first I wasn't confident of my observations, but now I have convinced >>myself. But I may be wrong ... I certainly have struggled with this >>'handedness' stuff :-) >> >>Q: Please post some independent confirmations telling me that you concur ... >>or explaining my error :-) >> >> you are right >>Q: I have not tried this in Chime ... can someone check it out and >>confirm that it behaves the same way? >> >>Q: Can someone also confirm that the chime 'move' command about the y >>axis is also left-handed? >> >> >>Unfortunately, this has pretty big implications for someone who has a >>large investment in existing scripts (Eric?). It means that all moves and >>rotates around the Y axis need to be negated. At least it isn't difficult. >> >>My goal for Jmol has been to get as close as possible to 100% RasMol/Chime >>script compatibility, to ease the migration path for people who have >>existing scripts. But this might be a pretty big change for people who >>have an investment in tutorials/courseware. >> >>As I see it, the options are pretty similar to the Axis Orientation >>question: >> >> 1. Jmol should only support RasMol/Chime rotations >> - people have made an investment in existing >> RasMol/Chime scripts >> - it works fine, leave it alone >> - people are used to seeing it behave this way >> - it doesn't really matter, no one has looked >> at it for years so nobody really cares >> >> #!RasMol >> 2. Jmol should be completely right-handed >> - the system should be consistently right-handed >> - the fact that y rotates backwards is a design >> flaw that should be corrected, not propogated >> - people have been confused by this for years >> - noone is going to use existing scripts anyway >> - OR, those who have scripts can easily change them >> - OR, just write a script converter that will >> fix existing scripts ... just negate the parameter >> to 'rotate y ' and 'move x z ...' >> commands >> >> #!Jmol -version 10 >> 3. Jmol should offer both >> - it is easy to support both >> Q: What should the default orientation be in Jmol? >> >> as old scripts didn't have an interpreter line, implicates #!RasMol >> Q: What should the script command be to change >> the setting? >> >> #!Jmol -version 10 set axis right #!RasMol set axis on >> Q: Is this *exactly* the same switch that controls >> the Y axis orientation? >> >> Yes, to minimize confusion. There should only be a minimum of different dialects, therefore it may even be better not to use the set axis command but something like: set Jmol on >> >> >>I am interested in your thoughts and feedback. >> >> >>Thanks, >>Miguel >> >> ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <50647.80.58.16.235.1076978243.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: RasMol rotations about axes Date: Tue, 17 Feb 2004 23:15:00 +0100 (CET) To: rasmol@lists.umass.edu Cc: yaya@bernstein-plus-sons.com, jmol-users@lists.sourceforge.net > I think you are right. OK > Once again, the best fix would be a > command line switch. Yes. We can put a user-setting in the Jmol application and a PARAM value to the applet in order to control this. > Changing the default would break lots of scripts. Maintaining compatibility with existing RasMol/Chime scripts is fundamentally important to Jmol. Otherwise, we would be using another scripting language. > Clearly Jmol is an independent program and its developers > can do whatever they think best, but with over a million > existing rasmol users worldwide, providing them with > a program that works in a similar fashion when they are > using a browser might be a good idea. Agreed. Jmol currently tries to mimic the RasMol behavior and will continue to try to do so. After spending so much time studying/worrying about this issue, I now think that it is relatively easy to support both Y orientations/behaviors. My tentative plan is to tie the Y axis orientation and the Y rotation direction to the same switch/setting. When you are in this 'as-yet-unnamed' mode, then the Y axis points up and the Y rotation is right-handed. Thanks for your help. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- 2 PDB Discussion List , pdb_education@swarthmore.edu, rasmol@lists.umass.edu X-Virus-Scanned: Symantec AntiVirus Scan Engine ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Completion of Bioinformatics Tutorial Date: Tue, 17 Feb 2004 19:52:34 -0500 To: Swiss-PdbViewer Discussion , Hi, Structural Biologists! If you are looking for ways to introduce your students -- or yourself -- to bioinformatics, take at look at my recently updated and expanded Bioinformatics: A Tutorial for Beginners Exploring Human Visual Pigments at http://www.usm.maine.edu/~rhodes/Goodies/Matics.html Besides updating to accommodate minor changes in some of the bioinformatics sites, I added a brief look at QuickPDB for those who have never used a structure viewer. And now the tutorial ends with hands-on homology modeling of human peropsin, a visual-pigment-like substance of unknown function (possibly a retinal isomerase). This exercise adds ProSite, the ExPDB structure database, and Swiss-Model to the many tools covered in the tutorial. The homology modeling exercise is an optional part at the end of the tutorial, requiring experience with DeepView (Swiss-PdbViewer). I will appreciate comments, suggestions and corrections. If there are additional sites that you would like the tutorial to include, let me know. I'll try to get to know them and include them. I'd also like to thank many of you for helpful suggestions about this tutorial and my other web teaching resources in structural biology. Cheers! Gale Rhodes, Professor of Chemistry University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 http://www.usm.maine.edu/~rhodes ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <50647.80.58.16.235.1076978243.squirrel@www.howards.org> <4031A3AB.6060002@sympatico.ca> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: RasMol rotations about axes Date: Wed, 18 Feb 2004 00:06:21 +0100 (CET) To: rasmol@lists.umass.edu Cc: diane.demers@sympatico.ca, jmol-users@lists.sourceforge.net Jean-Philippe, Thank you for taking the time to write such a detailed response. > In fact, as the Jmol code gets written, > it is normal that some features seem (to the development team at least) > to be better designed in another way than they were in Chime/Rasmol. Correct. With the benefit of hind-sight and much more powerful machines ... > There are advantages to keep the current scripting format > [snip] as well as to change it [snip]. Agreed. > There is the third option for Jmol to be able to interpret two scripting > languages that has not been discussed a lot. It's certain that there > are some disadvantages to that: need for a more complex interpreter, > need for a mechanism to distinguish the two scripting language, more > hassle for the script developer. This issue has been raised a few times, and I will take the blame/credit/responsibility for the fact that there has not been more discussion about it. My *strong* position is that Jmol needs to provide a migration path for existing Chime users. This implies that we need to have a hi-fidelity RasMol/Chime script interpreter. Once this phase of Jmol is done, and the Chime migration 'bridge' is built, then we can start to look at other extensions. The rendering engine is very much separated from the scripting engine in Jmol. And adding support for another language would not be difficult. The difficult task will be defining that language. > However, in my mind, two facts stand > clear. First, there is too much stuff out there that already uses the > Chime/Rasmol scripting language so that we can say, "no one is going to > use existing scripts anyway". Agreed. > Of course, it would be easy to modify the > current scripts - I guess there will code to change anyway when we will > definitely move to Jmol - but how time and labour-consuming this will > be! Second fact, there will be a demand for the addition of new features > to Jmol and, along with each new feature, there will be a new command > added to the scripting language (and the new command will generate a > syntax error if run in Chime/Rasmol). This is a good description of the issues which we are trying to balance. > Here I discuss some ways this option could be implemented in Jmol. > First, a script has an effect either on the molecule display or on the > "state" of the molecule in the software memory. If two languages are > supported, they can have a direct effect on the molecule; this choice > would require two interpreters. Your description is accurate. And the architecture will support this. > Alternatively, one language could be > translated into the other and the latter will affect the loaded > molecule. (Interestingly, it is stated in the Chime documentation that > CSML (a mere scripting language) is supported by Chime, in addition to > Rasmol scripts. A CSML script is just translated into a Rasmol script > and then sent to be executed). This choice would require only a script > interpreter, but also a translator. I was not aware that Chime had this kind of 'CSML' support. The direct translation option is interesting. I believe that if we were to do any translating we would be translating RasMol script into something that had a little more formal grammar and more semantic power. > It is also now a good time to think about the evolution of Jmol. I take > as an asset that the development of Jmol will be rapid and continuous: > addition of several features but nothing can be done perfectly at first, > so there will be adjustments made to the implemented features. How can > the scripting language used by Jmol cope with that? Should a script > specify the version of the language in which it is written? That is one advantage of sticking to the RasMol/Chime scripting commands until we have achieved 99% compatibility. We can avoid a lot of these issues. (As I write this I realize that perhaps I made a mistake by posting these 'axis-orientation' issues. We don't have 99% compatibility yet, so I should keep my mouth closed and keep working at high speed :-) > Nevertheless, HTML has the !DOCTYPE tag to identify the version of the > language used. However, it would be cumbersome to have an interpreter or > a translation if there are dozens of versions of different languages. That certainly would be cumbersome. > This brings us to the second problem: how to tell which language or > which version a script uses. This reminds me that Mr. Bernstein had > suggested to implement a command switch, a compromise that IMO does not > solve the problems involved: It would add a new command (for sure not > recognized by Chime, which could even less interpret the other scripting > language) and would allow the sudden switching of language into a > script, a situation that could introduce some confusion in the coding > and interpretation of scripts. For the two facts stated below, it would > not be a good idea to make a compromise language that would mix new and > old, apples and oranges :-) . I agree that mixing scripting languages sounds like a bad idea. > A solution could be to include the script > specifications as comments at the beginning of the script. Another > solution could be to handle each format differently. Each format could > have its own file extension and MIME type. I don't know yet how scripts > are handled in Jmol but there could be a way of telling the script > specifications to the applet, with a PARAM tag for instance. These will be good issues for us to think through if/when Jmol supports another scripting language. And your proposed solutions are good food for thought. > This was my two cents; I hope it will help the development of Jmol or > that it will create more debates among us, Rasmolers, Chimeleons and > Jmolers. And thank you once again for taking the time to write. !Adios! Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2727.1300 X-MSMail-priority: Normal References: <50647.80.58.16.235.1076978243.squirrel@www.howards.org> <4031CBEF.1040804@imb-jena.de> ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: RasMol rotations about axes Date: Tue, 17 Feb 2004 23:01:08 -0800 To: rasmol@lists.umass.edu > There is an other problem with the RasMol translate, it only translates > in % of the view, especially since RasMol is able to load and > manipulate up to 5 different molecules, it would be very useful to allow > translation in A units e.g. translate x 50.0 would translate the selected molecule > 50 A to the right side, not half out of the viewing area. From: "Jan Reichert" Since the effect of the translate command depends of the view, values along the y-axis and the x-axis are not homogeneous in rasmol scripts. Therefore the rasmol system is not only not fully right-handed, but is also not normalized! Depending of the shape of the view, e.g. square or rectangle, moves are different. These problems are extremely critical when multiple molecules are loaded together in the same "world" and make it virtually impossible to save and to restore properly a multimolecule session with the current rasmol scripting. For those interested in how these problems were addressed in RasTop 2.0 and after, I wrote a little paragraph in RasTop help called "rastop world" (see page rastopworld.htm in help folder, download at www.geneinfinity.org/rastop). Don't hesitate to run the software, rastop world is fun to play with! Philippe Valadon ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com References: <50647.80.58.16.235.1076978243.squirrel@www.howards.org> <4031CBEF.1040804@imb-jena.de> <002c01c3f5ec$fc0c0900$4406cb40@Tranquilo> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: RasMol rotations about axes Date: Wed, 18 Feb 2004 13:27:52 -0500 (EST) To: rasmol@lists.umass.edu I will be more than happy to add a variant on the translation commands in 2.7.3 to allow translation by Angstoms and/or RasMol units, but changing the meaning of the current commands would break many, many existing scripts. I would suggest the following: translate [-] value [units] where the permitted values for the axis parameter would be "x", "y" or "z" and the permitted values of the units parameter would be "percent" "Angstroms" (or just "A") or "rasmolunits" (or just "units") or blank. In the first case the motion would be given in percentage of half the screen (the default when the units parameter is blank). In the second case the mostion would be in true Angstroms. In the third case the motion would be in RasMol units (1/250 of an Angstrom). In addition we could add a command set translation units [percent|Angstroms|rasmolunits] to modify the default. I agree that the left handed rotation around Y and the -Y axis labelling of the Y axis in the Windows version is not an ideal choice. I propose to augment the set axes command as follows to address these issues: set axes set axes [x ] [y ] [z ] set axes label [-] set axes label [[-] x ] [[-] y ] [[-] z ] set axes rotation [-] set axes rotation [[-] x ] [[-] y ] [[-] z ] which would allow the user complete control over whether axes appear or not, over whether individual axes appear or not, over whether all axis labels appear or not and at which end, over whether individual axes have labels appear or not and at which end and over the sense of rotation for all axes or for one axis at a time. The current unix and Mac defaults for set axes on would be equivalent to set axes x on y on z on set axes label x on y on z on set axes rotation x -y z The current windows default would be set axes x on y on z on set axes label x on -y on z on set axes rotation x -y z It would then be simple to move over for new scripts to the more sensible defaults: set axes x on y on z on set axes label x on y on z on set axes rotation x y z As we build up a new set of defaults we could then add one more command set default where setup would be the name of a "standard" set of default settings all packaged together (e.g. oldunix, oldwindows, newcommon, etc.) This way we would not break any existing scripts, but could move towards common choices that satisfy current demands. Regards, Herbert ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Tue, 17 Feb 2004, Philippe wrote: > From: "Jan Reichert" > > There is an other problem with the RasMol translate, it only translates > > in % of the view, especially since RasMol is able to load and > > manipulate up to 5 different molecules, it would be very useful to allow > > translation in A units e.g. translate x 50.0 would translate the > selected molecule > > 50 A to the right side, not half out of the viewing area. > > Since the effect of the translate command depends of the view, values along > the y-axis and the x-axis are not homogeneous in rasmol scripts. Therefore > the rasmol system is not only not fully right-handed, but is also not > normalized! Depending of the shape of the view, e.g. square or rectangle, > moves are different. These problems are extremely critical when multiple > molecules are loaded together in the same "world" and make it virtually > impossible to save and to restore properly a multimolecule session with the > current rasmol scripting. For those interested in how these problems were > addressed in RasTop 2.0 and after, I wrote a little paragraph in RasTop help > called "rastop world" (see page rastopworld.htm in help folder, download at > www.geneinfinity.org/rastop). Don't hesitate to run the software, rastop > world is fun to play with! > > Philippe Valadon > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <50647.80.58.16.235.1076978243.squirrel@www.howards.org> <4031CBEF.1040804@imb-jena.de> <002c01c3f5ec$fc0c0900$4406cb40@Tranquilo> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: RasMol rotations about axes Date: Wed, 18 Feb 2004 20:09:11 +0100 (CET) To: rasmol@lists.umass.edu Philippe wrote: [snip] > For those interested in how > these problems were addressed in RasTop 2.0 and after, I wrote a little > paragraph in RasTop help called "rastop world" (see page rastopworld.htm > in help folder, download at www.geneinfinity.org/rastop). Phillipe, Is this help page available on the web? (I *will* install RasTop, but today I don't have the time to focus on it :-) Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: enhanced translation command Date: Wed, 18 Feb 2004 21:55:52 +0100 (CET) To: rasmol@lists.umass.edu Herbert said: > I will be more than happy to add a variant on the translation > commands in 2.7.3 to allow translation by Angstoms I was thinking along similar lines. > and/or RasMol units, I would vote for not propogating RasMol units ... see below ... > but changing the meaning of the current commands > would break many, many existing scripts. I would suggest the > following: > > translate [-] value [units] > > where the permitted values for the axis parameter would be "x", "y" or > "z" and the permitted values of the units parameter would be > "percent" "Angstroms" (or just "A") or "rasmolunits" (or just "units") > or blank. What about dropping the [units] term? If the value is a decimal number, then it will be interpreted as Angstroms. This is basically consistent with the other commands, where decimal numbers specify angstroms. The problem I have with the units term is that I think it would imply that the units term could be used with all the commands ... and I don't think we want to take that step. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- 2 PDB Discussion List , pdb_education@swarthmore.edu, rasmol@lists.umass.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Bruce Southey Subject: Re: Completion of Bioinformatics Tutorial Date: Wed, 18 Feb 2004 15:23:15 -0600 To: Gale Rhodes Cc: Swiss-PdbViewer Discussion , Hi, This is great work. I do agree that "Bioinformatics for Dummies" is a great book except for not using the Biology Workbench. Along the same lines, "The Complete Idiot's Guide to Decoding Your Genes" by Linda Tagliaferro and Mark Vincent Bloom is very good about genetics and biotechnology. You will find that the Biology Workbench (http://workbench.sdscu.edu) provides an integrated suite of bioinformatics including more tools and databases that actually makes it far easier to move between the different tools and databases. From example, when viewing the records of a PDB sequence entry there is a link that allows you to view the structure using Protein Explorer and a link to the entry at the PDB site. At the Biology Student Workbench (http://bsw.ncsa.uiuc.edu), we have a number of tutorials on using the Biology Workbench (Curricular Materials link) as well as the Student Interface to the Biology Workbench that is easier to use than the Biology Workbench. Similar material developed by teachers can be found at the Inquiry Page (http://www.inquiry.uiuc.edu/). This information makes the Biology Workbench much easier to use. If you or anyone else has questions on this, I will be happy to attempt to answer them. Regards Bruce Southey southey@uiuc.edu ---- Original message ---- >Date: Tue, 17 Feb 2004 19:52:34 -0500 >From: Gale Rhodes >Subject: Completion of Bioinformatics Tutorial >To: Swiss-PdbViewer Discussion , 2 PDB Discussion List , pdb_education@swarthmore.edu, rasmol@lists.umass.edu > >Hi, Structural Biologists! > >If you are looking for ways to introduce your students -- or yourself >-- to bioinformatics, take at look at my recently updated and expanded > >Bioinformatics: A Tutorial for Beginners >Exploring Human Visual Pigments >at http://www.usm.maine.edu/~rhodes/Goodies/Matics.html > >Besides updating to accommodate minor changes in some of the >bioinformatics sites, I added a brief look at QuickPDB for those who >have never used a structure viewer. And now the tutorial ends with >hands-on homology modeling of human peropsin, a visual-pigment-like >substance of unknown function (possibly a retinal isomerase). This >exercise adds ProSite, the ExPDB structure database, and Swiss-Model to >the many tools covered in the tutorial. The homology modeling exercise >is an optional part at the end of the tutorial, requiring experience >with DeepView (Swiss-PdbViewer). > >I will appreciate comments, suggestions and corrections. If there are >additional sites that you would like the tutorial to include, let me >know. I'll try to get to know them and include them. > >I'd also like to thank many of you for helpful suggestions about this >tutorial and my other web teaching resources in structural biology. > >Cheers! > > >Gale Rhodes, Professor of Chemistry >University of Southern Maine >PO Box 9300 >Portland, Maine 04104-9300 >http://www.usm.maine.edu/~rhodes > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <50647.80.58.16.235.1076978243.squirrel@www.howards.org> <4031CBEF.1040804@imb-jena.de> <002c01c3f5ec$fc0c0900$4406cb40@Tranquilo> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: axes rotation extensions -- was Re: RasMol rotations about axes Date: Wed, 18 Feb 2004 22:35:13 +0100 (CET) To: rasmol@lists.umass.edu Cc: jmol-users@lists.sourceforge.net Herbert wrote: > set axes rotation [-] > set axes rotation [[-] x ] [[-] y ] [[-] z ] > > which would allow the user complete control ... over the > sense of rotation for all axes or for one axis at a time. Whatever we decide to do on this will be implemented in Jmol as well. I am reluctant to say it, but I think this is giving the script writer *too much* control. I think that I would rather see two states 1. compatible 2. right-handed I personally don't think there is any reason to have any more than that. I do not know what the command syntax should be. Plus, I think that it would be best if this was tied to the +Y axis orientation. That is, when you go into 'right-handed' mode (or whatever it is called) then you get right-handed rotations plus the +Y axis pointing upwards. I am interested to hear what other people think ... Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: axis labelling -- was Re: RasMol rotations about axes Date: Wed, 18 Feb 2004 22:37:19 +0100 (CET) To: rasmol@lists.umass.edu Cc: yaya@bernstein-plus-sons.com, jmol-users@lists.sourceforge.net Herbert said: > I agree that the left handed rotation around Y and the -Y axis > labelling of the Y axis in the Windows version is not an ideal choice. > I propose to augment the set axes command as follows to address > these issues: > > set axes > set axes [x ] [y ] [z ] > set axes label [-] > set axes label [[-] x ] [[-] y ] [[-] z ] [snip] > > which would allow the user complete control over whether axes > appear or not, over whether individual axes appear or not, over > whether all axis labels appear or not and at which end, over whether > individual axes have labels appear or not and at which end First, regarding labels ... This would certainly give complete control. And if people want this level of control then that is the way we should implement it ... in RasMol 2.7.3 *and* in Jmol. Personally, I don't see the value of enabling the axes one at a time. But if someone thinks there is value in it then we should do it. Same goes for controlling the labelling of the individual axes ... I personally don't see any value in it, but if someone can argue that it has real value then we should do it. Regarding the positioning of the label ... I would propose that they are always on the positive end of the axes. I don't think that people need to put labels on the negative ends of the axes. That presents a backwards-compatibility issue for windows, but I suggest that you should consider the windows labelling a 'bug' and therefore this change in orientation as a 'bug fix' ... no need to maintain backward compatibility. To eliminate possible confusion over the axis orientation, Jmol labels the axes as "+X", "+Y", and "+Z". That would be a change from traditional RasMol labelling, but something that you may want to consider. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <50647.80.58.16.235.1076978243.squirrel@www.howards.org> <4031CBEF.1040804@imb-jena.de> <002c01c3f5ec$fc0c0900$4406cb40@Tranquilo> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: default state -- was Re: RasMol rotations about axes Date: Wed, 18 Feb 2004 22:45:20 +0100 (CET) To: rasmol@lists.umass.edu Cc: yaya@bernstein-plus-sons.com, jmol-users@lists.sourceforge.net Herbert said: > As we build up a new set of defaults we could then add > one more command > > set default > > where setup would be the name of a "standard" set of default > settings all packaged together (e.g. oldunix, oldwindows, > newcommon, etc.) This way we would not break any existing > scripts, but could move towards common choices that satisfy > current demands. I think that this sounds like a *very* good idea. One thing ... it isn't clear to me why we would want to make the platform distinction (you said 'oldunix, oldwindows'). If there is a need to make some type of platform distinction, then we may want to consider a hyphenated or dotted name so that it could be optional: old old.unix old.windows Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Bruce Southey Subject: Re: axes rotation extensions -- was Re: RasMol rotations about axes Date: Wed, 18 Feb 2004 16:06:50 -0600 To: rasmol@lists.umass.edu Hi, The issue that I want to point out is that a user may end up (unknownly) using a combination of command options. For example, loading an old script and then load a new script within the same session. This is likely to be very common in teaching or following someones script and then adding to it. This could make the second script do the 'incorrect' thing. I would think that most scripts are derived from playing with the Rasmol or Jmol so the script writer would workout some combination to obtain what they wanted anyhow. A complete control approach is likely result in better scripts especially for other people to understand. Regards Bruce Southey southey@uiuc.edu ---- Original message ---- >Date: Wed, 18 Feb 2004 22:35:13 +0100 (CET) >From: Miguel Howard >Subject: axes rotation extensions -- was Re: RasMol rotations about axes >To: rasmol@lists.umass.edu >Cc: jmol-users@lists.sourceforge.net > >Herbert wrote: > >> set axes rotation [-] >> set axes rotation [[-] x ] [[-] y ] [[-] z ] >> >> which would allow the user complete control ... over the >> sense of rotation for all axes or for one axis at a time. > >Whatever we decide to do on this will be implemented in Jmol as well. > >I am reluctant to say it, but I think this is giving the script writer >*too much* control. > >I think that I would rather see two states > 1. compatible > 2. right-handed > >I personally don't think there is any reason to have any more than that. > >I do not know what the command syntax should be. > > >Plus, I think that it would be best if this was tied to the +Y axis >orientation. That is, when you go into 'right-handed' mode (or whatever it >is called) then you get right-handed rotations plus the +Y axis pointing >upwards. > >I am interested to hear what other people think ... > > > >Miguel > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <9d5c24bf.1443ed0f.895db00@expms1.cites.uiuc.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: axes rotation extensions -- was Re: RasMol rotations about axes Date: Wed, 18 Feb 2004 23:50:38 +0100 (CET) To: southey@uiuc.edu, rasmol@lists.umass.edu Bruce wrote: > The issue that I want to point out is that a user may end up (unknownly) > using a combination of command options. > For example, loading an old > script and then load a new script within the same session. I believe what Herbert proposed was adding these as script commands, not as command line options. In general, I assume that the options would be reset to the defaults when a user does a 'zap' to load a new model. > This is likely to be very common in teaching Hmmm ... if a teacher turned some students loose on a set of scripts without understanding the scripts, then I would say that the teacher didn't do his/her homework :-) I don't see how this is different from any other script that one pay pick up and try to use. If you run a script that changes all the atoms green then when you run another script it my not look like you expected on the screen. > or following someones script and > then adding to it. This could make the second script do the 'incorrect' > thing. It seems to me that this is a risk that one always takes when one starts modifying someone else's code ... regardless of whether there is a 'new' command in there or not. > I would think that most scripts are derived from playing with the Rasmol > or Jmol so the script writer would workout some combination to obtain > what they wanted anyhow. > A complete control approach is likely result in > better scripts especially for other people to understand. If this sentence is referring to axis rotations then I strongly disagree. Visualizing 3D rotations and getting orientations right is very difficult. Many systems computer graphics systems have standardized on a right-handed system with right-handed rotations. This standardization is a very good thing because it helps people build on a general base of experience and expectations. Unfortunately, RasMol has a 'design flaw' regarding the Y axis rotation ... and we need to deal with it. I do not think that giving people the control to 'roll their own' rotational systems will not result in better scripts that are easier to understand. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com References: <50647.80.58.16.235.1076978243.squirrel@www.howards.org> <4031CBEF.1040804@imb-jena.de> <002c01c3f5ec$fc0c0900$4406cb40@Tranquilo> <43083.80.58.16.235.1077140720.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: default state -- was Re: RasMol rotations about axes Date: Wed, 18 Feb 2004 18:24:24 -0500 (EST) To: Miguel Howard Cc: rasmol@lists.umass.edu, jmol-users@lists.sourceforge.net The distinction between oldunix and oldwindows is simply a recognition of the fact that they don't work precisely the same way. A dotted notation is OK by me. Any other people have opinions? This code will be written in the next couple of weeks. ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Wed, 18 Feb 2004, Miguel Howard wrote: > Herbert said: > > >> As we build up a new set of defaults we could then add > >> one more command > >> > >> set default > >> > >> where setup would be the name of a "standard" set of default > >> settings all packaged together (e.g. oldunix, oldwindows, > >> newcommon, etc.) This way we would not break any existing > >> scripts, but could move towards common choices that satisfy > >> current demands. > > I think that this sounds like a *very* good idea. > > One thing ... it isn't clear to me why we would want to make the platform > distinction (you said 'oldunix, oldwindows'). > > If there is a need to make some type of platform distinction, then we may > want to consider a hyphenated or dotted name so that it could be optional: > old > old.unix > old.windows > > Miguel > > > > [*** Normal Termination ***] > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com References: <59969.80.58.16.235.1077140239.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: axis labelling -- was Re: RasMol rotations about axes Date: Wed, 18 Feb 2004 18:52:26 -0500 (EST) To: rasmol@lists.umass.edu Cc: jmol-users@lists.sourceforge.net The fine-grained set of commands is just as easy to implement as the broader set and with respect to the labels and rotation allows simple, yet complete simulation of both all the current behaviors and a pure right-handed system. The complete control over axes and labels one at a time is just for odd cases where one of the axes happens to obscure some fine detail someone wanted to show. Most people would have three axes with three labels. However, on reflection, I would suggest extending set axes [x ] [y ] [z ] to set axes [signed|unsigned] [[+|-]x ] [[+|-]y ] [[+|-]z ] to allow display of half axes if desired. (See below for signed|unsigned). With respect to just treating the windows Y-label as a bug, I agree that it is a bug, but, since it really does change the image, and somebody might care, what is the harm in allowing them to recreate what they are used to. This way when they move to Linux they can keep the behavior they are used to. With respect to signed labels, I would add the optional flags "signed" or "unsigned" to the set axes commands. This would have the nice effect of allowing the people who are used to the windows Y label placement to keep it, but also to add a minus sign so that it would also be an accurate label. The it would no longer be a bug. Regards, Herbert ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Wed, 18 Feb 2004, Miguel Howard wrote: > Herbert said: > > >> I agree that the left handed rotation around Y and the -Y axis > >> labelling of the Y axis in the Windows version is not an ideal choice. > >> I propose to augment the set axes command as follows to address > >> these issues: > >> > >> set axes > >> set axes [x ] [y ] [z ] > >> set axes label [-] > >> set axes label [[-] x ] [[-] y ] [[-] z ] > > [snip] > > >> > >> which would allow the user complete control over whether axes > >> appear or not, over whether individual axes appear or not, over > >> whether all axis labels appear or not and at which end, over whether > >> individual axes have labels appear or not and at which end > > First, regarding labels ... > > This would certainly give complete control. And if people want this > level of control then that is the way we should implement it ... in > RasMol 2.7.3 *and* in Jmol. > > Personally, I don't see the value of enabling the axes one at a time. > But if someone thinks there is value in it then we should do it. > > Same goes for controlling the labelling of the individual axes ... I > personally don't see any value in it, but if someone can argue that it > has real value then we should do it. > > Regarding the positioning of the label ... I would propose that they are > always on the positive end of the axes. I don't think that people need > to put labels on the negative ends of the axes. > > That presents a backwards-compatibility issue for windows, but I suggest > that you should consider the windows labelling a 'bug' and therefore > this change in orientation as a 'bug fix' ... no need to maintain > backward compatibility. > > To eliminate possible confusion over the axis orientation, Jmol labels > the axes as "+X", "+Y", and "+Z". That would be a change from > traditional RasMol labelling, but something that you may want to > consider. > > Miguel > > > > > [*** Normal Termination ***] > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- about axes User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; de-AT; rv:1.6) Gecko/20040113 X-Accept-Language: de,en References: <50647.80.58.16.235.1076978243.squirrel@www.howards.org> <4031CBEF.1040804@imb-jena.de> <002c01c3f5ec$fc0c0900$4406cb40@Tranquilo> <50370.80.58.16.235.1077140113.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: [Jmol-users] axes rotation extensions -- was Re: RasMol rotations Date: Thu, 19 Feb 2004 01:45:53 +0100 To: rasmol@lists.umass.edu Miguel Howard schrieb: >Herbert wrote: > > > >>set axes rotation [-] >> set axes rotation [[-] x ] [[-] y ] [[-] z ] >> >>which would allow the user complete control ... over the >>sense of rotation for all axes or for one axis at a time. >> >> > >Whatever we decide to do on this will be implemented in Jmol as well. > >I am reluctant to say it, but I think this is giving the script writer >*too much* control. > >I think that I would rather see two states > 1. compatible > 2. right-handed > > I agree, but I don't argue against controlling everything (I would like to control default cpk color scheme, too:-) >I personally don't think there is any reason to have any more than that. > >I do not know what the command syntax should be. > > set default compatible versus set default or set default [ | [ | [ |[ ]]]] e.g. set default MolScript would implicate set default cartoon HELIX ribbon set default color phosphor magenta set default color carbon [0, 0, 255] which is not true, but this is an example set default axis right-handed which itself contains set default rotation axis +x +y +z set default orientation axis [+y up] set default label axis x on y on z on > > > The wrong side labeling of the RasWin y axis, I consider as a bug, too. >Plus, I think that it would be best if this was tied to the +Y axis >orientation. That is, when you go into 'right-handed' mode (or whatever it >is called) then you get right-handed rotations plus the +Y axis pointing >upwards. > >I am interested to hear what other people think ... > > I agree, set default axis right-handed should itself contain set default rotation axis +x +y +z set default orientation axis [+y up] set default label axis x on y on z on Regards, Jan > > >Miguel > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2727.1300 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: RasMol rotations about axes Date: Wed, 18 Feb 2004 23:06:40 -0800 To: rasmol@lists.umass.edu Some comments: > translate [-] value [units] versus > translate [-] value with a decimal number interpreted as Angstroms. I agree with the second solution and I think that Miguel is very right in saying that this is consistent with the other commands. The translation command is restricted to +/- 100%, in order to keep the molecule always in the view. Maybe for that reason, values in Angstrom were not allowed in the initial design. Unfortunately, at high zoom, parts of the molecule often cannot be seen on screen because of this limitation. I would also drop the +/- 100% restriction on translation. There was a while ago a request for a translate command combining values for the three axis such as: translate [x [-] ] [y [-] ] [z [-] ]. I think this is a good command and I would add it too. > set axes rotation, etc. I see as well only two systems; a classical rasmol scripting which is the default when nothing makes to believe that it isn't and a new, right-handed, etc., scripting system. The principle of backward compatibility indicates that a script written in a different and newer system should not generate a warning in the classical system. This is only obtained when the corresponding command start by the letter #, which normally indicates a comment. Therefore I am again a proponent of versioning system using a magic tag at the start of the script. In any cases, the different solutions presented here imply that all scripts written in the newer system will have a special command indicating their state. Sound's to me like a form a tagging. There are other reasons to believe that versioning is important. For example a solid MIME type would result from the use of a magic tag, saving of worksessions need to remember which exact version of the scripting system they used at creation, variants of jmol may need to indicate their own differences, etc. > Miguel wrote: Is this help page available on the web? RasTop help is not available on the web, but it is a good suggestion - I'll try to find the time to do it. RasTop addresses problems with multimolecule environment and world scripting and is divergent from RasMol 2.7.2.1, although it shares most of the code. Briefly RasTop implements the following elements: - A world origin, which permits to reset the scenery easily; - Translation values in the 3 axes are expressed in percent of the smallest size of the screen/window/canvas and there is no limitation of the translation values; - Commands that operate at the world level systematically use the syntax "world". For example "translate x 50" translates the active molecule to 50% and "translate world x 50" does the same on all molecules + origin independently of the status of the "rotate all" command. In RasMol 2.7.2.1 "rotate all" followed by "translate x 50" does move all molecules. I find this way very confusing, and in theory the state of your gui could interfere with running scripts; - There is a "scale" command which indicates in Angstrom the value of the smallest side of the screen/window/canvas. In RasMol, the effect of the zoom command depends on the size of the loaded molecule; in a multimolecule environment this becomes quickly a real mess. The "scale " command overcomes this problem by unambiguously indicating the zoom level; - There is also a "position" command, but I just realized that it is equivalent to a translate command with values in RU/Angstrom on the 3 axes simultaneously - see above; - There are a few other things, but less important, such as a bunch of reset variants, multiple coordinate systems, etc. Regards, Philippe Valadon ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: RasTop -- was Re: RasMol rotations about axes Date: Thu, 19 Feb 2004 18:28:16 +0100 (CET) To: valadon@ix.netcom.com, rasmol@lists.umass.edu Phillipe, >> Miguel wrote: >>Is this help page available on the web? > RasTop help is not available on the web, but it is a good suggestion - > I'll try to find the time to do it. I only asked because I don't currently have access to a Win32 machine. But I wanted to read the document that you wrote describing how you chose to address the translation issues. I am not a chemist and am not familiar with the molecular visualization software (other than Jmol). Therefore, I frankly didn't know that RasTop existed. However, I am now very interested in downloading RasTop and seeing how you chose to extend and add functionality ... once I get my Win32 machine back :-) Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- axes Importance: Normal References: <50647.80.58.16.235.1076978243.squirrel@www.howards.org> <4031CBEF.1040804@imb-jena.de> <002c01c3f5ec$fc0c0900$4406cb40@Tranquilo> <43083.80.58.16.235.1077140720.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: [Jmol-users] Re: default state -- was Re: RasMol rotations about Date: Thu, 19 Feb 2004 18:36:41 +0100 (CET) To: jmol-users@lists.sourceforge.net Cc: yaya@bernstein-plus-sons.com, rasmol@lists.umass.edu Herbert wrote: > The distinction between oldunix and oldwindows is simply a recognition > of the fact that they don't work precisely the same way. I see. > A dotted notation is OK by me. I would say that the dotted notation would only make sense if there really is a true hierarchy of options. >> >> where setup would be the name of a "standard" set of default >> >> settings all packaged together (e.g. oldunix, oldwindows, >> >> newcommon, etc.) Now that I reread this, maybe there really isn't a hierarchy. Other than oldunix, oldwindows, newcommon, what did you have in mind? Separately, we may want to avoid words like 'old' and 'new' ... what is new today quickly becomes old :-) Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- axes Importance: Normal References: <59969.80.58.16.235.1077140239.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: [Jmol-users] Re: axis labelling -- was Re: RasMol rotations about Date: Thu, 19 Feb 2004 18:45:47 +0100 (CET) To: jmol-users@lists.sourceforge.net Cc: yaya@bernstein-plus-sons.com, rasmol@lists.umass.edu Herbert wrote: > The fine-grained set of commands is just as easy to implement as the > broader set Hmmm ... while it may be 'just as easy' for you, it is not quite as easy for me :-) [snip] > However, on reflection, I would suggest > > extending > set axes [x ] [y ] [z ] > to > set axes [signed|unsigned] > [[+|-]x ] [[+|-]y ] [[+|-]z ] > > to allow display of half axes if desired. (See below for > signed|unsigned). Regarding the display of half-axes, I would like to see if others think there is value. > With respect to just treating the windows Y-label as a bug, I agree that > it is a bug, but, since it really does change the image, and somebody > might care, what is the harm in allowing them to recreate what they are > used to. Personally, I would say that if they like the version with the bug then they should keep using the version that has the bug. > With respect to signed labels, I would add the optional flags "signed" > or "unsigned" to the set axes commands. This would have the nice effect > of allowing the people who are used to the windows Y label placement to > keep it, but also to add a minus sign so that it would also be an > accurate label. The it would no longer be a bug. I like signed|unsigned Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- about axes Importance: Normal References: <50647.80.58.16.235.1076978243.squirrel@www.howards.org> <4031CBEF.1040804@imb-jena.de> <002c01c3f5ec$fc0c0900$4406cb40@Tranquilo> <50370.80.58.16.235.1077140113.squirrel@www.howards.org> <40340741.3050709@imb-jena.de> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: [Jmol-users] axes rotation extensions -- was Re: RasMol rotations Date: Thu, 19 Feb 2004 18:54:37 +0100 (CET) To: rasmol@lists.umass.edu Cc: jr@imb-jena.de Jan wrote: >>I think that I would rather see two states >> 1. compatible >> 2. right-handed >> > I agree, but I don't argue against controlling everything This expression will not translate very well ... Does the phrase 'give them enough rope to hang themselves' mean anything? > (I would like to control default cpk color scheme, too:-) Actually, I agree with you on this one ... I think that colors *should* be under user control :-) [snip] > The wrong side labeling of the RasWin y axis, I consider as a bug, too. > >>Plus, I think that it would be best if this was tied to the +Y axis >> orientation. That is, when you go into 'right-handed' mode (or whatever >> it is called) then you get right-handed rotations plus the +Y axis >> pointing upwards. >> >>I am interested to hear what other people think ... >> >> > I agree, > set default axis right-handed > should itself contain > set default rotation axis +x +y +z > set default orientation axis [+y up] > set default label axis x on y on z on I am not sure why we would need the word 'default' on these. ? Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <007701c3f6b6$ec626ce0$6d06cb40@Tranquilo> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: RasMol rotations about axes Date: Thu, 19 Feb 2004 19:24:47 +0100 (CET) To: rasmol@lists.umass.edu Cc: valadon@ix.netcom.com > Some comments: > >> translate [-] value [units] > versus >> translate [-] value with a decimal number interpreted as >> Angstroms. > > I agree with the second solution and I think that Miguel is very right > in saying that this is consistent with the other commands. > The > translation command is restricted to +/- 100%, in order to keep the > molecule always in the view. Interesting ... I though that by definition translate x|y|z (-)100 meant that it was out of view. > Maybe for that reason, values in Angstrom > were not allowed in the initial design. I suspect that nobody asked for it so nobody ever implemented it. > Unfortunately, at high zoom, > parts of the molecule often cannot be seen on screen because of this > limitation. I would also drop the +/- 100% restriction on translation. I do not understand what you are trying to say. > There was a while ago a request for a translate command combining > values > for the three axis such as: translate [x [-] ] [y [-] ] > [z [-] ]. I think this is a good command and I would add it too. I could go for that. (One could take the next step and add an optional 'time' parameter, but I don't think we should start that discussion until we get some simpler issues resolved :-) >> set axes rotation, etc. > I see as well only two systems; a classical rasmol scripting which is > the default when nothing makes to believe that it isn't and a new, > right-handed, etc., scripting system. The principle of backward > compatibility indicates that a script written in a different and newer > system should not generate a warning in the classical system. This is > only obtained when the > corresponding command start by the letter #, which normally indicates a > comment. Therefore I am again a proponent of versioning system using a > magic tag at the start of the script. I am not sure that putting a magic version comment solves the problem. An old system will not die when it sees the comment ... but it will die a few lines later when it dies on some random new/extended command ... like 'set axes rotate ...' If you want to introduce versioning then I think you should introduce a version tag as a command. That way, if a 'new' script is run on old software, it will die on the line that has the version number. I think that might be more clear to the person who encounters the bug. And when they search the web they will find information about this 'version' command, rather than documentation about how to use the 'set axes rotate ...' command > In any cases, the different solutions presented here imply that all > scripts written in the newer system will have a special command > indicating their state. Sound's to me like a form a tagging. There are > other reasons to believe that versioning is important. For example a > solid MIME type would result from the use of a magic tag, saving of > worksessions need to remember which exact version of the scripting > system they used at creation, variants of jmol may need to indicate > their own differences, etc. Good point. This clear version identification is something we should think about. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- <2146324.1077227101618.JavaMail.root@misspiggy.psp.pas.earthlink.net> ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: RasMol rotations about axes Date: Thu, 19 Feb 2004 13:45:01 -0800 (GMT-08:00) To: rasmol@lists.umass.edu Miguel wrote: >Interesting ... I though that by definition > translate x|y|z (-)100 >meant that it was out of view. The translation command is in fact not behaving propely in rasmol. For example, start a session with rasmol 2.6.4 or 2.7.2.1 and load a molecule, I use usually 1CRN. The molecule opens at zoom 100, the command "translate x|y (-) 100" moves the molecule just of the screen. Ok for me, the molecule is not in the view anymore, but just off of it. Now, zoom out, for example zoom 50 or smaller. The molecule becomes smaller. With the mouse drag it in all directions. You will find that moves are limited to a square that is smaller than the view. Inversely, zoom in and drag. There are now areas that cannot be seen on the edges. In conclusion, the behavior of the translate command is as expected only at and around "zoom 100". Remember that 2.6.4 has a lot of unfinished points. I believe that the intended design was to have the translate command to work at all zoom values like at zoom 100. For this reason the use of RU/Angstrom values were not possible (yet) since it would have broken the limitations of the translation command. Of course only Roger Sayle knows about that and it is just speculation. In a multimolecule environement, it is not possible to limit translation. The world needs to keep its integrity even when one molecule is send far away by rotating around another molecule. In any case, if we loose a molecule we still have the reset command to get things back. My point is that we should drop the limitation on translation, i.e. authorize any percentage values in the translate command, even those superior to 100, and perhaps implement the translate command as described in the manual at all zoom values. Philippe Valadon ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: mailing list courtesy and respect Date: Fri, 20 Feb 2004 02:35:19 +0100 (CET) To: southey@uiuc.edu, rasmol@lists.umass.edu We have recently had discussions about possibly extending the RasMol scripting language. I posted some messages and asked for feedback. Bruce Southey responded to one of those messages and offered his opinion. I disagreed with Bruce's message. Unfortunately, I responded with a rather critical and harsh tone. That was inappropriate and it was a mistake. Bruce responded in good faith to a posting in a public forum. While it is OK to have a difference of opinion, it was uncourteous and disrespectful for me to respond with a critical tone. And it is counterproductive to the idea of a forum ... where we are supposed to be encouraging the exchange of ideas. I apologize. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: en-us, en X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Richard Harrington Subject: transformation matrix Date: Fri, 20 Feb 2004 18:39:26 +0000 To: rasmol@lists.umass.edu Dear all, I'm trying to use Rasmol to implement a transformation matrix given by a structural alignment that I can apply to one of the molecules I load into Rasmol whilst keeping the other molecule(s) constant. (I'm using the UCB enhanced rasmol, so can load multiple molecules. I've never used transformation matrices before, and cannot find any documentation of how exactly to implement them in Rasmol. matrix: | 0.597 0.494 0.632 | |x| | -69.456 | | -0.275 -0.614 0.740 | x |y| + | -9.966 | | 0.754 -0.615 -0.231 | |z| | 29.702 | commands into Rasmol: > rotate x 0.597 > rotate y -0.275 > rotate z 0.754 > rotate x 0.494 > rotate y -0.614 > rotate z -0.615 > rotate x 0.632 > rotate y 0.740 > rotate z -0.231 > translate x -69.456 > translate y -9.966 > translate z 29.702 I have an original output from the structrual alignment tool, but would like to load the molecules separately into Rasmol to utilise some Rasmol scripts. Unfortunately the above commands don't reproduce the original alignment, and I've double checked the matrix values. I've tried a couple of different ways, but to no avail - if you have any insight on this, that'd be great. In general, is the best way to implement a transformation matrix in rasmol by using a sequence of rotations and translations? Many thanks, Richie -- _______________________________________________ Richard Harrington, Men's Boat Club Captain, Homerton College. PhD student, ATP Synthase Group, MRC-Dunn Human Nutrition Unit, Cambridge University. e-mail: rah@mrc-dunn.cam.ac.uk telephone: +44 (0) 1223 252861 mobile: 07817 927175 _______________________________________________ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-MSMail-priority: Normal References: <50647.80.58.16.235.1076978243.squirrel@www.howards.org> <4031CBEF.1040804@imb-jena.de> <002c01c3f5ec$fc0c0900$4406cb40@Tranquilo> <43083.80.58.16.235.1077140720.squirrel@www.howards.org> <33083.212.128.142.26.1077212201.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Arkadiusz Chrzastek Subject: unsubscribe rasmol Date: Fri, 20 Feb 2004 19:47:11 +0100 To: rasmol@lists.umass.edu BeetleSystems ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: lpotapov@pceg1.weizmann.ac.il ++++------+------+------+------+------+------+------+------+------+------+ From: Vladimir Potapov Subject: Re: transformation matrix Date: Fri, 20 Feb 2004 21:03:24 +0200 (IST) To: rasmol@lists.umass.edu Hello Richard, As you correctly showed, the transformation matrix is composed of a rotation matrix and a translation vector. But the values in rotation matrix do not represent angles (Euler angles) that you can use in "rotate" command. Given a rotation matrix you can calculate three Euler angles. See "Q37. How do I convert a rotation matrix to Euler angles?" in "Matrix and Quaternion FAQ" http://www.flipcode.com/documents/matrfaq.html This is a nice page that explains all details about mathematical representation of rotations and other things. Knowing three Euler angles you perform rotations you need: rotate x EulerX rotate y EulerY rotate z EulerZ Regards, Vladimir Potapov -- Department of Plant Sciences Weizmann Institute of Science Rehovot 76100 ISRAEL vladimir.potapov@weizmann.ac.il Tel: +972-8-9342717 Fax: +972-8-9469124 On Fri, 20 Feb 2004, Richard Harrington wrote: > Dear all, > > I'm trying to use Rasmol to implement a transformation matrix given by a structural alignment that I can apply to one of the molecules I load into Rasmol whilst keeping the other molecule(s) constant. (I'm using the UCB enhanced rasmol, so can load multiple molecules. I've never used transformation matrices before, and cannot find any documentation of how exactly to implement them in Rasmol. > > matrix: > > | 0.597 0.494 0.632 | |x| | -69.456 | > | -0.275 -0.614 0.740 | x |y| + | -9.966 | > | 0.754 -0.615 -0.231 | |z| | 29.702 | > > commands into Rasmol: > > > rotate x 0.597 > > rotate y -0.275 > > rotate z 0.754 > > rotate x 0.494 > > rotate y -0.614 > > rotate z -0.615 > > rotate x 0.632 > > rotate y 0.740 > > rotate z -0.231 > > translate x -69.456 > > translate y -9.966 > > translate z 29.702 > > I have an original output from the structrual alignment tool, but would like to load the molecules separately into Rasmol to utilise some Rasmol scripts. Unfortunately the above commands don't reproduce the original alignment, and I've double checked the matrix values. I've tried a couple of different ways, but to no avail - if you have any insight on this, that'd be great. > > In general, is the best way to implement a transformation matrix in rasmol by using a sequence of rotations and translations? > > Many thanks, > > Richie ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- <2146324.1077227101618.JavaMail.root@misspiggy.psp.pas.earthlink.net> X-X-Sender: yaya@epsilon.pair.com References: <2146324.1077227101618.JavaMail.root@misspiggy.psp.pas.earthlink.net> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: RasMol rotations about axes Date: Fri, 20 Feb 2004 23:18:57 -0500 (EST) To: Philippe Cc: rasmol@lists.umass.edu Allowing larger percentages than 100 should be feasible, but there are two things wrong with trying to solve this problem by labeling the current behavior as a bug and changing it in the zoom-sensitive way Phillipe proposes: 1. It will break lots of existing scripts. 2. It produces very strange behavior when you zoom an image that has already been translated. The first issue is the important one, but it is interesting to consider the second one to see why we should be careful about hasty "bug fixes". Suppose we were to change RasMol so that translate 100 would move a molecule just off the screen and would do just that after a zoom 50, a zoom 100 and a zoom 200. If the molecule is 200 Angstroms wide, then at zoom 100, then a translate x 50 will move the molecule by 100 Angstroms to the right after applying all rotations. Under the current implementation it also moves the molecule by 100 Angstroms to the right at all other zoom values, so we can translate first and then zoom or zoom first and then translate, and we will get the same image. Under Phillipe's proposal, the molecule would move by different amounts if we zoom first and then translate: commands motion zoom 50 translate x 50 200 Angstroms right zoom 100 translate x 50 100 Angstroms right zoom 200 translate x 50 50 Angstroms right Now supposed we follow the "zoom 50; translate x 50" by a "zoom 200". Where should the molecule be now? Do we honor the "translate x 50" in the new context and move 150 Angstroms to the left, or do we convert the "translate x 50" into "translate x 200" to keep the rotation center in the same place relative to the molecule. One can get used to anything, but is this approach really what RasMol users want to get used to? I think we can do better by leaving the current behavior alone and just adding new command variants to support more general translation commands. With so many scripts out there and so many users, it seems sensible to keep existing scripts operational, even if they depend on features that some people feel are bugs. -- Herbert ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Thu, 19 Feb 2004, Philippe wrote: > Miguel wrote: > > >Interesting ... I though that by definition > > translate x|y|z (-)100 > >meant that it was out of view. > > The translation command is in fact not behaving propely in rasmol. For > example, start a session with rasmol 2.6.4 or 2.7.2.1 and load a > molecule, I use usually 1CRN. The molecule opens at zoom 100, the > command "translate x|y (-) 100" moves the molecule just of the screen. > Ok for me, the molecule is not in the view anymore, but just off of it. > > Now, zoom out, for example zoom 50 or smaller. The molecule becomes > smaller. With the mouse drag it in all directions. You will find that > moves are limited to a square that is smaller than the view. Inversely, > zoom in and drag. There are now areas that cannot be seen on the edges. > > In conclusion, the behavior of the translate command is as expected only > at and around "zoom 100". Remember that 2.6.4 has a lot of unfinished > points. I believe that the intended design was to have the translate > command to work at all zoom values like at zoom 100. For this reason the > use of RU/Angstrom values were not possible (yet) since it would have > broken the limitations of the translation command. Of course only Roger > Sayle knows about that and it is just speculation. > > In a multimolecule environement, it is not possible to limit > translation. The world needs to keep its integrity even when one > molecule is send far away by rotating around another molecule. In any > case, if we loose a molecule we still have the reset command to get > things back. > > My point is that we should drop the limitation on translation, i.e. > authorize any percentage values in the translate command, even those > superior to 100, and perhaps implement the translate command as > described in the manual at all zoom values. > > Philippe Valadon > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2727.1300 X-MSMail-priority: Normal References: <2146324.1077227101618.JavaMail.root@misspiggy.psp.pas.earthlink.net> ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: RasMol rotations about axes Date: Fri, 20 Feb 2004 22:50:45 -0800 To: rasmol@lists.umass.edu Herbert J. Bernstein wrote: > I think we can do better by leaving the > current behavior Absolutly, these arguments are totally convincing. That was actually a side point of my discussion which turns out to make little sens. The main point is that we need freedom of translation. Just a little bit of freedom :-) ! Philippe Valadon ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; de-AT; rv:1.6) Gecko/20040113 X-Accept-Language: de, en-us, en References: <59969.80.58.16.235.1077140239.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: axis labelling -- was Re: RasMol rotations about axes Date: Mon, 23 Feb 2004 16:06:54 +0100 To: rasmol@lists.umass.edu Herbert J. Bernstein schrieb: >The fine-grained set of commands is just as easy to implement as the >broader set and with respect to the labels and rotation allows simple, >yet complete simulation of both all the current behaviors and a pure >right-handed system. The complete control over axes and labels one >at a time is just for odd cases where one of the axes happens to obscure >some fine detail someone wanted to show. Most people would have >three axes with three labels. However, on reflection, I would suggest > >extending > set axes [x ] [y ] [z ] >to > set axes [signed|unsigned] > [[+|-]x ] [[+|-]y ] [[+|-]z ] > >to allow display of half axes if desired. (See below for >signed|unsigned). > > I had not much use for special axis labeling and half axis. Axis are to help with orientation during the manipulation and I would turn them off before printing (in contrary to unitcell), but this is just my personal opinion. >With respect to just treating the windows Y-label as a bug, I agree that >it is a bug, but, since it really does change the image, and somebody >might care, what is the harm in allowing them to recreate what they are > > this wouldn't be a good idea, because it *is* wrong. y values are increasing in the opposite direction in RasWin. If there would be a lebeling option for coordinates e.g. label "%8.3x %8.3y %8.3z" everybody woud see the confusion with current RasWin y axis label. I would like to see the insertion code get interpreted in RasMol, too, and suggest to use upcase %I (which is currently the same as %i) for label generation load pdb pdb1hag.ent select [Gly]1^F.Ca:E/0 cpk 50 label "%5i [%n]%r^%I:%c.%a;%A/%M\n%2e%C %8.3x %8.3y %8.3z %b" select [Gly]1^D.Ca:E/0 cpk Regards, Jan >used to. This way when they move to Linux they can keep the behavior >they are used to. > >With respect to signed labels, I would add the optional flags "signed" >or "unsigned" to the set axes commands. This would have the nice effect >of allowing the people who are used to the windows Y label placement to >keep it, but also to add a minus sign so that it would also be an >accurate label. The it would no longer be a bug. > >Regards, > Herbert > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal References: <4036545E.2000100@mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: transformation matrix Date: Tue, 24 Feb 2004 09:58:58 +0100 To: rasmol@lists.umass.edu I think that your problem is that you want to split a given rotation to the sum of a series of rotations. Take into consideration that rotations are not additive. For example: rot x 40, rot y 40 will give a different a result as rot x 20, rot y 20, rot x 20, rot y 20. Dr. Tamas E. Gunda ------------------------------------ University of Debrecen Medical and Health Science Center Dept. of Pharmaceutical Chemistry POBox 36 H-4010 Debrecen Hungary e-mail: tgunda*AT*puma.unideb.hu ----- Original Message ----- Sent: Friday, February 20, 2004 7:39 PM From: "Richard Harrington" Subject: transformation matrix To: > Dear all, > > I'm trying to use Rasmol to implement a transformation matrix given by a structural alignment that I can apply to one of the molecules I load into Rasmol whilst keeping the other molecule(s) constant. (I'm using the UCB enhanced rasmol, so can load multi > > matrix: > > | 0.597 0.494 0.632 | |x| | -69.456 | > | -0.275 -0.614 0.740 | x |y| + | -9.966 | > | 0.754 -0.615 -0.231 | |z| | 29.702 | > > commands into Rasmol: > > > rotate x 0.597 > > rotate y -0.275 > > rotate z 0.754 > > rotate x 0.494 > > rotate y -0.614 > > rotate z -0.615 > > rotate x 0.632 > > rotate y 0.740 > > rotate z -0.231 > > translate x -69.456 > > translate y -9.966 > > translate z 29.702 > > I have an original output from the structrual alignment tool, but would like to load the molecules separately into Rasmol to utilise some Rasmol scripts. Unfortunately the above commands don't reproduce the original alignment, and I've double checked the > > In general, is the best way to implement a transformation matrix in rasmol by using a sequence of rotations and translations? > > Many thanks, > > Richie > > -- > > _______________________________________________ > > Richard Harrington, > Men's Boat Club Captain, > Homerton College. > > PhD student, > ATP Synthase Group, > MRC-Dunn Human Nutrition Unit, > Cambridge University. > > e-mail: rah@mrc-dunn.cam.ac.uk > telephone: +44 (0) 1223 252861 > mobile: 07817 927175 > _______________________________________________ > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="--866757349145641" X-IP: 100.103.64.211 ++++------+------+------+------+------+------+------+------+------+------+ From: "ramesh kertis" Subject: Sillyest Stuff Everchicle Date: Fri, 27 Feb 2004 16:56:00 -0600 To: radkins@bio.umass.edu, rashie@bio.umass.edu, rasmol-digest@bio.umass.edu ----866757349145641

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a

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----866757349145641-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 boundary="Boundary_(ID_rGkeKpmwS5oNOuab1dUxHg)" X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: John Nixon Subject: Feedback request Date: Wed, 03 Mar 2004 15:06:27 +0000 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_rGkeKpmwS5oNOuab1dUxHg) Dear Chime users I have recently moved and updated a Chime tutorial on the mechanism of Rubisco and scripted it to work in both Netscape 4 and Microsoft Internet Explorer 6 using CHIME version 2.6 SP4. The original site was moved on the Birkbeck server and disappeared behind a password : The revised site may now be freely accessed at http://www.scicom.demon.co.uk/ see also http://photoscience.la.asu.edu/photosyn/photoweb/default.html#Rubisco Any feedback (e.g.concerning browser issues, page loading time...) on the updated site would be welcome at feedback@scicom.demon.co.uk Forgive the naivety of a non-programmer: is it meaningful to ask if there is a subset of the Chime command language that is likely to survive 'foreseeable changes in browser capability ? Thanks John --Boundary_(ID_rGkeKpmwS5oNOuab1dUxHg) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_rGkeKpmwS5oNOuab1dUxHg)-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Rasmol / RDB Date: Fri, 05 Mar 2004 14:23:53 +0000 (GMT) To: Rasmol Mailing List Hi, Making complex selects in rasmol is a bit like querying a relational database. Could rasmol be integrated with the free mysql libraries, and store a PDB file internally in some accepted PDB schema? Then selects could be optimized using regular and geometric indexes. Should I write a grant proposal ;) Also, why doesn't rasmol use the standard(?) readline? The number of times I have typed Ctrl-W or del is astonishing! Cheers, Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- LIST Jmol users , LIST PDB Education ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: example animation in Jmol Date: Mon, 08 Mar 2004 09:45:29 -0500 To: LIST rasmol , hi all, shows an example of a Chime animation converted directly to Jmol (version 10pre6, just released). fans of the Lehninger Chime tutorials (a.k.a. Biochemistry in 3D) may recognize this one from the beginning of the Bacteriorhodopsin module ;-) a 'direct' conversion means that this animation has not been upgraded to take advantage of Jmol features, like percent-based van der Waals radii. please make me feel good - visit the above site with a browser that is NOT netscape 4. :-) comments or problems, please let me know! regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- LIST PDB Education ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: example animation in Jmol Date: Mon, 08 Mar 2004 10:35:09 -0500 To: rasmol@lists.umass.edu Cc: LIST Jmol users , at 9.45a EDT on 2004 March 08 Monday timothy driscoll said: > hi all, > > > > shows an example of a Chime animation converted directly to Jmol > (version 10pre6, just released). fans of the Lehninger Chime > tutorials (a.k.a. Biochemistry in 3D) may recognize this one from the > beginning of the Bacteriorhodopsin module ;-) > several people have noted that the above page does not work well in Firefox 0.8, myself included, on Linux or OSX. generally, a page reload solves the problem, whatever it is. if you have problems with any other browsers, please let me know! thanks, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.6487.1 Thread-Topic: example animation in Jmol Thread-Index: AcQFHIoSUAchFaHdQa6Ejdq0U1zriAAB+Qlg content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: X-OriginalArrivalTime: 08 Mar 2004 15:55:24.0308 (UTC) FILETIME=[C4927D40:01C40525] ++++------+------+------+------+------+------+------+------+------+------+ From: "Thomson, Alan" Subject: RE: example animation in Jmol Date: Mon, 08 Mar 2004 15:55:24 +0000 To: rasmol@lists.umass.edu I tried, Internet Explorer version 6.0,2800.1106 on XP service pack 2 A) It takes ages to download (Over a 100 Gbyte line) 3-4 min B) There is a script error 1: Jmol executing script ... 2: script brdemo.spt 3: load brdemo.pdb 4: restrict none 5: 0 atoms selected 6: reset 7: rotate z 61 8: rotate y -1 9: rotate x 87 10: translate x -4 11: translate y -1 12: zoom 100 13: select model=1 hetero ret solvent or not and and 14: ScriptException:variable undefined Script line:select (model=1 and (hetero and not (RET or solvent))) File:brdemo.spt Line number:14 As a result you only see a black screen until you right click when the maanual system seems to work OK Dr Alan Thomson Dept Biological Sciences Lancaster University LANCASTER LA1 4YQ UK Tel (Direct Line) 01524 593792 -----Original Message----- On Behalf Of timothy driscoll Sent: 08 March 2004 14:45 From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu] Subject: example animation in Jmol To: LIST rasmol; LIST Jmol users; LIST PDB Education hi all, shows an example of a Chime animation converted directly to Jmol (version 10pre6, just released). fans of the Lehninger Chime tutorials (a.k.a. Biochemistry in 3D) may recognize this one from the beginning of the Bacteriorhodopsin module ;-) a 'direct' conversion means that this animation has not been upgraded to take advantage of Jmol features, like percent-based van der Waals radii. please make me feel good - visit the above site with a browser that is NOT netscape 4. :-) comments or problems, please let me know! regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: "J. Ricky Cox" Subject: Re: example animation in Jmol Date: Mon, 08 Mar 2004 11:00:00 -0600 To: rasmol@lists.umass.edu I am running Windows 2000 with Netscape 7.0.  It took about 15 seconds to load and it looks great...

Ricky


At 10:35 AM 3/8/2004 -0500, you wrote:
at 9.45a EDT on 2004 March 08 Monday timothy driscoll said:

> hi all,
>
> <http://www.molvisions.com/community/jmol/jm_dev_bin3d.html>
>
> shows an example of a Chime animation converted directly to Jmol
> (version 10pre6, just released).  fans of the Lehninger Chime
> tutorials (a.k.a. Biochemistry in 3D) may recognize this one from the
> beginning of the Bacteriorhodopsin module ;-)
>

several people have noted that the above page does not work well in
Firefox 0.8, myself included, on Linux or OSX.  generally, a page reload
solves the problem, whatever it is.

if you have problems with any other browsers, please let me know!

thanks,

:tim

--
timothy driscoll
molvisions - molecular graphics & visualization
<http://www.molvisions.com/>
usa:north carolina:wake forest

----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- LIST Jmol users ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: RE: example animation in Jmol Date: Mon, 08 Mar 2004 12:04:02 -0500 To: rasmol@lists.umass.edu, LIST PDB Education , at 3.55p EDT on 2004 March 08 Monday Thomson, Alan said: > I tried, Internet Explorer version 6.0,2800.1106 on XP service pack 2 > damn, it worked fine here! ;-) > A) It takes ages to download (Over a 100 Gbyte line) 3-4 min > my apologies. there is a speed issue in Jmol 10pre6 that we are currently debugging. this will be fixed as soon as possible. > B) There is a script error > this was my fault - because my test browsers weren't throwing visible errors on it. the script error should be repaired now. (clear your browser cache if you revisit.) thanks to all for your prompt feedback! it is extremely helpful. :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest > -----Original Message----- > From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu] > On Behalf Of timothy driscoll > Sent: 08 March 2004 14:45 > To: LIST rasmol; LIST Jmol users; LIST PDB Education > Subject: example animation in Jmol > > > hi all, > > > > shows an example of a Chime animation converted directly to Jmol > (version 10pre6, just released). fans of the Lehninger Chime > tutorials (a.k.a. Biochemistry in 3D) may recognize this one from the > beginning of the Bacteriorhodopsin module ;-) > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: "galaeasy.002062" Subject: Re: example animation in Jmol Date: Mon, 08 Mar 2004 20:12:46 +0100 To: rasmol@lists.umass.edu sorry, but i cant read a blue text over a black page, can u ? giuseppe striccoli ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_Eu33d48QLGifEcIqm639sQ)" X-scanner: scanned by Inflex 1.0.12.3 References: ++++------+------+------+------+------+------+------+------+------+------+ From: adriano ceccarelli Subject: Re: example animation in Jmol Date: Mon, 08 Mar 2004 23:04:49 +0100 To: rasmol@lists.umass.edu --Boundary_(ID_Eu33d48QLGifEcIqm639sQ) Hi Tim, I tried it with Safari and OSX 10.3 It takes a while to load, approx 30 sec, but the disappointing thing is that as soon as I close the browser window, Safari "quits unexpectedly" as they say. Graphically it looks gorgeous. Regard Adriano l giorno 08/mar/04, alle 15:45, timothy driscoll ha scritto: > hi all, > > > > shows an example of a Chime animation converted directly to Jmol > (version 10pre6, just released). fans of the Lehninger Chime tutorials > (a.k.a. Biochemistry in 3D) may recognize this one from the beginning > of > the Bacteriorhodopsin module ;-) > > a 'direct' conversion means that this animation has not been upgraded > to > take advantage of Jmol features, like percent-based van der Waals > radii. > > please make me feel good - visit the above site with a browser that is > NOT netscape 4. :-) > > comments or problems, please let me know! > > > regards, > > :tim > > -- > timothy driscoll > molvisions - molecular graphics & visualization > > usa:north carolina:wake forest > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > > Prof. Adriano Ceccarelli Dip. Scienze Cliniche e Biologiche Osp. San Luigi Gonzaga Regione Gonzole 10 10043 Orbassano Torino tel 0116708109 fax 0112368109 e-mail: adriano.ceccarelli@unito.it _____________________________________________________________________ For your security, this mail has been scanned and protected by Inflex --Boundary_(ID_Eu33d48QLGifEcIqm639sQ) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_Eu33d48QLGifEcIqm639sQ)-- X-MSMail-Priority: High boundary="_B5188_25F_E__6_.B9" ++++------+------+------+------+------+------+------+------+------+------+ From: "Admin" Subject: ADV: Attention All School Staff, Teachers and Students: Date: Tue, 09 Mar 04 13:14:01 GMT To: libbik@bio.umass.edu This is a multi-part message in MIME format. --_B5188_25F_E__6_.B9 Attention All School Staff, Teachers and Students: You Must Respond By 5 P.M. Wednesday, March 10, 2004. Through a special arrangement, Avtech Direct is offering a limited allotment of BRAND NEW, top of-the-line, name-brand desktop computers at more than 50% off MSRP to all Staff Members, Teachers and Students who respond to this message before 5 P.M., Wednesday, March 10, 2004. All desktop computers are brand-new packed in their original boxes, and come with a full manufacturer's warranty plus a 100% satisfaction guarantee. These professional grade Desktops are fully equipped with 2004 next generation technology, making these the best performing computers money can buy. Avtech Direct is offering these feature rich, top performing Desktop Computers with the latest Intel technology at an amazing price to all who call: 1-800-884-9510 by 5 P.M. Wednesday, March 10, 2004 The fast and powerful AT-2400 series Desktop features: * Intel 2.0Ghz Processor for amazing speed and performance * 128MB DDR RAM, --- Upgradeable to 1024 * 20 GB UDMA Hard Drive, --- Upgradeable to 80 GB * 52X CD-Rom Drive, --- Upgradeable to DVD/CDRW * 1.44 Floppy disk drive * Next Generation Technology * ATI Premium video and sound * Full Connectivity with Fax modem/Lan/IEE 1394/USB 2.0 * Soft Touch Keyboard and scroll mouse * Internet Ready * Network Ready * 1 Year parts and labor warranty * Priority customer service and tech support MSRP $699 ........................................ Your Cost $297 How to qualify: 1. You must be a Staff member, Teacher or Student: 2. All desktop computers will be available on a first come first serve basis. 3. You must call 1-800-884-9510 by 5 P.M. Wednesday, March 10, 2004 and we will hold the desktops you request on will call. 4. You are not obligated in any way. 5. 100% Satisfaction Guaranteed. Call Avtech Direct 1-800-884-9510 before 5 P.M. Wednesday, March 10, 2004 If you wish to unsubscribe from this list, please go to: http://www.computeradvice.org/unsubscribe.asp --_B5188_25F_E__6_.B9-- User-Agent: Microsoft-Entourage/10.1.4.030702.0 ++++------+------+------+------+------+------+------+------+------+------+ From: "S. Renee Judd" Subject: Re: example animation in Jmol Date: Mon, 08 Mar 2004 23:27:27 -0600 To: rasmol@lists.umass.edu Safari 1.2 v125 in OSX 10.3.2 did *not* quit for me after closing the tutorial window. srj -- S. Renee Judd Assistant Professor, Natural Science Department College of Arts and Sciences National-Louis University rjudd@nl.edu > From: adriano ceccarelli > Reply-To: rasmol@lists.umass.edu > Date: Mon, 08 Mar 2004 23:04:49 +0100 > To: rasmol@lists.umass.edu > Subject: Re: example animation in Jmol > > Hi Tim, > > I tried it with Safari and OSX 10.3 > It takes a while to load, approx 30 sec, but the disappointing thing is > that as soon as I close the browser window, Safari "quits unexpectedly" > as they say. > > Graphically it looks gorgeous. > > Regard > > Adriano > > > > l giorno 08/mar/04, alle 15:45, timothy driscoll ha scritto: > >> hi all, >> >> >> >> shows an example of a Chime animation converted directly to Jmol >> (version 10pre6, just released). fans of the Lehninger Chime tutorials >> (a.k.a. Biochemistry in 3D) may recognize this one from the beginning >> of >> the Bacteriorhodopsin module ;-) >> >> a 'direct' conversion means that this animation has not been upgraded >> to >> take advantage of Jmol features, like percent-based van der Waals >> radii. >> >> please make me feel good - visit the above site with a browser that is >> NOT netscape 4. :-) >> >> comments or problems, please let me know! >> >> >> regards, >> >> :tim >> >> -- >> timothy driscoll >> molvisions - molecular graphics & visualization >> >> usa:north carolina:wake forest >> >> ---------------------------------------------------------------- >> rasmol-+ >> >> To change your address, unsubscribe, view previous messages/history, >> receive messages as weekly digests, or for any other information >> about the RasMol EMail List, please go to >> http://www.umass.edu/microbio/rasmol/raslist.htm >> >> ---------------------------------------------------------------- >> rasmol-- >> >> > Prof. Adriano Ceccarelli > Dip. Scienze Cliniche e Biologiche > Osp. San Luigi Gonzaga > Regione Gonzole 10 10043 > Orbassano Torino > tel 0116708109 > fax 0112368109 > e-mail: adriano.ceccarelli@unito.it > > > _____________________________________________________________________ > For your security, this mail has been scanned and protected by Inflex > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.6487.1 Thread-Topic: example animation in Jmol Thread-Index: AcQFlEK8JZSul1dDRPeO4qsPxqMQKAAJX0dQ content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: X-OriginalArrivalTime: 09 Mar 2004 09:36:13.0894 (UTC) FILETIME=[F6AE8E60:01C405B9] ++++------+------+------+------+------+------+------+------+------+------+ From: "Thomson, Alan" Subject: RE: example animation in Jmol Date: Tue, 09 Mar 2004 09:36:13 +0000 To: rasmol@lists.umass.edu Internet Explorer now fixed Alan Thomson -----Original Message----- On Behalf Of timothy driscoll Sent: 08 March 2004 17:04 From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu] Subject: RE: example animation in Jmol To: rasmol@lists.umass.edu; LIST PDB Education; LIST Jmol users at 3.55p EDT on 2004 March 08 Monday Thomson, Alan said: > I tried, Internet Explorer version 6.0,2800.1106 on XP service pack 2 > damn, it worked fine here! ;-) > A) It takes ages to download (Over a 100 Gbyte line) 3-4 min > my apologies. there is a speed issue in Jmol 10pre6 that we are currently debugging. this will be fixed as soon as possible. > B) There is a script error > this was my fault - because my test browsers weren't throwing visible errors on it. the script error should be repaired now. (clear your browser cache if you revisit.) thanks to all for your prompt feedback! it is extremely helpful. :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest > -----Original Message----- > From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu] > On Behalf Of timothy driscoll > Sent: 08 March 2004 14:45 > To: LIST rasmol; LIST Jmol users; LIST PDB Education > Subject: example animation in Jmol > > > hi all, > > > > shows an example of a Chime animation converted directly to Jmol > (version 10pre6, just released). fans of the Lehninger Chime > tutorials (a.k.a. Biochemistry in 3D) may recognize this one from the > beginning of the Bacteriorhodopsin module ;-) > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: example animation in Jmol Date: Tue, 09 Mar 2004 05:27:59 -0500 To: rasmol@lists.umass.edu at 11.04p EDT on 2004 March 08 Monday adriano ceccarelli said: > Hi Tim, > > I tried it with Safari and OSX 10.3 It takes a while to load, approx > 30 sec, but the disappointing thing is that as soon as I close the > browser window, Safari "quits unexpectedly" as they say. > argh; that is disappointing. I'm not sure why Safari would do that but I'll look at it again. this is my first attempt at casting an animation from Chime to Jmol, so I knew there would be trouble. :-) > Graphically it looks gorgeous. > thanks for the feedback, Adriano! regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest > l giorno 08/mar/04, alle 15:45, timothy driscoll ha scritto: > > > hi all, > > > > > > > > shows an example of a Chime animation converted directly to Jmol > > (version 10pre6, just released). fans of the Lehninger Chime > > tutorials (a.k.a. Biochemistry in 3D) may recognize this one from > > the beginning of the Bacteriorhodopsin module ;-) > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: example animation in Jmol Date: Tue, 09 Mar 2004 05:30:38 -0500 To: rasmol@lists.umass.edu at 8.12p EDT on 2004 March 08 Monday galaeasy.002062 said: > sorry, but i cant read a blue text over a black page, can u ? > giuseppe striccoli > hi Giuseppe, I can, yes - but I'm on a Mac, where the gamma is higher. the links at my site in general are much duskier on Windows. sorry 'bout that. so... were you able to view to the animation? regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Inbal Tuvi-Arad Subject: RE: example animation in Jmol Date: Tue, 09 Mar 2004 14:30:05 +0200 To: "'rasmol@lists.umass.edu'" Hi, I'm working with Internet Explorer version 5.50.4897.2300 on Microsoft Windows 2000, and it does not work. __________________________________ Dr. Inbal Tuvi-Arad Department of Natural Sciences The Open University of Israel POB 39328, Tel Aviv, 61392, Israel. Tel: 972-3-640-3704 Fax: 972-3-646-5465 Email: inbaltu@openu.ac.il __________________________________ -----Original Message----- Sent: Monday, March 08, 2004 7:04 PM From: timothy driscoll [mailto:molvisions@mac.com] Subject: RE: example animation in Jmol To: rasmol@lists.umass.edu; LIST PDB Education; LIST Jmol users at 3.55p EDT on 2004 March 08 Monday Thomson, Alan said: > I tried, Internet Explorer version 6.0,2800.1106 on XP service pack 2 > damn, it worked fine here! ;-) > A) It takes ages to download (Over a 100 Gbyte line) 3-4 min > my apologies. there is a speed issue in Jmol 10pre6 that we are currently debugging. this will be fixed as soon as possible. > B) There is a script error > this was my fault - because my test browsers weren't throwing visible errors on it. the script error should be repaired now. (clear your browser cache if you revisit.) thanks to all for your prompt feedback! it is extremely helpful. :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest > -----Original Message----- > From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu] > On Behalf Of timothy driscoll > Sent: 08 March 2004 14:45 > To: LIST rasmol; LIST Jmol users; LIST PDB Education > Subject: example animation in Jmol > > > hi all, > > > > shows an example of a Chime animation converted directly to Jmol > (version 10pre6, just released). fans of the Lehninger Chime > tutorials (a.k.a. Biochemistry in 3D) may recognize this one from the > beginning of the Bacteriorhodopsin module ;-) > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- LIST Jmol users ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: FOLLOWUP: Re: example animation in Jmol Date: Tue, 09 Mar 2004 09:01:16 -0500 To: rasmol@lists.umass.edu, LIST PDB Education , at 11.04p EDT on 2004 March 08 Monday adriano ceccarelli said: > Hi Tim, > > I tried it with Safari and OSX 10.3 > It takes a while to load, approx 30 sec, but the disappointing thing > is that as soon as I close the browser window, Safari "quits > unexpectedly" as they say. > greetings all, many thanks to everyone who provided (and continue to provide) helpful feedback about this animation. with your help, and Miguel's, I have rewritten the page: the animation no longer tries to play immediately, and I have added a Play button, and a Reset. I have removed all of the command line and message box code as well, since that seemed to be mucking up some browsers (especially Mozilla flavors) and was not necessary in this context. please note that the first time you load the Jmol applet it may take 20-30 seconds. after the first time, though, it resides in your local cache and should load much faster. the page is using the recent public beta of Jmol (10pre6). I have tested it thusly: Mac 10.2.3 :: Safari 1.2 no problems. Mozilla 1.6 no problems. Firefox 0.8 no problems. Camino 0.7 seems to work. Java output shows some bugs, characterized by Camino as 'total weirdness'. some odd screen redraw or repaint issues. Netscape 7.1 no problems. OmniWeb 4.5 no problems. Internet Explorer 5.2.2 no problems (brief screen 'flash' at the animation start). Opera 5.0b applet does not load. iCab 2.9.7 seems to work. screen redraw issue causes the Jmol applet to flash when a script is played, but no major problems. Mac 9.2.2 :: Netscape 4.79 ponderous to load and run, but it does work. eventually. Internet Explorer 5 no problems. (!) Windows2000 :: Internet Explorer 6 no problems. Mozilla 1.6 no problems. if you continue to have problems with the animation, especially using one of the above browsers, please feel free to let me know on the list or off. your comments are extremely helpful, and hopefully we can iron out the remaining problems in short order. if you are running Linux, feel free to add your own observations about your system (I do not have a working Linux system yet, so can not test that platform). ditto for folks with other Windows systems. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest > > l giorno 08/mar/04, alle 15:45, timothy driscoll ha scritto: > > > hi all, > > > > > > > > shows an example of a Chime animation converted directly to Jmol > > (version 10pre6, just released). fans of the Lehninger Chime > > tutorials (a.k.a. Biochemistry in 3D) may recognize this one from > > the beginning of the Bacteriorhodopsin module ;-) > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: example animation in Jmol Date: Tue, 09 Mar 2004 20:16:01 +0000 (GMT) To: rasmol@lists.umass.edu :( My mozilla (old verion) fails... Error: document.jmolapplet.script is not a function. On Tue, 9 Mar 2004, timothy driscoll wrote: > at 8.12p EDT on 2004 March 08 Monday galaeasy.002062 said: > > > sorry, but i cant read a blue text over a black page, can u ? > > giuseppe striccoli > > > > hi Giuseppe, > > I can, yes - but I'm on a Mac, where the gamma is higher. the links at > my site in general are much duskier on Windows. sorry 'bout that. > > so... > > were you able to view to the animation? > > > > > regards, > > :tim > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- LIST Jmol users X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: FOLLOWUP: Re: example animation in Jmol Date: Tue, 09 Mar 2004 20:17:46 +0000 (GMT) To: rasmol@lists.umass.edu Cc: LIST PDB Education , Mozilla 1.2.1 Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.2.1) Gecko/20030225 On Tue, 9 Mar 2004, timothy driscoll wrote: > at 11.04p EDT on 2004 March 08 Monday adriano ceccarelli said: > > Hi Tim, > > > > I tried it with Safari and OSX 10.3 > > It takes a while to load, approx 30 sec, but the disappointing thing > > is that as soon as I close the browser window, Safari "quits > > unexpectedly" as they say. > > > > greetings all, > > many thanks to everyone who provided (and continue to provide) helpful > feedback about this animation. with your help, and Miguel's, I have > rewritten the page: > > > > the animation no longer tries to play immediately, and I have added a > Play button, and a Reset. I have removed all of the command line and > message box code as well, since that seemed to be mucking up some > browsers (especially Mozilla flavors) and was not necessary in this > context. > > please note that the first time you load the Jmol applet it may take > 20-30 seconds. after the first time, though, it resides in your local > cache and should load much faster. > > the page is using the recent public beta of Jmol (10pre6). I have tested > it thusly: > > Mac 10.2.3 :: > Safari 1.2 > no problems. > Mozilla 1.6 > no problems. > Firefox 0.8 > no problems. > Camino 0.7 > seems to work. Java output shows some bugs, characterized by > Camino as 'total weirdness'. some odd screen redraw or > repaint issues. > Netscape 7.1 > no problems. > OmniWeb 4.5 > no problems. > Internet Explorer 5.2.2 > no problems (brief screen 'flash' at the animation start). > Opera 5.0b > applet does not load. > iCab 2.9.7 > seems to work. screen redraw issue causes the Jmol applet to > flash when a script is played, but no major problems. > > Mac 9.2.2 :: > Netscape 4.79 > ponderous to load and run, but it does work. eventually. > Internet Explorer 5 > no problems. (!) > > Windows2000 :: > Internet Explorer 6 > no problems. > Mozilla 1.6 > no problems. > > > if you continue to have problems with the animation, especially using > one of the above browsers, please feel free to let me know on the list > or off. your comments are extremely helpful, and hopefully we can iron > out the remaining problems in short order. if you are running Linux, > feel free to add your own observations about your system (I do not have > a working Linux system yet, so can not test that platform). ditto for > folks with other Windows systems. > > > regards, > > :tim > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline User-Agent: Mutt/1.4i References: <9E0C9032-714C-11D8-8900-000A95CDD040@unito.it> ++++------+------+------+------+------+------+------+------+------+------+ From: Michael Sternberg Subject: Re: example animation in Jmol Date: Tue, 09 Mar 2004 14:33:21 -0600 To: rasmol@lists.umass.edu Hello Tim, On Tue, Mar 09, 2004 at 09:01:16AM -0500, timothy driscoll wrote: > many thanks to everyone who provided (and continue to provide) helpful > feedback about this animation. with your help, and Miguel's, I have > rewritten the page: > > > > the animation no longer tries to play immediately, and I have added a > Play button, and a Reset. I have removed all of the command line and > message box code as well, since that seemed to be mucking up some > browsers (especially Mozilla flavors) and was not necessary in this > context. Your example loads and the animation runs flawlessly with Mozilla and Sun's Java under Linux: Mozilla 1.2.1 (X11; U; Linux i686; en-US; rv:1.2.1) Gecko/20030225 Java(TM) Plug-in 1.4.1_02-b06 The Browser came one packaged with the distro, which is RedHat-9. I also tried Konqueror 3.1-12 with the same Java plugin handler. The applet loads and runs (in a separate window), and has some reluctance bringing up the context menu (right menu button). These issues may be related to my Java settings for Konqueror though. - file that one under "yes, mostly" :-) I greatly appreciate the recent developments with JMol -- these are major breaktroughs in cross-platform accessibility. Best Regards, -- Michael Sternberg, Ph.D. | Argonne National Laboratory phone: (630) 252-7020 fax: -9555 | Materials Science Div., Building 200 email: sternberg.at.anl.gov | 9700 S Cass Ave, Argonne, IL 60439-4831 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: example animation in Jmol Date: Tue, 09 Mar 2004 16:38:55 -0500 To: rasmol@lists.umass.edu at 8.16p EDT on 2004 March 09 Tuesday Dan Bolser said: > > :( > > My mozilla (old verion) fails... > > Error: document.jmolapplet.script is not a function. > :-( indeed, but not too bad. what version of Mozilla are you using? I use some javascript to check browser and decide how to send commands to Jmol - you may be getting caught in that. your version will tell me. many thanks, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: RE: example animation in Jmol Date: Tue, 09 Mar 2004 16:40:15 -0500 To: rasmol@lists.umass.edu at 2.30p EDT on 2004 March 09 Tuesday Inbal Tuvi-Arad said: > Hi, > I'm working with Internet Explorer version 5.50.4897.2300 on Microsoft > Windows 2000, and it does not work. > __________________________________ > Dr. Inbal Tuvi-Arad > Department of Natural Sciences > The Open University of Israel thank you very much - that is a browser that I do not have available for testing, but I know is still popular. I will work on debugging the problem. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: example animation in Jmol Date: Tue, 09 Mar 2004 16:52:54 -0500 To: rasmol@lists.umass.edu at various times on 2004 March 09 Tuesday Dan Bolser said: > > My mozilla (old verion) fails... > > Error: document.jmolapplet.script is not a function. > > Mozilla 1.2.1 > > Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.2.1) Gecko/20030225 > but at 2.33p EDT on 2004 March 09 Tuesday Michael Sternberg said: > Your example loads and the animation runs flawlessly with Mozilla > and Sun's Java under Linux: > > Mozilla 1.2.1 (X11; U; Linux i686; en-US; rv:1.2.1) Gecko/20030225 > Java(TM) Plug-in 1.4.1_02-b06 > > The Browser came one packaged with the distro, which is RedHat-9. if I had to guess, I would say your two systems are running different JVMs but it would be only a guess. I will have to check with the Linux experts that I know and figure this out. it should work, for what *that* is worth ;-) sorry Dan; stay tuned... regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest > On Tue, 9 Mar 2004, timothy driscoll wrote: > > > > > were you able to view to the animation? > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline User-Agent: Mutt/1.4i References: ++++------+------+------+------+------+------+------+------+------+------+ From: Michael Sternberg Subject: Re: example animation in Jmol Date: Tue, 09 Mar 2004 17:34:12 -0600 To: rasmol@lists.umass.edu Hello, On Tue, Mar 09, 2004 at 04:52:54PM -0500, timothy driscoll wrote: > at various times on 2004 March 09 Tuesday Dan Bolser said: > > My mozilla (old verion) fails [..] > > Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.2.1) Gecko/20030225 > at 2.33p EDT on 2004 March 09 Tuesday Michael Sternberg said: > > Your example loads and the animation runs flawlessly with Mozilla > > and Sun's Java under Linux: > > Mozilla 1.2.1 (X11; U; Linux i686; en-US; rv:1.2.1) Gecko/20030225 > > Java(TM) Plug-in 1.4.1_02-b06 Tim is most likely correct - I used the pre-installed Mozilla, and switched the Java VM to the one from Sun. I just upgraded to the current version, which also works nicely with Tim's example. Mozilla's "about:plugins" says: Java(TM) Plug-in 1.4.2_04-b05 Steps to upgrade: Get the "J2SE v 1.4.2_04" package from: http://java.sun.com/j2se/1.4.2/download.html Follow the instructions to install the package AND register it with the browsers: http://java.sun.com/j2se/1.4.2/jre/install-linux.html Regards, Michael ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Inbal Tuvi-Arad Subject: RE: example animation in Jmol Date: Wed, 10 Mar 2004 13:29:07 +0200 To: "'rasmol@lists.umass.edu'" Hi Tim, I don't know what you fixed, but it works now and it is very nice. Best regards Inbal __________________________________ Dr. Inbal Tuvi-Arad Department of Natural Sciences The Open University of Israel POB 39328, Tel Aviv, 61392, Israel. Tel: 972-3-640-3704 Fax: 972-3-646-5465 Email: inbaltu@openu.ac.il __________________________________ -----Original Message----- Sent: Tuesday, March 09, 2004 11:40 PM From: timothy driscoll [mailto:molvisions@mac.com] Subject: RE: example animation in Jmol To: rasmol@lists.umass.edu at 2.30p EDT on 2004 March 09 Tuesday Inbal Tuvi-Arad said: > Hi, > I'm working with Internet Explorer version 5.50.4897.2300 on Microsoft > Windows 2000, and it does not work. > __________________________________ > Dr. Inbal Tuvi-Arad > Department of Natural Sciences > The Open University of Israel thank you very much - that is a browser that I do not have available for testing, but I know is still popular. I will work on debugging the problem. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: RE: example animation in Jmol Date: Wed, 10 Mar 2004 06:54:49 -0500 To: rasmol@lists.umass.edu at 1.29p EST on 2004 March 10 Wednesday Inbal Tuvi-Arad said: > Hi Tim, > I don't know what you fixed, but it works now and it is very nice. > > Best regards > > Inbal LOL - not a thing! maybe just a good night's sleep helped the server ;-) thanks for letting me know, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest > -----Original Message----- > From: timothy driscoll [mailto:molvisions@mac.com] > Sent: Tuesday, March 09, 2004 11:40 PM > To: rasmol@lists.umass.edu > Subject: RE: example animation in Jmol > > > at 2.30p EDT on 2004 March 09 Tuesday Inbal Tuvi-Arad said: > > > Hi, > > I'm working with Internet Explorer version 5.50.4897.2300 on > Microsoft > > Windows 2000, and it does not work. > > __________________________________ > > Dr. Inbal Tuvi-Arad > > Department of Natural Sciences > > The Open University of Israel > > > thank you very much - that is a browser that I do not have available for > testing, but I know is still popular. I will work on debugging the > problem. > > regards, > > :tim > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: DNA/protein models in glass Date: Thu, 11 Mar 2004 10:37:51 -0500 To: rasmol@lists.umass.edu Dear Colleagues: I recently learned about a technology that makes beautiful physical models of 3D objects inside a glass block. Bathsheba Grossman, a sculptor, has pioneered use of this technology for macromolecular models as well as other scientific and mathematical models (http://www.bathsheba.com/crystal/). Don't miss her page on macromolecules (http://www.crystalprotein.com). You may get a clearer idea of the size of her DNA model from my photo at http://www.umass.edu/microbio/rasmol/history.htm#sculpt (scroll down a bit till you see the glass model by Bathsheba Grossman). Models of new macromolecular structures using this technology will generally cost roughly $250 for the first copy, and roughly $120 for additional copies (or somewhat less, depending on the size of the glass block chosen). Please see http://www.bathsheba.com/crystal/ -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein folding kit, DNA construction for teaching Date: Thu, 11 Mar 2004 10:43:57 -0500 To: rasmol@lists.umass.edu 3DMolecularDesigns.com is now offering a nifty hands-on protein folding kit for classes, using very inexpensive toobers, see http://www.rpc.msoe.edu/3dmd/tfoldings.php (and also my Toobers in Science Education site, http://www.umass.edu/molvis/toobers/) Soon they will offer a plastic DNA construction kit, see http://www.rpc.msoe.edu/3dmd/dnainfo.php (cost not yet set). -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Andy Bates Subject: Chime button problem with 'load' Date: Mon, 15 Mar 2004 09:29:16 +0000 To: rasmol@lists.umass.edu Cc: elizabeth Hi I have a short Chime tutorial called 'Why is DNA a helix?', which I have been using for quite a while now: http://www.liv.ac.uk/~bates/Stackframe.html We have just come to modify it and have found a strange fault. The 'embed' buttons that include a 'load' command in the script work fine first time through, but on returning to the start and trying them again, they seem to pause or stop halfway through the script - a second click of the button gives the desired result. An example of one of the embed tags is below: Button tags without 'load' seem to work fine. This problem does not occur on a Mac with Chime 2.6, and as far as I know did not several years ago on Windows, but does on: Windows 2000 (5.00.2195 SP2) with Chime 2.6 SP4 or 5 with IE 6 (6.0.2800.1106) Any confirmation of the fault or any thoughts gratefully received. Thanks a lot, Andy Bates -- Dr Andrew D. Bates School of Biological Sciences University of Liverpool The Biosciences Building Crown Street Liverpool L69 7ZB UK Tel-(+44) (0)151 795 4563 Fax-(+44) (0)151 795 4410 Mobile-(+44) (0)797 324 7956 http://www.liv.ac.uk/~bates/ Liverpool - European Capital of Culture 2008 http://www.liverpoolculture.com/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Chime button problem with 'load' Date: Mon, 15 Mar 2004 16:56:25 -0500 To: rasmol@lists.umass.edu Dear Andy, I have not looked at your tutorial, but from your description I think I know where the problem is. Scripts that have commands that refer to disk files (commands: load, script) don't work properly in IE. They work fine in Netscape 4.8. For IE, best to design your tutorials with only one PDB file per page, and load it with the src="" in the embed tag, then use "reset" as the first command in button scripts, omitting the load command. Please see http://molvis.sdsc.edu/protexpl/ie.htm for a list of Chime problems in IE. Note the item ".pdb file loading kills remainder of script". Let me know if this doesn't identify the problem. -Eric At 3/15/2004, you wrote: >Hi > >I have a short Chime tutorial called 'Why is DNA a helix?', which I have >been using for quite a while now: > >http://www.liv.ac.uk/~bates/Stackframe.html > >We have just come to modify it and have found a strange fault. The >'embed' buttons that include a 'load' command in the script work fine >first time through, but on returning to the start and trying them again, >they seem to pause or stop halfway through the script - a second click of >the button gives the desired result. An example of one of the embed tags >is below: > >type="application/x-spt" button=push align=bottom target="struct" >startspin=no script=" > zap > load pdb/Stack.pdb > color chain > wireframe 20 > rotate x 100 > rotate y 10 > zoom 150 > restrict *:a > refresh > center *:a"> > >Button tags without 'load' seem to work fine. > >This problem does not occur on a Mac with Chime 2.6, and as far as I know >did not several years ago on Windows, but does on: > >Windows 2000 (5.00.2195 SP2) with Chime 2.6 SP4 or 5 with IE 6 (6.0.2800.1106) > >Any confirmation of the fault or any thoughts gratefully received. > >Thanks a lot, > >Andy Bates >-- >Dr Andrew D. Bates School of Biological Sciences University of Liverpool > The Biosciences Building Crown Street > Liverpool L69 7ZB UK > Tel-(+44) (0)151 795 4563 Fax-(+44) (0)151 795 4410 > Mobile-(+44) (0)797 324 7956 > http://www.liv.ac.uk/~bates/ > >Liverpool - European Capital of Culture 2008 >http://www.liverpoolculture.com/ > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime 2.6 SP6 fixes "pbd" ChimeShim bug Date: Sun, 21 Mar 2004 16:24:53 -0500 To: rasmol@lists.umass.edu Cc: chime-team@mdli.com Chime 2.6 SP4 fixed a serious bug in the Chime installer, but introduced a new one. A typographical error put "pbd" (instead of "pdb") in the Windows registry. When clicking on a URL to a .pdb file (in Internet Explorer only) the file would sometimes fail to display, reporting a ChimeShimLibrary error. Also, if a PDB file were saved from Chime, it might be saved with the filename ending in .pbd. Although I had reported this problem to MDL, this bug was not fixed in Chime 2.6 SP5. Bob Dickey at MDL kindly initiated release of Chime 2.6 SP6 (now available) to correct this bug. I have tested SP6 and it appears to fix the "pbd" bug. Also it reports its version correctly with the "show version" command, and works correctly in Protein Explorer in both Netscape and Internet Explorer in cursory tests. Thanks, Bob!! I have just released two new documents: Step by Step: Downloading and Installing MDL Chime http://www.umass.edu/microbio/chime/getchime.htm Version History of MDL Chime http://www.umass.edu/microbio/chime/chimvers.htm -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- jmol-developers@lists.sourceforge.net ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime script command overview revised, updated Date: Sun, 21 Mar 2004 16:29:57 -0500 To: rasmol@lists.umass.edu, jmol-users@lists.sourceforge.net, I have just revised, updated and expanded the section 'About Chime' at my main Molecular Visualization page, http://www.umass.edu/microbio/chime/index.html#about This section now explains how the command language in Chime evolved, and ended up being documented in two separate non-overlapping manuals (the RasMol Reference Manual, and the MDL Chime Script Reference Manual). It also newly provides links to overviews of select commands, colors, and bond determination and display in Chime, and to the MDL Chime Embed Tag Parameter Reference Manual. I have also revised the document on browser compatibility with Chime, and created a new document with step by step instructions for downloading and installing Chime. Finally, I created a new document listing the history of Chime versions and key changes in each version, also linked at the URL above. -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Ian Musgrave Subject: Strange problem with pages using Chime 2.6 SP6 Date: Mon, 22 Mar 2004 10:27:51 +1030 To: rasmol@lists.umass.edu G'Day All I have just installed Chime 2.6 SP6, (updated from Chime 2.6 SP3) and my page now has a weird problem, not previously seen in earlier versions of Chime. If you go to http://home.mira.net/~reynella/chime/adr_tuta.htm You will see I have a tutorial set up with three chime panels. The first and last panels display okay, just as they always did (I'm using Communicator 4.77 running on Windows 2000 5.00.2195 service pack4) The middle panel displays "click here to get plug-in", needless to say the other panels are working so the plug-in must exist. When I view the local copy of the very same files on my hard disk (using the same navigator/Windows combination, it works fine!!! Similarly, http://home.mira.net/~reynella/chime/artemisinin.htm shows a "click here to get plugin" panel, while the local copy works just fine. http://home.mira.net/~reynella/chime/ang_tuta.htm shows all panels with no problems. The only thing I can think of is that the offending panels display mol files, but MDL MOL files are explicitly stated as being handled, and why do local mol files display, but not those over the internet?? Any clues people? Cheers! Ian =============================================================== Ian F. Musgrave Ph.D, ian.musgrave@adelaide.edu.au Senior Lecturer, Dept. Clinical and Experimental Pharmacology University of Adelaide, SA, 5005, Australia Phone +61 8 83033905 Fax +61 8 8224 0685 CRICOS Provider Number 00123M And now a word from our lawyers...... ----------------------------------------------------------- This email message is intended only for the addressee(s) and contains information that may be confidential and/or copyright. If you are not the intended recipient please notify the sender by reply email and immediately delete this email. Use, disclosure or reproduction of this email by anyone other than the intended recipient(s) is strictly prohibited. No representation is made that this email or any attachments are free of viruses. Virus scanning is recommended and is the responsibility of the recipient. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-language: en Content-disposition: inline X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: PHILLIP W BARAK Subject: Re: Strange problem with pages using Chime 2.6 SP6 Date: Sun, 21 Mar 2004 18:06:18 -0600 To: rasmol@lists.umass.edu Don't know if this is a Chime 2.6 SP6 problem. On your page, my machine w/ NS 4.79, Chime 2.6 SP4, and Win2000 shows a blank middle panel where presumably the Chime should be...no offer of a plugin source, either. --Phillip Barak ----- Original Message ----- ++++------+------+------+------+------+------+------+------+------+------+ From: Ian Musgrave Subject: Strange problem with pages using Chime 2.6 SP6 Date: Sunday, March 21, 2004 5:57 pm > G'Day All > > I have just installed Chime 2.6 SP6, (updated from Chime 2.6 SP3) > and my > page now has a weird problem, not previously seen in earlier > versions of > Chime. > If you go to http://home.mira.net/~reynella/chime/adr_tuta.htm > > You will see I have a tutorial set up with three chime panels. The > first > and last panels display okay, just as they always did (I'm using > Communicator 4.77 running on Windows 2000 5.00.2195 service pack4) > The > middle panel displays "click here to get plug-in", needless to say > the > other panels are working so the plug-in must exist. When I view > the local > copy of the very same files on my hard disk (using the same > navigator/Windows combination, it works fine!!! Similarly, > http://home.mira.net/~reynella/chime/artemisinin.htm shows a > "click here to > get plugin" panel, while the local copy works just fine. > http://home.mira.net/~reynella/chime/ang_tuta.htm shows all panels > with no > problems. > > The only thing I can think of is that the offending panels display > mol > files, but MDL MOL files are explicitly stated as being handled, > and why do > local mol files display, but not those over the internet?? > > Any clues people? > Cheers! Ian > > =============================================================== > Ian F. Musgrave Ph.D, ian.musgrave@adelaide.edu.au > Senior Lecturer, Dept. Clinical and Experimental Pharmacology > University of Adelaide, SA, 5005, Australia > Phone +61 8 83033905 Fax +61 8 8224 0685 > > CRICOS Provider Number 00123M > > And now a word from our lawyers...... > ----------------------------------------------------------- > This email message is intended only for the addressee(s) and > contains > information that may be confidential and/or > copyright. If you are not the intended recipient please notify > the sender > by reply email and immediately delete > this email. Use, disclosure or reproduction of this email by > anyone other > than the intended recipient(s) is strictly > prohibited. No representation is made that this email or any > attachments > are free of viruses. Virus scanning is > recommended and is the responsibility of the recipient. > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Strange problem with pages using Chime 2.6 SP6 Date: Sun, 21 Mar 2004 20:36:26 -0500 To: rasmol@lists.umass.edu Ian Musgrave sent [10.27a gmt 2004 March 22 Monday] : >G'Day All > >I have just installed Chime 2.6 SP6, (updated from Chime 2.6 SP3) >and my page now has a weird problem, not previously seen in earlier >versions of Chime. If you go to >http://home.mira.net/~reynella/chime/adr_tuta.htm > >You will see I have a tutorial set up with three chime panels. The >first and last panels display okay, just as they always did (I'm >using Communicator 4.77 running on Windows 2000 5.00.2195 service >pack4) The middle panel displays "click here to get plug-in", >needless to say the other panels are working so the plug-in must >exist. When I view the local copy of the very same files on my hard >disk (using the same navigator/Windows combination, it works fine!!! >Similarly, http://home.mira.net/~reynella/chime/artemisinin.htm >shows a "click here to get plugin" panel, while the local copy works >just fine. http://home.mira.net/~reynella/chime/ang_tuta.htm shows >all panels with no problems. > >The only thing I can think of is that the offending panels display >mol files, but MDL MOL files are explicitly stated as being handled, >and why do local mol files display, but not those over the >internet?? > but is your server set up to serve mol files correctly, as Chime? that is the first thing that occurs to me... regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Ian Musgrave Subject: Re: Strange problem with pages using Chime 2.6 SP6 Date: Mon, 22 Mar 2004 10:57:08 +1030 To: rasmol@lists.umass.edu G'Day All At 06:06 PM 21/03/2004 -0600, you wrote: >Don't know if this is a Chime 2.6 SP6 problem. On your page, my machine w/ >NS 4.79, Chime 2.6 SP4, and Win2000 shows a blank middle panel where >presumably the Chime should be...no offer of a plugin source, either. Under Mozilla 1.6, with the IE plug-ins copied to the Mozilla plug-in directory (see http://dragon.unideb.hu/%7Egundat/Chimetest/mozilla.html but remember to copy ChimeShim.dll as well), I get a blank middle panel as well. But again, Mozzilla opens the local hard disk copy perfectly. Cheers! Ian =============================================================== Ian F. Musgrave Ph.D, ian.musgrave@adelaide.edu.au Senior Lecturer, Dept. Clinical and Experimental Pharmacology University of Adelaide, SA, 5005, Australia Phone +61 8 83033905 Fax +61 8 8224 0685 CRICOS Provider Number 00123M And now a word from our lawyers...... ----------------------------------------------------------- This email message is intended only for the addressee(s) and contains information that may be confidential and/or copyright. If you are not the intended recipient please notify the sender by reply email and immediately delete this email. Use, disclosure or reproduction of this email by anyone other than the intended recipient(s) is strictly prohibited. No representation is made that this email or any attachments are free of viruses. Virus scanning is recommended and is the responsibility of the recipient. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal X-Virus-Scanned: Yes References: <5.2.1.1.0.20040322095230.024a2a90@mail.staff.adelaide.edu.au> ++++------+------+------+------+------+------+------+------+------+------+ From: Duane Sears Subject: Re: Strange problem with pages using Chime 2.6 SP6 Date: Sun, 21 Mar 2004 18:49:03 -0800 To: rasmol@lists.umass.edu Cc: Ian Musgrave Ian, All three of your Chime windows appeared without a problem with Internet Explorer 6.028 running on either Windows XP or Windows 98. My suggestion is that you simply try reloading the web page in the browser with the refresh button. Cheers, Duane __________________________________ Duane W. Sears Department of Molecular, Cellular, and Developmental Biology University of California Santa Barbara, CA 93106-9610 Office (voice): 805-893-3499 Fax: 805-893-5081 Lab: 805-893-4272 ----- Original Message ----- Sent: Sunday, March 21, 2004 3:57 PM From: "Ian Musgrave" Subject: Strange problem with pages using Chime 2.6 SP6 To: > G'Day All > > I have just installed Chime 2.6 SP6, (updated from Chime 2.6 SP3) and my > page now has a weird problem, not previously seen in earlier versions of > Chime. > If you go to http://home.mira.net/~reynella/chime/adr_tuta.htm > > You will see I have a tutorial set up with three chime panels. The first > and last panels display okay, just as they always did (I'm using > Communicator 4.77 running on Windows 2000 5.00.2195 service pack4) The > middle panel displays "click here to get plug-in", needless to say the > other panels are working so the plug-in must exist. When I view the local > copy of the very same files on my hard disk (using the same > navigator/Windows combination, it works fine!!! Similarly, > http://home.mira.net/~reynella/chime/artemisinin.htm shows a "click here to > get plugin" panel, while the local copy works just fine. > http://home.mira.net/~reynella/chime/ang_tuta.htm shows all panels with no > problems. > > The only thing I can think of is that the offending panels display mol > files, but MDL MOL files are explicitly stated as being handled, and why do > local mol files display, but not those over the internet?? > > Any clues people? > Cheers! Ian > > =============================================================== > Ian F. Musgrave Ph.D, ian.musgrave@adelaide.edu.au > Senior Lecturer, Dept. Clinical and Experimental Pharmacology > University of Adelaide, SA, 5005, Australia > Phone +61 8 83033905 Fax +61 8 8224 0685 > > CRICOS Provider Number 00123M > > And now a word from our lawyers...... > ----------------------------------------------------------- > This email message is intended only for the addressee(s) and contains > information that may be confidential and/or > copyright. If you are not the intended recipient please notify the sender > by reply email and immediately delete > this email. Use, disclosure or reproduction of this email by anyone other > than the intended recipient(s) is strictly > prohibited. No representation is made that this email or any attachments > are free of viruses. Virus scanning is > recommended and is the responsibility of the recipient. > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-pair-Authenticated: 209.197.6.81 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: RasMol_2.7.2.1.1 testers needed Date: Sun, 21 Mar 2004 22:09:41 -0500 To: pdb-l@rcsb.org, rasmol@lists.umass.edu RasMol 2.7.2.1.1, the final production reference release of the RasMol 2.7.2 series is ready for release. This release will be the base upon which the 2.7.3 development series of releases will be built. The links for binaries have been changed to make it easier for us to release new binaries as they become available, but this reorganization increases the risk that we may have created dead links, or mismatched links against particular binaries. Testers are needed to test the web page at: http://www.bernstein-plus-sons.com/software/RasMol_2.7.2.1.1 to catch any dead links or bad binaries. Please report problems to rasmol@bernstein-plus-sons.com. If you create any binaries we don't have listed, please post them on a web page and send an email with the URL, so we can add them to the main page. Users should not see any visible external difference between running 2.7.2.1 and running 2.7.2.1.1 except for correction to the handling of RCSB PDB mmCIF extensions data sets. -- H. J. Bernstein -- ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <5.2.1.1.0.20040322095230.024a2a90@mail.staff.adelaide.edu.au> ++++------+------+------+------+------+------+------+------+------+------+ From: Ian Musgrave Subject: Re: Strange problem with pages using Chime 2.6 SP6 Date: Mon, 22 Mar 2004 14:43:12 +1030 To: rasmol@lists.umass.edu G'Day All At 06:49 PM 21/03/2004 -0800, Duane Sears wrote: >Ian, > >All three of your Chime windows appeared without a problem with Internet >Explorer 6.028 running on either Windows XP or Windows 98. My suggestion is >that you simply try reloading the web page in the browser with the refresh >button. No, that doesn't help at all. Timothy Driscoll suggested that my server may not be set up to serve mol files correctly, but the fact that you can see it suggests otherwise. Cheers! Ian =============================================================== Ian F. Musgrave Ph.D, ian.musgrave@adelaide.edu.au Senior Lecturer, Dept. Clinical and Experimental Pharmacology University of Adelaide, SA, 5005, Australia Phone +61 8 83033905 Fax +61 8 8224 0685 CRICOS Provider Number 00123M And now a word from our lawyers...... ----------------------------------------------------------- This email message is intended only for the addressee(s) and contains information that may be confidential and/or copyright. If you are not the intended recipient please notify the sender by reply email and immediately delete this email. Use, disclosure or reproduction of this email by anyone other than the intended recipient(s) is strictly prohibited. No representation is made that this email or any attachments are free of viruses. Virus scanning is recommended and is the responsibility of the recipient. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Strange problem with pages using Chime 2.6 SP6 Date: Mon, 22 Mar 2004 04:39:05 -0500 To: rasmol@lists.umass.edu Ian Musgrave sent [2.43p gmt 2004 March 22 Monday] : >G'Day All > >At 06:49 PM 21/03/2004 -0800, Duane Sears wrote: >>Ian, >> >>All three of your Chime windows appeared without a problem with >>Internet Explorer 6.028 running on either Windows XP or Windows 98. >> My suggestion is that you simply try reloading the web page in the >>browser with the refresh button. > >No, that doesn't help at all. Timothy Driscoll suggested that my >server may not be set up to serve mol files correctly, but the fact >that you can see it suggests otherwise. > >Cheers! Ian > hi Ian, I still suggest it is a server configuration problem. IE, as was noted on the Jmol list recently, uses the file extension to determine how to handle a file. Netscape, Mozilla, etc. use MIME type from the server. so if the server is not sending the correct MIME type, IE users don't care as long as their local Chime is configured correctly. I can see all three structures here on win2k IE6, but I can't see the mol file on Netscape 4 on the same machine, or my Mac. (all using Chime 2.6 SP3.) for attribution's sake, here is the relevant post from Phil Barak to the Jmol users list: PHILLIP W BARAK sent [10.55a gmt 2004 March 19 Friday] : >----- Original Message ----- >From: Philip Bays >Date: Friday, March 19, 2004 10:10 am >Subject: Re: [Jmol-users] Re: MIME types > >>This is not exactly what I meant. I have this vague memory >>(senility is setting in!) that when we first began using Chime many >>years ago, the campus IT staff had to do something on their end >>before the local machines would properly display structures, even >>though chime was installed on the local machine. Am I remembering >>correctly, and is there something we need to do in the present case? > >Not senility, just a bad dream! > >Indeed, servers delivering chemical formats to be interpreted by >Chime had to be set up on the servers to send a MIME type with it >(similar to pdf, wrl, doc, etc.) Without it, Netscape browsers would >not correctly interpret the contents as chem files (unless they were >local, which led to aggravating situations when things would display >correctly _locally_ but break when posted on a server.) > >As it happened, MS Internet Explorer broke all the MIME rules and >simply made decisions based on the file extension, ignoring any >associated MIME info from the server. So Chime contents would work >on IE in the absence of getting the techies involved. Not a bug, but >a feature? > >--Phillip Barak > regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <5.2.1.1.0.20040322144120.02c22b70@mail.staff.adelaide.edu.au> ++++------+------+------+------+------+------+------+------+------+------+ From: Ian Musgrave Subject: Re: Strange problem with pages using Chime 2.6 SP6 Date: Tue, 23 Mar 2004 15:58:06 +1030 To: rasmol@lists.umass.edu, timothy driscoll G'Day ALl At 04:39 AM 22/03/2004 -0500, timothy driscoll wrote: >Ian Musgrave sent [2.43p gmt 2004 March 22 Monday] : > >At 06:49 PM 21/03/2004 -0800, Duane Sears wrote: > >>Ian, > >> > >>All three of your Chime windows appeared without a problem with > >>Internet Explorer 6.028 running on either Windows XP or Windows 98. > >> My suggestion is that you simply try reloading the web page in the > >>browser with the refresh button. > > > >No, that doesn't help at all. Timothy Driscoll suggested that my > >server may not be set up to serve mol files correctly, but the fact > >that you can see it suggests otherwise. > > > >Cheers! Ian > > > >hi Ian, > >I still suggest it is a server configuration problem. IE, as was noted >on the Jmol list recently, uses the file extension to determine how to >handle a file. Netscape, Mozilla, etc. use MIME type from the server. >so if the server is not sending the correct MIME type, IE users don't >care as long as their local Chime is configured correctly. Okay, I see what you mean. So what do I tell my IT people to do to get the server configured correctly? Cheers! Ian =============================================================== Ian F. Musgrave Ph.D, ian.musgrave@adelaide.edu.au Senior Lecturer, Dept. Clinical and Experimental Pharmacology University of Adelaide, SA, 5005, Australia Phone +61 8 83033905 Fax +61 8 8224 0685 CRICOS Provider Number 00123M And now a word from our lawyers...... ----------------------------------------------------------- This email message is intended only for the addressee(s) and contains information that may be confidential and/or copyright. If you are not the intended recipient please notify the sender by reply email and immediately delete this email. Use, disclosure or reproduction of this email by anyone other than the intended recipient(s) is strictly prohibited. No representation is made that this email or any attachments are free of viruses. Virus scanning is recommended and is the responsibility of the recipient. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Strange problem with pages using Chime 2.6 SP6 Date: Tue, 23 Mar 2004 03:51:00 -0500 To: rasmol@lists.umass.edu Ian Musgrave sent [3.58p gmt 2004 March 23 Tuesday] : >G'Day ALl > >At 04:39 AM 22/03/2004 -0500, timothy driscoll wrote: >>Ian Musgrave sent [2.43p gmt 2004 March 22 Monday] : >>> >>>No, that doesn't help at all. Timothy Driscoll suggested that my >>>server may not be set up to serve mol files correctly, but the >>>fact that you can see it suggests otherwise. >>> >>>Cheers! Ian >>> >>hi Ian, >> >>I still suggest it is a server configuration problem. IE, as was >>noted on the Jmol list recently, uses the file extension to >>determine how to handle a file. Netscape, Mozilla, etc. use MIME >>type from the server. so if the server is not sending the correct >>MIME type, IE users don't care as long as their local Chime is >>configured correctly. > >Okay, I see what you mean. So what do I tell my IT people to do to >get the server configured correctly? > add the appropriate MIME type association to their tables. you can get a pdf of them here: for mol files, the server needs to associate the MIME type chemical/x-mdl-molfile with mol files. hope that helps, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- A M C Ekwue , a.delago@qmul.ac.uk, a.j.robinson@qmul.ac.uk, a.kumar@qmul.ac.uk, a.shahneh@qmul.ac.uk, ah9156@qmul.ac.uk, akykhan2001@yahoo.com, alcollinson@hotmail.com, ALKHRISHA@hotmail.com, Aman Bembey , amassey12@hotmail.com, amc@accelrys.com, Andrew Chan , angela_zheung@hotmail.com, anildutt28@hotmail.com, annie@wanguk.com, arc , atitlikerabbits@yahoo.co.uk, b.ashcroft@qmul.ac.uk, b.murphy@qmul.ac.uk, "Bai, Zhonghu" , bealgordon@hotmail.com, Benny Kong , benny_dino@hotmail.com, Bing Liu , Bi-Qiong , gx101@soton.ac.uk, bluesky122299@yahoo.com, "'C. Wu'" , c.y.ku@qmul.ac.uk, c.y.kuan@qmul.ac.uk, cathy_uk_eh@yahoo.co.uk, catiecao1977@yahoo.co.uk, ccchen , ceylan_m@hotmail.com, Chai Chin Stevens , charlottehird1@hotmail.com, chencontact@yahoo.co.uk, chun.zhang@btinternet.com, clearwatergoldmine@hotmail.com, clnvm410@hotmail.com, collen889x@yahoo.com.cn, CSSA QMUL , CSSA Queen Mary , Cumberbatch , d.hu@qmul.ac.uk, dane87@hotmail.com, darrenchin@hotmail.com, davidchang01uk@yahoo.com.cn, dd ff , donaldzh , Dr G Ren , "Dr. Jochen Zuegge" , dreams013@yahoo.co.uk, eddykeen23@hotmail.com, emilaonyema@yahoo.com, evangelosmelas@yahoo.co.uk, ex6110@qmul.ac.uk, ez02157@qmul.ac.uk, ez03024@qmul.ac.uk, ez03170@qmul.ac.uk, f.c.gomes-de-sousa@qmul.ac.uk, Fan.Huajun@epamail.epa.gov, fangyen wong , fangyufeng@hotmail.com, Fi , Francesc , frankwang0086@yahoo.com, g.clackett@qmul.ac.uk, g.s.serebe@qmul.ac.uk, g.willats@qmul.ac.uk, gbdevereese@hotmail.com, geeking@263.net, george wong , Gerardo , Wei-Na Yang , Caroline , Coxia , Jerry , John , Jonny , Lucy , Ming , Mutin , Philippe Pouliot , Raj , Rong , Tim , Tom , Ven , Xiao , Yan , Yang , Yun , Zhu-Sheng , GS W , guiukbt , Guo Huang , h.hay@lse.ac.uk, h.l.hsu@qmul.ac.uk, h.m.t.u.herath@qmul.ac.uk, Haixue Yan , he xia , hf_chris@hotmail.com, oksunnyman@hotmail.com, Hilary Eboji , hon_steven@hotmail.com, hotmale_mev@hotmail.com, Huaitao Zhang , hugh , hugh fain , I.I.leonidov@qmul.ac.uk, i.papadopoulos@qmul.ac.uk, isgrieve@hotmail.com, Iskhander , J Gad , J Jalili , J.arhin@qmul.ac.uk, j.Grabowski@qmul.ac.uk, Jan Labanowski , Jason Sun , jayjaybond@hotmail.com, jeff3tse@yahoo.com, Jen , Jen Tung , Jianhui Xia at QMUL , Jie Fang , Jim Phillips , Jin Gu , Jingbo , Jo , jontylerrocks@hotmail.com, Joseph_Xie , jtwelsch@hotmail.com, k.berketis@qmul.ac.uk, k.gong@qmul.ac.uk, k.khamoushi@qmul.ac.uk, kelly_xin_sh , kenyccw@hotmail.com, Kish , kongqw@dcs.kcl.ac.uk, krishna6996@hotmail.com, kyungjin yun , l.yang@qmul.ac.uk, lawrence.leung@btinternet.com, Letting Agency , Li JIN , Li Ming , Liisa Holm , Litao Fu , lujiang_l@yahoo.co.uk, lukexu78@hotmail.com, M.L.Hartley@qmul.ac.uk, M.L.Hickson@qmul.ac.uk, m.m.mohebi@qmul.ac.uk, m.o.gad@qmul.ac.uk, mabaena30@hotmail.com, maggs_g_v@hotmail.com, mark@macbeet.fsnet.co.uk, markysparky44@hotmail.com, martin , mehr_unnisa@hotmail.com, melinda_nofear@yahoo.co.uk, Miao He , miaoxin_uk@yahoo.com, Min Zhao , mss1@cec.wustl.edu, Na Yao , just for you , Just Me , Michel Neo , "Braces wanted!!! :$" , Alfred Lee , confirm-s2-NGBEHJfNVNP=M8lei=fenUNz8U8-r.li=qmul.ac.uk@yahoogroups.com, L Liu , Rong , Rong Ding , ngvicki@hotmail.com, O Afejuku , o.d.verclos@qmul.ac.uk, o.opaleye@qmul.ac.uk, Ding rong , "Prof. Lu" , "Prof. Wang" , Roderic_yj@163.com, "D. 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Zhang" , y.chen@qmul.ac.uk, yangshijian168@hotmail.com, Yu , Yu Wang , yu zeng , yue.chen@elec.qmul.ac.uk, yzzj1@hotmail.com, z.guo@qmul.ac.uk, z.y.li@qmul.ac.uk, zhanglei0421@hotmail.com, Zhen Qin , zhenyun Shi , ZhiDong Zhang , Zhigang Kong , zhiping zeng , zhoubellling@hotmail.com, zhubao74@hotmail.com, =?utf-8?B?56WlIOWFiSDpg5E=?= X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 boundary="Boundary_(ID_qVKBWAagnRfn2coUHzhOCg)" X-MSMail-priority: Normal X-Sender-Host-Address: 138.37.43.64 X-QM-Scan-Virus: virusscan says the message is clean X-QM-Scan-Virus: ClamAV says the message is clean ++++------+------+------+------+------+------+------+------+------+------+ From: Ru-Zhen Li Subject: ShARE Date: Tue, 23 Mar 2004 14:52:49 +0000 To: ? ? , ? ? , This is a multi-part message in MIME format. --Boundary_(ID_qVKBWAagnRfn2coUHzhOCg) My dear friend, Because of some contact between us before, I got your email address, if you are NOT currently a student in college/university or a newly graduate, please ignore this email and sorry for this. If you are either a brilliant student or a newly graduate, and if you fancy economies but you cannot find a place to present your idea, or if you are interested in economies but don't know where to start, or if you are learning economies and you want to share your ideas with other people to get improvement more quickly, I am greatly honored to introduce ShARE http://www.share-economy.org, a place for young, brilliant people to give, to get and to inspire ideas about reginal economies. it is founded by students, maintained by students and developed by students. we are sponsored by a pioneer in innovation consulting : Altran http://www.altran.net/en/ the idea is simple: research, share, debate we now have branches in many hot places: Shanghai, Taipei, Tokyo, Singapore, Paris, Hongkong in 1.5 years! and now, we have come to London! come on and join us! meet brilliant people, share bring ideas and get yourself more brilliant! to get more details, just email me : Ru-Zhen Li (r.li@qmul.ac.uk) Thank you very much for your time and sorry if this email disturbe you. Best Regards, Ru-Zhen ********************************************************************** Ms Ru-Zhen Li 0044-020-78826327 r.li@qmul.ac.uk http://www.freewebs.com/lrz/ Materials Department Queen Mary University of London E1 4NS ********************************************************************** --Boundary_(ID_qVKBWAagnRfn2coUHzhOCg) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_qVKBWAagnRfn2coUHzhOCg)-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal X-Sender-Host-Address: 138.37.43.64 X-QM-Scan-Virus: virusscan says the message is clean X-QM-Scan-Virus: ClamAV says the message is clean ++++------+------+------+------+------+------+------+------+------+------+ From: Ru-Zhen Li Subject: wrong email ===> ShARE Date: Tue, 23 Mar 2004 22:11:35 +0000 To: rasmol@lists.umass.edu My dear friend, The last email about ShARE has been sent mistakenly by my friend, if you are my Prof, my superior, my professional collaborator, my non-personal friend or live outside London or anyone who shouldn't have received that email, I am extremely sorry for the mistake. if you are my personal friend, and if you are interested, please contact LingXia at lingxia_zhao@hotmail.com instead of myself. Best regards, Ru-Zhen ********************************************************************** Ms Ru-Zhen Li 0044-020-78826327 r.li@qmul.ac.uk http://www.freewebs.com/lrz/ Materials Department Queen Mary University of London E1 4NS ********************************************************************** ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MSMail-Priority: High boundary=".BCC.F79DA_5A.D0EA8_8." ++++------+------+------+------+------+------+------+------+------+------+ From: "Admin" Subject: ADV: Attention All School Staff, Teachers and Students: Date: Tue, 30 Mar 04 01:17:13 GMT To: nnor@bio.umass.edu This is a multi-part message in MIME format. --.BCC.F79DA_5A.D0EA8_8. Attention All School Staff, Teachers and Students: You Must Respond By 5 P.M. Tuesday, March 30, 2004. Through a special arrangement, Avtech Direct is offering a limited allotment of BRAND NEW, top of-the-line, name-brand desktop computers at more than 50% off MSRP to all Staff Members, Teachers and Students who respond to this message before 5 P.M., Tuesday, March 30, 2004. All desktop computers are brand-new packed in their original boxes, and come with a full manufacturer's warranty plus a 100% satisfaction guarantee. These professional grade Desktops are fully equipped with 2004 next generation technology, making these the best performing computers money can buy. Avtech Direct is offering these feature rich, top performing Desktop Computers with the latest Intel technology at an amazing price to all who call: 1-800-884-9510 by 5 P.M. Tuesday, March 30, 2004 The fast and powerful AT-2400 series Desktop features: * Intel 2.0Ghz Processor for amazing speed and performance * 128MB DDR RAM, --- Upgradeable to 1024 * 20 GB UDMA Hard Drive, --- Upgradeable to 80 GB * 52X CD-Rom Drive, --- Upgradeable to DVD/CDRW * 1.44 Floppy disk drive * Next Generation Technology * ATI Premium video and sound * Full Connectivity with Fax modem/Lan/IEE 1394/USB 2.0 * Soft Touch Keyboard and scroll mouse * Internet Ready * Network Ready * 1 Year parts and labor warranty * Priority customer service and tech support MSRP $699 ........................................ Your Cost $297 How to qualify: 1. You must be a Staff member, Teacher or Student: 2. All desktop computers will be available on a first come first serve basis. 3. You must call 1-800-884-9510 by 5 P.M. Tuesday, March 30, 2004 and we will hold the desktops you request on will call. 4. You are not obligated in any way. 5. 100% Satisfaction Guaranteed. Call Avtech Direct 1-800-884-9510 before 5 P.M. Tuesday, March 30, 2004 If you wish to unsubscribe from this list, please go to: http://www.computeradvice.org/unsubscribe.asp --.BCC.F79DA_5A.D0EA8_8.-- ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: PE in Mac Classic Date: Wed, 31 Mar 2004 15:31:22 -0500 To: rasmol@lists.umass.edu Hi All, Is anyone using Protein Explorer in the Mac Classic environment? Or have you tried and given up? We'd like to get some feedback on whether PE is working well in Classic (it is not, for us). Please reply off-list to friedar@nsm.umass.edu. Thanks! Frieda (on behalf of the PE Team) Frieda Reichsman, PhD Educational Multimedia Specialist Molecules in Motion Interactive Molecular Structures http://www.MoleculesInMotion.com 94 Pratt Corner Road Shutesbury, MA 01072 413-253-2405 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <5FCF50EE-8352-11D8-B430-000A95774552@nsm.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Margulies, David (NIAID/NIH)" Subject: Re: PE in Mac Classic Date: Wed, 31 Mar 2004 16:59:10 -0500 To: rasmol@lists.umass.edu Yes, Using communicator 4.7 in classic on a G5 running os X (10.3.3) I have proteinexplorer (at least the web version, notthe local install) running fine. I believe I also have it running on a Powerbook G4. Had to do the usual chime install, but that went pretty well lately. D On Mar 31, 2004, at 3:31 PM, Frieda Reichsman wrote: > Hi All, > > Is anyone using Protein Explorer in the Mac Classic environment? Or > have you tried and given up? We'd like to get some feedback on whether > PE is working well in Classic (it is not, for us). Please reply > off-list to friedar@nsm.umass.edu. > Thanks! > > Frieda > (on behalf of the PE Team) > > > > Frieda Reichsman, PhD > Educational Multimedia Specialist > > Molecules in Motion > Interactive Molecular Structures > http://www.MoleculesInMotion.com > > 94 Pratt Corner Road > Shutesbury, MA 01072 > 413-253-2405 > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Schremmer, Bruno (NIH/NHLBI)" Subject: RE: PE in Mac Classic Date: Wed, 31 Mar 2004 17:04:11 -0500 To: "'rasmol@lists.umass.edu'" Yes thank you for the distinction, I must have given up installing it on my Mac. If you have an answer please forward it to me. Bruno Schremmer > ---------- > From: Margulies, David (NIH/NIAID) > Reply To: rasmol@lists.umass.edu > Sent: Wednesday, March 31, 2004 4:59 PM > To: rasmol@lists.umass.edu > Subject: Re: PE in Mac Classic > > Yes, Using communicator 4.7 in classic on a G5 running os X (10.3.3) I > have proteinexplorer (at least the web version, notthe local install) > running fine. > > I believe I also have it running on a Powerbook G4. Had to do the > usual chime install, but that went pretty well lately. > > > D > > On Mar 31, 2004, at 3:31 PM, Frieda Reichsman wrote: > > > Hi All, > > > > Is anyone using Protein Explorer in the Mac Classic environment? Or > > have you tried and given up? We'd like to get some feedback on whether > > PE is working well in Classic (it is not, for us). Please reply > > off-list to friedar@nsm.umass.edu. > > Thanks! > > > > Frieda > > (on behalf of the PE Team) > > > > > > > > Frieda Reichsman, PhD > > Educational Multimedia Specialist > > > > Molecules in Motion > > Interactive Molecular Structures > > http://www.MoleculesInMotion.com > > > > 94 Pratt Corner Road > > Shutesbury, MA 01072 > > 413-253-2405 > > > > ---------------------------------------------------------------- > > rasmol-+ > > > > To change your address, unsubscribe, view previous messages/history, > > receive messages as weekly digests, or for any other information > > about the RasMol EMail List, please go to > > http://www.umass.edu/microbio/rasmol/raslist.htm > > > > ---------------------------------------------------------------- > > rasmol-- > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <5FCF50EE-8352-11D8-B430-000A95774552@nsm.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Christopher Masi Subject: Re: PE in Mac Classic Date: Wed, 31 Mar 2004 22:23:05 -0500 To: rasmol@lists.umass.edu Cc: friedar@nsm.umass.edu Protein Explorer works here. I have a local install of PE running in OS X 10.3.3's Classic environment on a PB G3. Honestly, I don't use it much, but it launches and loads molecules. The buttons that I have tried also work. Chris On Mar 31, 2004, at 3:31 PM, Frieda Reichsman wrote: > Hi All, > > Is anyone using Protein Explorer in the Mac Classic environment? Or > have you tried and given up? We'd like to get some feedback on whether > PE is working well in Classic (it is not, for us). Please reply > off-list to friedar@nsm.umass.edu. > Thanks! > > Frieda > (on behalf of the PE Team) > > > > Frieda Reichsman, PhD > Educational Multimedia Specialist > > Molecules in Motion > Interactive Molecular Structures > http://www.MoleculesInMotion.com > > 94 Pratt Corner Road > Shutesbury, MA 01072 > 413-253-2405 > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer main site down/use UMass site Date: Thu, 01 Apr 2004 12:38:19 -0500 To: rasmol@lists.umass.edu Unexpectedly the main Protein Explorer server URL has stopped working (proteinexplorer.org which goes to http://molvis.sdsc.edu/protexpl). This also affects my DNA tutorial and molvisindex.org. I have notified the staff at SDSC. This probably happened yesterday or earlier. Until this is fixed, please use the UMass copies which are working fine. These UMass links are and have been accessible at http://www.umass.edu/microbio/chime/ namely Protein Explorer 1.982 at http://www.umass.edu/microbio/chime/explorer/frntdoor.htm and DNA at http://www.umass.edu/microbio/chime/dna If any one desperately needs PE 2.1 Alpha, I can set that up at UMass also -- currently it is only served from SDSC. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: ProteinExplorer.Org redirected Date: Thu, 01 Apr 2004 12:47:05 -0500 To: rasmol@lists.umass.edu Because of the problem at http://molvis.sdsc.edu, I have temporarily changed the domain proteinexplorer.org to go to the working UMass site. Note that to use the UMass site, you must click on the smaller print UMass "fallback" link at the bottom of the first page. The domain change can take up to 24 hours to propagate worldwide. I'll change it back to SDSC once their server is fixed. This temporary change restores service only to Protein Explorer 1.982. PE 2.1 Alpha and molvisindex.org will be out of service temporarily. However, PE 2.1 Alpha can be downloaded from UMass at http://www.umass.edu/microbio/distrib/pe_alpha.htm -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: ProteinExplorer.Org redirected Date: Thu, 01 Apr 2004 12:58:39 -0500 To: rasmol@lists.umass.edu Eric Martz sent [12.47p gmt 2004 April 01 Thursday] : >Because of the problem at http://molvis.sdsc.edu, I have temporarily >changed the domain proteinexplorer.org to go to the working UMass >site. > >Note that to use the UMass site, you must click on the smaller print >UMass "fallback" link at the bottom of the first page. > >The domain change can take up to 24 hours to propagate worldwide. >I'll change it back to SDSC once their server is fixed. > >This temporary change restores service only to Protein Explorer >1.982. PE 2.1 Alpha and molvisindex.org will be out of service >temporarily. However, PE 2.1 Alpha can be downloaded from UMass at >http://www.umass.edu/microbio/distrib/pe_alpha.htm > and if you are really desperate, PE 2.1 alpha is available at this url as well: regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-description: Mail message body X-ELTE-SpamVersion: MailScanner 4.26.8-itk2 (ELTE 1.1) SpamAssassin 2.63 ClamAV 0.65 X-ELTE-VirusStatus: clean X-ELTE-SpamCheck: no X-ELTE-SpamCheck-Details: score=-4.74, required 5.9, BAYES_00 -4.90, NO_REAL_NAME 0.16 X-ELTE-SpamLevel: X-ELTE-SpamScore: -4 X-MIME-Autoconverted: from Quoted-printable to 8bit by marlin.bio.umass.edu id i37B2eM00511 ++++------+------+------+------+------+------+------+------+------+------+ From: nyitray@cerberus.elte.hu Subject: 3D contest and 3D literacy Date: Wed, 07 Apr 2004 13:03:11 +0200 To: rasmol@lists.umass.edu Dear Colleagues, The 2005 FEBS-IUBMB Congress will be organized in Budapest, Hungary (see at http://www.febs-iubmb-2005.com/). The main topics of the Congress will be the Protein World. As a part of the Science is Fun program the organizers want to have a 3D modeling contest on July 4th 2005 between 13:30 and 16:30 in the Internet center of the Congress. We would be thankful for any ideas on this (e.g. what kind of tasks might be given for this relatively short time; what 3D tools could be used from the Internet to accomplish the task; what were the evaluation criteria). Authors of good ideas will be acknowledged in all Congress documents. The person who will submit the best proposal and who is willing to assemble the contest will be invitied to the Congress. We are also planning to organizing a Science Education Symposium focusing on "3D literacy" in biochemical education. I would also appreciate any suggestions or proposals for speakers (we want maximum four). If anyone of the Rasmolian community is interested to attend our Conference at Budapest, you are most welcome in our beautiful city! (fill out the online registration form on the conference web page). Our motto is "Science is Fun: a Conference for your Creativity" Please, send replies directly to Laszlo Nyitray at nyitray@cerberus.elte.hu by May 31st 2004 the latest. p.s. Please, let me know if you are aware of any other e-mail list server/newsgroup related to the above topics to where I can send my inquiry letter.*********************************** Laszlo Nyitray, PhD Associate Professor Dept.Biochemistry, Eotvos University Budapest, Pázmány P. sétány 1/C H-1117 Hungary tel:361-381-2171 fax:361-381-2172 e-mail:nyitray@cerberus.elte.hu xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer 2.2 Alpha Released Date: Wed, 21 Apr 2004 22:16:04 -0400 To: rasmol@lists.umass.edu Protein Explorer 2.2 Alpha was released April 19. It supercedes PE 2.1 Alpha (released July 2003). PE 1.982 Beta is still available at proteinexplorer.org -- click the red and magenta link near the top of PE 1.982 Beta's FrontDoor to get to PE 2.2 Alpha. Changes in PE 2.2 Alpha include: 1. Better control of the window size when PE opens a new session (because resizing the window after you see the molecule causes problems). See the bottom of the middle gray box on the FrontDoor for the new window size controls and help. 2. Addition of subheadings and clarified wording on the "Features of the Molecule" page (thanks to Frieda Reichsman for suggesting most of these changes). "Features of the molecule" should now work on the Macintosh (unlike in PE 2.1 -- thanks to Diana Ditmore for work on the Macintosh fix). 3. Addition of several "slides" on Global Protein Structure Issues, such as "What percentage of the proteins of the human genome have known structure?", the structural genomics initiative, and success rates in protein crystallography. See also the new section entitled "About Protein Structure" on the FrontDoor (bottom of right-hand gray box). 4. Troubleshooting, the Help/Index/Glossary (including rules of thumb for interpreting R value and Free R among many other additions), Future Plans and some other documents were updated. A bug in PE 2.2 Alpha that prevented it from starting in Internet Explorer was fixed this morning (April 21) for the on-line version -- this bug remains in the downloadable version, which may require that you use Netscape 4.8. I plan to update the downloadable version in a week or so. PE Alpha can be downloaded from the Download link on the *2.2 Alpha* FrontDoor. Within a week or so we will provide a separate downloadable .sit file for Macintoshes, which will avoid problems the older downloads have on OSX. Mac users should be sure to upgrade to Chime 2.6 SP3, and Windows users to Chime 2.6 SP6. Step by step instructions for navigating MDL's Chime download site were recently provided: http://www.umass.edu/microbio/chime/getchime.htm More details about the changes are available by clicking on the large red version number at the top of the FrontDoor, or by going directly to http://molvis.sdsc.edu/pe_alpha/protexpl/vers_pe.htm#versionhistory Please let me know about any problems. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Rasmol startup data... Date: Thu, 22 Apr 2004 09:36:30 +0100 (BST) To: Rasmol Mailing List Hi, When I start rasmol on a structure directly I get some nice summary data, for example... Molecule name ......... SULFATE ADENYLYLTRANSFERASE; Classification ........ TRANSFERASE Secondary Structure ... No Assignment Experiment Technique .. Y DIFFRACTION - SINGLE CRYSTAL Number of Chains ...... 10 Number of Groups ...... 3060 (1877) Number of Atoms ....... 24450 (2210) Number of Bonds ....... 25386 However, when I start rasmol using a script (I am using the "load inline ... exit pdb-file" syntax) I don't get the above output - it is suppressed. Is there a rasmol command line function which I can call in my script to get rasmol to output the above kind of summary data? Cheers, Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7b) Gecko/20040421 X-Accept-Language: de, en-us, en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: Rasmol startup data... Date: Thu, 22 Apr 2004 10:34:29 +0200 To: rasmol@lists.umass.edu Dan Bolser wrote: >Hi, > >When I start rasmol on a structure directly I get some nice summary data, >for example... >... >Is there a rasmol command line function which I can call in my script to >get rasmol to output the above kind of summary data? > > show info will do this, Regards, Jan ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: Rasmol startup data... Date: Thu, 22 Apr 2004 11:42:09 +0100 (BST) To: rasmol@lists.umass.edu On Thu, 22 Apr 2004, Jan Reichert wrote: > Dan Bolser wrote: > > >Hi, > > > >When I start rasmol on a structure directly I get some nice summary data, > >for example... > >... > >Is there a rasmol command line function which I can call in my script to > >get rasmol to output the above kind of summary data? > > > > > show info > > will do this, > Regards, Jan *) Thanks! > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Errors-to: jefffinnan@aol.com ++++------+------+------+------+------+------+------+------+------+------+ From: jefffinnan@aol.com Subject: jefffinnan's AOL Address Card Date: Thu, 29 Apr 2004 12:15:57 -0400 (EDT) To: rasmol@lists.umass.edu --Boundary_(ID_yG4k+C8WFPaDiIUPBQXdfQ) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_yG4k+C8WFPaDiIUPBQXdfQ)-- boundary="Boundary_(ID_SZldC716m2A9UTQEpJbIiw)" ++++------+------+------+------+------+------+------+------+------+------+ From: JeffFinnan@aol.com Subject: Conversion of MDL molfiles to PDB files Date: Thu, 29 Apr 2004 12:20:47 -0400 (EDT) To: rasmol@lists.umass.edu --Boundary_(ID_SZldC716m2A9UTQEpJbIiw) My interests lie in small molecules. I like the detail in molfiles such as multiple bonds. However, sometimes I would like the same detail in a PDB file. I have used BABEL and ArgusLab to convert molfiles to PBD files. However, bond detail is lost. I have come across PDB files that do show bond detail on the Web. I was wondering if there was something out there that could do my desired conversion. Thanks, Jeff --Boundary_(ID_SZldC716m2A9UTQEpJbIiw) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_SZldC716m2A9UTQEpJbIiw)-- X-MSMail-Priority: High boundary="72.BA6A.86_F" ++++------+------+------+------+------+------+------+------+------+------+ From: "Admin" Subject: ADV: Attention All School Staff: Teachers, Students and Faculty Members: Date: Mon, 03 May 04 13:59:58 GMT To: oreilly@bio.umass.edu This is a multi-part message in MIME format. --72.BA6A.86_F Attention All School Staff: Teachers, Students and Faculty Members: You Must Respond By 5 P.M. Tuesday, May 4, 2004. Through a special arrangement, Avtech Direct is offering a limited allotment of BRAND NEW, top of-the-line, name-brand desktop computers at more than 50% off MSRP to all Teachers, Students,Faculty and Staff, who respond to this message before 5 P.M., Tuesday, May 4, 2004. All desktop are brand-new, packed in their original boxes, and come with a full manufacturer's warranty plus a 100% satisfaction guarantee. These professional grade Desktops are fully equipped with 2004 next generation technology, making these the best performing computers money can buy. Avtech Direct is offering these feature rich, top performing Desktop Computers with the latest Intel technology at an amazing price to all who call: 1-800-884-9510 by 5 P.M. Tuesday, May 4, 2004 The fast and powerful AT-2400 series Desktop features: * Intel 2.0Ghz Processor for amazing speed and performance * 128MB DDR RAM, --- Upgradeable to 1024 * 20 GB UDMA Hard Drive, --- Upgradeable to 80 GB * 52X CD-Rom Drive, --- Upgradeable to DVD/CDRW * 1.44 Floppy disk drive * Next Generation Technology * ATI Premium video and sound * Full Connectivity with Fax modem/Lan/IEE 1394/USB 2.0 * Soft Touch Keyboard and scroll mouse * Internet Ready * Network Ready * 1 Year parts and labor warranty * Priority customer service and tech support MSRP $699 ........................................ Your Cost $297 How to qualify: 1. You must be a Teacher, Student, Faculty or Staff Member: 2. All desktop computers will be available on a first come first serve basis. 3. You must call 1-800-884-9510 by 5 P.M. Tuesday, May 4, 2004 and we will hold the desktops you request on will call. 4. You are not obligated in any way. 5. 100% Satisfaction Guaranteed. Call Avtech Direct 1-800-884-9510 before 5 P.M. Tuesday, May 4, 2004 If you wish to unsubscribe from this list, please go to: http://www.computeradvice.org/unsubscribe.asp --72.BA6A.86_F-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 boundary="Boundary_(ID_uGOijFPwkqR9tjbSSanVsQ)" X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Ilan Samish Subject: 3Dsig: Structural Bioinformatics Meeting. Last announcement + update Date: Thu, 06 May 2004 15:08:27 +0200 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_uGOijFPwkqR9tjbSSanVsQ) ***************************************************** STRUCTURAL BIOINFORMATICS (3D SIG) ***************************************************** 29-30 July 2004, Glasgow, UK (immediately preceding ISMB/ECCB 2004) ABSTRACTS ARE ACCEPTED TILL MAY 24th !! http://3dsig.weizmann.ac.il/ -------------------------------------------------------------------------- TOPICS WILL INCLUDE: *3D data-mining, *3D programming modules, *Docking & protein-protein/ligand interaction prediction, *Membrane protein assembly prediction, *Secondary structure & domain assignment, *Structure-based function prediction, * Structural databases, *Structural genomics, *Structure prediction, * Structure representation, *Geometry & energetics in protein structure & function ---------------------------------------------------------------------------- * 2-day innovative, stimulating meeting Dinner and evening session included * 8 talks by invited speakers, 20 chosen from abstracts The program committee is looking for fresh, effective voices, and fresh, potentially high impact, ideas and results Confirmed speakers and round table discussants include: Phil Bourne, Cyrus Chothia, John Moult, Rob Russel, Luis Serrano, Michael Sternberg, Ron Unger, Gunnar von Heijne * Novel LAPTOP Poster Session: All abstracts presented on laptops rather than by traditional posters This is an experiment in communication aimed at more intensive interactions between presenters and participants. ABSTRACTS ARE ACCEPTED TILL MAY 24th !! AUTHOR LIST is available online: http://3dsig.weizmann.ac.il/3dsig/2004/listallauthors.html Full abstracts and detailed program will be available during June. * Sponsorship opportunities are still available. See website for sponsorship possibilities. _______________________________ SCIENTIFIC COMMITTEE: John Moult (Chair) - CARB, USA; Phil Bourne - UCSD, USA; Luis Serrano - EMBL, Germany; Michael Sternberg - Imperial College, UK; Ron Unger - BIU, Israel; HONORARY: David Gilbert - U. Glasgow, UK; Janet Thornton - EBI, UK ORGANIZING COMMITTEE: Ilan Samish & Marvin Edelman - WIS, Israel _______________________________ ! REGISTER NOW ! http://3dsig.weizmann.ac.il/ For questions/comments: 3dsig@weizmann.ac.il Sponsors: ROCHE, ISCB, WIS, NE Bioinfo Inst --Boundary_(ID_uGOijFPwkqR9tjbSSanVsQ) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_uGOijFPwkqR9tjbSSanVsQ)-- update Content-disposition: inline User-Agent: Mutt/1.4i References: <01e701c4336b$389fcad0$e3504d84@IBM66> ++++------+------+------+------+------+------+------+------+------+------+ From: Eugen Leitl Subject: Re: 3Dsig: Structural Bioinformatics Meeting. Last announcement + Date: Thu, 06 May 2004 14:36:34 +0200 To: rasmol@lists.umass.edu On Thu, May 06, 2004 at 03:08:27PM +0200, Ilan Samish wrote: > * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * > * ---REMAINDER OF MESSAGE TRUNCATED--- * > * This post contains a forbidden message format * > * (such as an attached file, a v-card, HTML formatting) * > * This mailing list only accepts PLAIN TEXT messages * > * If your postings display this message your mail program * > * is not set to send PLAIN TEXT ONLY and needs adjusting * > * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Please don't send HTML-only email to public mailing lists. -- Eugen* Leitl leitl ______________________________________________________________ ICBM: 48.07078, 11.61144 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE http://moleculardevices.org http://nanomachines.net ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-pair-Authenticated: 209.197.6.81 References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: RasMol_2.7.2.1.1 windows binary updated Date: Fri, 07 May 2004 17:12:25 -0400 To: pdb-l@rcsb.org, rasmol@lists.umass.edu Thanks to a trouble report by Julien Hering, an error in the build of the windows version of RasMol 2.7.2.1.1 was found and corrected. Those who downloaded an MS Windows 2.7.2.1.1 binary prior to 7 May 2004 from http://www.bernstein-plus-sons.com/software/RasMol_2.7.2.1.1/ may wish to download the updated binary. The errors was in use of an outdated source of mswin31.c, that failed to do two initializations, causing the screen to blank in some cases. The source and tar have been replaced in the release kit. The patch for mswin31.c is available at http://www.OpenRasMol.org/RasMol_2.7.3_pending/mswin31.c.patch There is no impact on the unix or mac versions. -- H. J. Bernstein -- ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer 2.3 Alpha Released Date: Sat, 08 May 2004 13:09:40 -0400 To: rasmol@lists.umass.edu Yesterday, I released Protein Explorer 2.3 Alpha. It is downloadable (really!) in a zipped .exe file for windows, or in a stuffed .sit file for Macs (with file types and creators that will enable easy use on OSX/Classic). This release improves checking for browser and Chime version compatibility. It rejects Safari and Opera with appropriate help messages. (Compatible browsers are listed at http://molvis.sdsc.edu/pe_alpha/protexpl/needbrow.htm?nosorry ) It also tests for "popup window swatters" and explains how to enable PE to work if you are using one. This version of PE requires MDL Chime 2.6 SP4 (Mac: 2.6 SP3). (For Windows, Chime 2.6 SP6 is strongly recommended because it fixes a serious bug, but 2.6 SP4 is acceptable if it works on your system.) Step by step instructions for navigating MDL's Chime download site were recently provided: http://www.umass.edu/microbio/chime/getchime.htm If these new version requirements for Chime are a problem for anyone whose computer labs cannot be changed quickly before the semester ends, the previous PE 2.2 Alpha remains available (not publically linked) at http://molvis.sdsc.edu/pe2.2/protexpl If I receive any requests based on such updating problems, I'll make a public link to PE 2.2 on the PE 2.3 FrontDoor, from now until September 1. In the Help/Index/Glossary (Reference Manual), the entries on "quality of the molecular model", "R value", "Free R" and "Ramachandran plots" are further improved. All-atom contact analysis (with the Richardsons group's MolProbity server) has been added to External Resources (see http://molvis.sdsc.edu/pe_alpha/protexpl/psbiores.htm#molprobity ). Further details on changes in this release are at http://molvis.sdsc.edu/pe_alpha/protexpl/vers_pe.htm#versionhistory I believe that PE 2.3 is quite solid, because I had time to do much more extensive testing than I did for 2.2. The only reason for designating 2.3 "Alpha" instead of "Beta" is that I still haven't had time to reinstate the Protein Comparator mode (in concert with the new 'Features of the Molecule' control panel). I plan to work towards making a full release of Protein Explorer next (no longer "Beta"), then later in the year releasing Tim Driscoll's script recorder (with "undo" button), and support for Presentations in Protein Explorer. Also Frieda Reichsman is well along in preparing a flash orientation "movie" with audio voice explanation, which we expect to release sometime this summer. Tim is now working on 'QuizMol', a javascript-based mechanism for posing questions and responding to answers, that will be suitable for incorporation into any browser-based tutorial. In 2005, I hope to begin converting PE to use the open-source Jmol applet instead of Chime. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: PE 2.3 problem: clear cache? Date: Sat, 08 May 2004 15:25:29 -0400 To: John Nixon Cc: rasmol@lists.umass.edu At 5/8/04, John Nixon wrote:
Hi Eric,
 
Just tested the new PE online - I got as far as the page
 
The Protein Explorer should appear automatically in a few moments, if you are using a compatible browser
 
then nothing.  Previous versions work fine.  I'm using Chime 2.6 SP6  Windows XP SP1 (Up to date) and IE6.
 
Best wishes
 
John

Dear John:

Thanks for letting me know! I have tested it on several WinXP up to date machines with the same IE6.0 SP1 and Chime 2.6 SP6 with perfect function (also Win98, Mac OSX) .

Suggest that you clear your IE cache and try again -- you may have old files in the cache.

IE: Tools, Internet Options, Temporary Internet Files, Delete Files.

I have seen one or two failures on the first (and sometimes second) try on a machine, presumably due to old copies in a cache (which might also exist on your campus as well as in your client browser). But by the 3rd try, it has always worked, and from then on, reliably.

Do let me know if this doesn't solve the problem.

-Eric


----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline User-Agent: Mutt/1.4i References: <000a01c43525$943e9d10$be0c313e@oemcomputer> <5.2.0.9.2.20040508152333.02238340@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eugen Leitl Subject: Re: PE 2.3 problem: clear cache? Date: Sun, 09 May 2004 22:41:38 +0200 To: rasmol@lists.umass.edu On Sat, May 08, 2004 at 03:25:29PM -0400, Eric Martz wrote: Please don't send HTML-only messages to public mailing lists. -- Eugen* Leitl leitl ______________________________________________________________ ICBM: 48.07078, 11.61144 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE http://moleculardevices.org http://nanomachines.net ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Protein Explorer for Mac OSX Date: Wed, 12 May 2004 13:32:06 -0400 To: "Virginia B. Pett" Cc: rasmol@lists.umass.edu At 5/10/04, you wrote: >Dear Eric, > >We would like to use Protein Explorer at The College of Wooster for our >Biochemistry and Molecular Biology majors, in the classroom and >laboratory. With respect to this goal we have two questions: > >When do you think PE will run on OS X? > >Is there a script capability in PE so that an instructor can save a >molecular display and start from that point in front of the class? > >Thanks for taking the time to answer these questions. I plan to develop a >workshop this summer for my teaching colleagues in molecular >visualization, and I'd like to feature PE as one of the most user-friendly >packages available. > >Sincerely, >Virginia B. Pett >Professor of Chemistry >The College of Wooster, Wooster, OH 44691 Dear Virginia: I am glad that you find Protein Explorer (PE) to be user friendly, and I encourage you to adopt it at Wooster. I retired from teaching in January, and I have 2 more years of NSF support for PE development. I expect to pour most of my energy into PE development for the next few years. Incidentally, Frieda Reichsman has nearly completed a Shockwave Flash "movie" with spoken explanation that gives an overview of how to use PE. We hope this will save class time by making it unnecessary for educators to give such an overview in class. We expect to release this PE demonstration "Getting Started in PE" during the summer. When released, it will be linked prominently on PE's FrontDoor just above the first Quick-Start. 1. OSX: PE-Chime works quite well now in the Classic environment under OSX. This is the only way you can use it with OSX, and it will be the only way for a few more years at least. You must use Netscape 4.7x/4.8 with PE on all Macs (OS8, 8, 10), because it is the only browser Chime works in on Macs. Instructions for downloading NS4.8: http://www.umass.edu/microbio/chime/netscape.htm Several people have told us that they use PE in OSX teaching computer labs with great success. The only way it was possible for me to develop PE, largely by myself, in a few years, was by building on the great 'chemical knowledge' and capabilities of MDL Chime. MDL has no plans to release a Chime for native OSX. In the long run, I hope to port PE to use the open-source Jmol java applet instead of Chime. This will make it available on essentially all common platforms and browsers. However, I have six years of code in PE now, and making that conversion will itself take over a year, I expect. I don't plan to begin it until I have released some near-completion modules in PE-Chime (see below). Jmol only became a viable alternative to Chime in 2004 (due to heroic volunteer work by Michael T. Howard). 2. Saving views to show classes during lectures: I expect to release PE with these capabilities later in 2004. Meanwhile, there are pre-releases available if you are game. 2A. Saving scripts. Tim Driscoll has developed a script recorder for Protein Explorer. Everything you do in a session is recorded, so you can play it back to arrive quickly at a view you like. The saved scripts can be stored in disk files for quick playback later. Although the script recorder itself is essentially completed, it needs to be fully integrated into PE (especially PE's documentation and context sensitive help) before it is publically released. In the meantime, PE 2.1 Alpha with the script recorder is available "as is" (still in development) from Tim's site, http://www.molvisions.com/projects/software/per.html The script recorder also provides an "undo" button. (Internally, this plays back the recorded script minus the last action.) Saved scripts can be played back now from the command line. See the link "Set Project Folder" under PE's message box. 2B. Presentations in Protein Explorer (PiPE). The mechanism to attach saved scripts to buttons for instant viewing in PE is still under development. A demo "as is, in development" version can be seen at http://www.umass.edu/microbio/chime/beta/pipes/pe_pre2.15/ There you can see a presentation that I used in a journal club here, and somewhat sketchy instructions for how to construct such a presentation. (That version of PE with the partial support for PiPE can be downloaded at http://www.umass.edu/microbio/chime/beta/pipes/download/). If you use it, please don't expect a LOT of help from me. I'll try to help, but I need to spend my time working towards a well-documented, fully functioning version of it! However, I offer what I have for those who are willing to spend some extra time with it "as is". Because I have covered some topics of wider interest, I have copied this to the MolVis email list. Sincerely, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- dcrjsr@kinemage.biochem.duke.edu, dcr@kinemage.biochem.duke.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: MolVisIndex.Org reorganized and expanded Date: Tue, 18 May 2004 22:22:59 -0400 To: rasmol@lists.umass.edu, jmol-users@lists.sourceforge.net Cc: bourne@sdsc.edu, tkramer@hampshire.edu, jsr@biochem.duke.edu, MolVisIndex.Org, the World Index of Molecular Visualization Resources, has been on-line since 2000, and is currently visited 500-700 times/week. It indexes hundreds of on-line resources contributed by over a hundred authors. I initiated molvisindex.org to provide a central listing of browser-based tutorials utilizing MDL Chime. Recently, some excellent alternative technologies have come forth including Jmol, BioEditor, and KiNG (Kinetic Images New Generation, the applet sequel to Kinemages). The main goal of molvisindex.org is to enable a visitor to find tutorials on a particular molecule or topic. It is not particularly useful to separate tutorials using different technologies into different indices, provided each entry indicates the technology it employs. Therefore I have redefined the main category (formerly restricted to Chime-based resources) as "Biochemical Structure Tutorials with Rotating/Interactive Molecular Displays" to embrace tutorials using non-Chime technologies. I have also added an exciting new category "Physical Molecular Models and Molecular Sculpture", and populated it initially with eight entries. A summary of the history and growth of the site has been added at the bottom of the main page. I encourage you to submit tutorials and resources, and to encourage others who may not subscribe to this list. To do so, at the main page, go to the appropriate category, click the link "Submit a new resource", fill out the form, and submit it. Sincerely, -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal X-MSMail-priority: Normal X-ContentStamp: 6:3:1557412487 X-MAIL-INFO: 3d3a739aabcbeb73ab93cbc3b7a7c3b7171e1e2fa3eacb8eae0e4f4fcec3 X-UNTD-OriginStamp: oImUnXrqkXxEz6wkAsNJjGp8Sc928MZGOxZRo+QAZ3gc6znkPf/BcQ== ++++------+------+------+------+------+------+------+------+------+------+ From: faphd Subject: RE: RASMOL digest 326 Date: Sun, 23 May 2004 18:18:24 -0700 To: rasmol@lists.umass.edu Hi Eric, I am having trouble getting the protein explorer to work. I had explorer 6.0 and am using windows 98. I couldn't get that to work with the chime so I loaded Netscape and the chime again. Nothing again. I get the blank screen but I can't open specific molecules. What am I doing wrong? Frank -----Original Message----- On Behalf Of RASter display of MOLecular structure Sent: Saturday, May 22, 2004 9:02 PM From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu] Subject: RASMOL digest 326 To: RASter display of MOLecular structure RASMOL Digest 326 Topics covered in this issue include: 1) MolVisIndex.Org reorganized and expanded by Eric Martz ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: convert rasmol units to A Date: Fri, 28 May 2004 13:24:39 -0400 To: LIST rasmol greetings, is there an easy way to convert RasMol units to Angstroms? for example, wireframe 200 means how many angstroms? many thanks, tim -- @molvisions ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal User-Agent: SquirrelMail/1.4.2 References: ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: Re: convert rasmol units to A Date: Fri, 28 May 2004 21:02:16 +0200 (CEST) To: rasmol@lists.umass.edu Tim wrote: > is there an easy way to convert RasMol units to Angstroms? for example, > > wireframe 200 > > means how many angstroms? there are 250 rasmol units/angstrom 200 rasmol units = 200/250 = 0.8 angstroms Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline User-Agent: KMail/1.6.1 X-Spam-Level: ++++------+------+------+------+------+------+------+------+------+------+ From: Boris Gorelik Subject: preventing rasmol from centering molecules Date: Sun, 30 May 2004 10:28:38 +0300 To: rasmol@lists.umass.edu Hi, Is there a way to prevent load command from centering molecules? In other words: how can one separate a complex of two molecules and then load them into rasmol separately without changing their relative position? Thanks in advance Boris Gorelik ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.8a2) Gecko/20040527 X-Accept-Language: en-us, en X-Spam-Status: No, hits=-3.5 required=5.0 tests=BAYES_20,EMAIL_ATTRIBUTION,IN_REP_TO,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_MOZILLA_UA version=2.55 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) References: <200405301028.38518.bgbg@pob.huji.ac.il> ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: preventing rasmol from centering molecules Date: Tue, 01 Jun 2004 10:09:54 +0200 To: rasmol@lists.umass.edu Boris Gorelik wrote: >Hi, >Is there a way to prevent load command from centering molecules? In other >words: how can one separate a complex of two molecules and then load them >into rasmol separately without changing their relative position? > > > in principle you may load the complex load complex.pdb restrict :a center selected show center remember this numbers save pdb a.pdb restrict :b center selected show center remember agin save pdb b.pdb load a.pdb molecule 2 rotate molecule center [] load b.pdb molecule 3 rotate molecule center [<*-1>] molecule all now :a and :b should be on the same position as in the start file (molecule 1) Regards, Jan ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MSMail-Priority: High boundary="8E_E..DB6ADA0" ++++------+------+------+------+------+------+------+------+------+------+ From: "Admin" Subject: ADV: Attention All School Staff: Teachers, Students and Faculty Members: Date: Mon, 07 Jun 04 21:29:13 GMT To: nnor@bio.umass.edu This is a multi-part message in MIME format. --8E_E..DB6ADA0 Attention All School Staff: Teachers, Students and Faculty Members: You Must Respond By 5 P.M. Wednesday, June 9, 2004. Through a special arrangement, Avtech Direct is offering a limited allotment of BRAND NEW, top of-the-line, name-brand desktop computers at more than 50% off MSRP to all Teachers, Students,Faculty and Staff, who respond to this message before 5 P.M., Wednesday, June 9, 2004. All desktop are brand-new, packed in their original boxes, and come with a full manufacturer's warranty plus a 100% satisfaction guarantee. These professional grade Desktops are fully equipped with 2004 next generation technology, making these the best performing computers money can buy. Avtech Direct is offering these feature rich, top performing Desktop Computers with the latest Intel technology at an amazing price to all who call: 1-800-884-9510 by 5 P.M. Wednesday, June 9, 2004 The fast and powerful AT-2400 series Desktop features: * Intel 2.0Ghz Processor for amazing speed and performance * 128MB DDR RAM, --- Upgradeable to 1024 * 20 GB UDMA Hard Drive, --- Upgradeable to 80 GB * 52X CD-Rom Drive, --- Upgradeable to DVD/CDRW * 1.44 Floppy disk drive * Next Generation Technology * ATI Premium video and sound * Full Connectivity with Fax modem/Lan/IEE 1394/USB 2.0 * Soft Touch Keyboard and scroll mouse * Internet Ready * Network Ready * 1 Year parts and labor warranty * Priority customer service and tech support MSRP $699 ........................................ Your Cost $297 How to qualify: 1. You must be a Teacher, Student, Faculty or Staff Member: 2. All desktop computers will be available on a first come first serve basis. 3. You must call 1-800-884-9510 by 5 P.M. Wednesday, June 9, 2004 and we will hold the desktops you request on will call. 4. You are not obligated in any way. 5. 100% Satisfaction Guaranteed. Call Avtech Direct 1-800-884-9510 before 5 P.M. Wednesday, June 9, 2004 If you wish to unsubscribe from this list, please go to: http://www.computeradvice.org/unsubscribe.asp Avtech Direct 22647 Ventura Blvd., Suite 374 Woodland Hills, CA 91364 --8E_E..DB6ADA0-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2739.300 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: RasTop 2.1 beta Date: Tue, 08 Jun 2004 19:43:54 -0700 To: rasmol@lists.umass.edu, pdb-l@rcsb.org Dear Friends, RasTop 2.1 is available for download at http://www.geneinfinity.org/rastop/download.htm. This is a beta version, meaning that feedback is encouraged before we do a final release, hopefully in a few weeks. This new version contains many bug fixes, a command line window as seen in the original RasMol, and support for translation. The code for the command line window was contributed by Christian Duqué. Thanks for all your comments & bug reports. RasTop integrates a powerful graphical user interface to RasMol molecular visualization software and is available for both Windows and Linux platforms. RasTop is getting increasingly popular as a teaching tool. Philippe Valadon San Diego, CA June 08, 2004 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 boundary="Boundary_(ID_HDzKvx5sVDcijdtYr2Xd7w)" X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: HYUN CHUL KIM Subject: How to turn off all atom display by the command line input Date: Thu, 10 Jun 2004 11:05:18 +0900 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_HDzKvx5sVDcijdtYr2Xd7w) I know how to turn off the all atom display and turn on the backbone type display at the same time(Click on the graphic menu bar: Display->Backbone But I don't know how I can turn off this all atom picture while backbone picture is still being displayed. When I enter the "backbone on/off", the all-atom picture still remains in the screen. I mean the all-atom picture(default) and backbone picture of same molecule. How can I do this? Thanks in advance Kim --Boundary_(ID_HDzKvx5sVDcijdtYr2Xd7w) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_HDzKvx5sVDcijdtYr2Xd7w)-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.6487.1 Thread-Topic: How to turn off all atom display by the command line input Thread-Index: AcROkAklLEp0iCK7TMaCDJfrkJNYvwAV4tDA content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: X-OriginalArrivalTime: 10 Jun 2004 12:39:05.0970 (UTC) FILETIME=[EAF73D20:01C44EE7] ++++------+------+------+------+------+------+------+------+------+------+ From: "Gorga, Frank" Subject: RE: How to turn off all atom display by the command line input Date: Thu, 10 Jun 2004 08:39:05 -0400 To: rasmol@lists.umass.edu Kim, The default "all-atom picture" as you call it is "officially" a "wireframe"... the command "wireframe off" will turn this off. Of course "wireframe on" will make it visible again. Hope this helps, --- Frank --------------------------------------------------- Frank R. Gorga, Ph.D. Dept. of Chemical Sciences Bridgewater State College Bridgewater, MA 02325 508-531-2827 / 508-531-4827 (fax) mailto:fgorga@bridgew.edu http://webhost.bridgew.edu/fgorga ----------------------------------------------------- -----Original Message----- On Behalf Of HYUN CHUL KIM Sent: Wednesday, June 09, 2004 10:05 PM From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu] Subject: How to turn off all atom display by the command line input To: rasmol@lists.umass.edu I know how to turn off the all atom display and turn on the backbone type display at the same time(Click on the graphic menu bar: Display->Backbone But I don't know how I can turn off this all atom picture while backbone picture is still being displayed. When I enter the "backbone on/off", the all-atom picture still remains in the screen. I mean the all-atom picture(default) and backbone picture of same molecule. How can I do this? Thanks in advance Kim ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: chain colors in rasmol Date: Fri, 11 Jun 2004 10:59:51 +0100 (BST) To: Rasmol Mailing List Hi, I find that 'color chain' with a large number of chains dosn't give very high 'contrast' results, with the result that I can't really see the different chains. Is their any way to alter this behaviour? (i.e a nice red / green / blue / ...) Cheers, Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_oJPqssUidN7lStVpDvSncA)" ++++------+------+------+------+------+------+------+------+------+------+ From: Malcolm Leissring Subject: selecting residues in RasTop Date: Fri, 11 Jun 2004 15:04:50 -0400 To: rasmol@lists.umass.edu --Boundary_(ID_oJPqssUidN7lStVpDvSncA) Simple question: How do you select individual atoms/residues/chains in RasTop? It is definitely not intuitive. M ---------- Malcolm A. Leissring, Ph.D. Center for Neurologic Diseases Brigham and Women's Hospital and Harvard Medical School HIM, Room 740 77 Avenue Louis Pasteur Boston, MA 02115 ph: (617) 525-5226 fax: (617) 525-5305 Webpage: http://darwin.bio.uci.edu/~malcolm/ --Boundary_(ID_oJPqssUidN7lStVpDvSncA) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_oJPqssUidN7lStVpDvSncA)-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2739.300 X-MSMail-priority: Normal References: <5.0.0.25.2.20040611150339.0213fe48@rics.bwh.harvard.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: selecting residues in RasTop Date: Sat, 12 Jun 2004 14:29:32 -0700 To: rasmol@lists.umass.edu >From Malcolm Leissring: > Simple question: How do you select individual atoms/residues/chains in > RasTop? It is definitely not intuitive. Dear Malcom, Press the TAB key (SPACE bar in old versions) to see the current selection. The simplest method for selection uses the mouse. On the first toolbar click the button labeled either "Atoms", "Residues", or "Chain" and then select part of the molecule with the mouse directly on screen . Press the Schift key at the same time to add the new selection to the previous one or the Control key to remove from it. It seems that the tooltips (texts with a yellow background that appear when the cursor stay over a button more than 1 second) are not explicite enough. Thanks for pointing this out. Philippe Valadon ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer "Demo" Flash Movies Available Date: Tue, 15 Jun 2004 23:13:38 -0400 To: rasmol@lists.umass.edu Frieda Reichsman has developed a series of interactive Flash movies with audio (voice) explanations, "Getting Started in Protein Explorer". I have just made these available in a new release of PE, version 2.4, at proteinexplorer.org. You will see them prominently linked just above the large Quick-Start at the FrontDoor. It is our hope that these introductory movies will enable more educators to use PE in class assignments, by freeing them from the need to introduce PE in a demonstration that uses lecture time. Of course they should also make it easier for anyone to get started with PE, including students, educators, and researchers. At present, the Demo is not yet downloadable for offline use. We will offer that later in the summer. (Presently, you can download either PE 2.3 Alpha [no Demo], or PE 1.982 Beta.) PE 2.4 also adds solutions to two problems that sometimes plague PE for Mac OS X users. Click on "Tips and Techniques" at the FrontDoor (also linked to Troubleshooting), or go directly to http://molvis.sdsc.edu/protexpl/pe_tips.htm#osx I have designated 2.4 a "Beta" release because it seems solid. However I still haven't implemented Protein Comparator in this version. Therefore, if you try to use Comparator you will be advised to use PE 1.982, now relocated to a secondary URL. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-MSMail-priority: Normal References: <5.2.0.9.2.20040615224953.015b9030@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Edward Mathenge Subject: Re: Protein Explorer "Demo" Flash Movies Available Date: Wed, 16 Jun 2004 18:56:11 +0900 To: rasmol@lists.umass.edu ----- Original Message ----- Sent: Wednesday, June 16, 2004 12:13 PM From: "Eric Martz" Subject: Protein Explorer "Demo" Flash Movies Available To: > Frieda Reichsman has developed a series of interactive Flash movies with > audio (voice) explanations, "Getting Started in Protein Explorer". I have > just made these available in a new release of PE, version 2.4, at > proteinexplorer.org. You will see them prominently linked just above the > large Quick-Start at the FrontDoor. > > It is our hope that these introductory movies will enable more educators to > use PE in class assignments, by freeing them from the need to introduce PE > in a demonstration that uses lecture time. Of course they should also make > it easier for anyone to get started with PE, including students, educators, > and researchers. > > At present, the Demo is not yet downloadable for offline use. We will offer > that later in the summer. (Presently, you can download either PE 2.3 Alpha > [no Demo], or PE 1.982 Beta.) > > PE 2.4 also adds solutions to two problems that sometimes plague PE for Mac > OS X users. Click on "Tips and Techniques" at the FrontDoor (also linked to > Troubleshooting), or go directly to > http://molvis.sdsc.edu/protexpl/pe_tips.htm#osx > > I have designated 2.4 a "Beta" release because it seems solid. However I > still haven't implemented Protein Comparator in this version. Therefore, if > you try to use Comparator you will be advised to use PE 1.982, now > relocated to a secondary URL. > > -Eric > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor Emeritus, Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MSMail-Priority: High boundary="FFE.E_.CA_5" ++++------+------+------+------+------+------+------+------+------+------+ From: "Admin" Subject: ADV: Attention All School Staff: Teachers, Students and Faculty Members: Date: Sun, 20 Jun 04 21:32:21 GMT To: nnor@bio.umass.edu This is a multi-part message in MIME format. --FFE.E_.CA_5 Attention All School Staff: Teachers, Students and Faculty Members: You Must Respond By 5 P.M. Tuesday, June 22, 2004. Through a special arrangement, Avtech Direct is offering a limited allotment of BRAND NEW, top of-the-line, name-brand desktop computers at more than 50% off MSRP to all Teachers, Students,Faculty and Staff, who respond to this message before 5 P.M., Tuesday, June 22, 2004. All desktop are brand-new, packed in their original boxes, and come with a full manufacturer's warranty plus a 100% satisfaction guarantee. These professional grade Desktops are fully equipped with 2004 next generation technology, making these the best performing computers money can buy. Avtech Direct is offering these feature rich, top performing Desktop Computers with the latest Intel technology at an amazing price to all who call: 1-800-884-9510 by 5 P.M. Tuesday, June 22, 2004 The fast and powerful AT-2400 series Desktop features: * Intel 2.0Ghz Processor for amazing speed and performance * 128MB DDR RAM, --- Upgradeable to 1024 * 20 GB UDMA Hard Drive, --- Upgradeable to 80 GB * 52X CD-Rom Drive, --- Upgradeable to DVD/CDRW * 1.44 Floppy disk drive * Next Generation Technology * ATI Premium video and sound * Full Connectivity with Fax modem/Lan/IEE 1394/USB 2.0 * Soft Touch Keyboard and scroll mouse * Internet Ready * Network Ready * 1 Year parts and labor warranty * Priority customer service and tech support MSRP $699 ........................................ Your Cost $297 How to qualify: 1. You must be a Teacher, Student, Faculty or Staff Member: 2. All desktop computers will be available on a first come first serve basis. 3. You must call 1-800-884-9510 by 5 P.M. Tuesday, June 22, 2004 and we will hold the desktops you request on will call. 4. You are not obligated in any way. 5. 100% Satisfaction Guaranteed. Call Avtech Direct 1-800-884-9510 before 5 P.M. Tuesday, June 22, 2004 Visit our website at http://www.avtechdirectcomputers.com If you wish to unsubscribe from this list, please go to: http://www.computeradvice.org/unsubscribe.asp Avtech Direct 22647 Ventura Blvd., Suite 374 Woodland Hills, CA 91364 --FFE.E_.CA_5-- 90+ Abstracts now online + Late abstracts still accepted http://3Dsig.weizmann.ac.il/ X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 boundary="Boundary_(ID_dT4fYpwRZ+Q9Fja1OLNA7A)" X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Ilan Samish Subject: 3Dsig Structural Bioinformatics Meeting, Date: Fri, 25 Jun 2004 13:01:18 +0300 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_dT4fYpwRZ+Q9Fja1OLNA7A) Dear Colleague, We would like to inform you that the 3Dsig Structural Bioinformatics Meeting (July 29-30 July 2004, Glasgow, Scotland, UK, part of the ISMB/ECCB Bioinformatics Conference) has opened all abstract material to the public. Whether you decide to come or not, you may want to view the online abstracts: http://3dsig.weizmann.ac.il/3dsig/2004/abstracts.html 3Dsig will have a novel laptop session where authors will be at their numbered stations with their laptops describing their work. The idea is to offer a semi-formal, yet intimate channel during 3Dsig to facilitate discussion of individual research. Abstracts are still accepted till June 30th. As the organization of the 3 panel discussions will be conducted in the upcoming days, you may want to send such an abstract quickly. Topics include: 3D data-mining; 3D programming modules; docking and protein-protein/ligand interaction prediction; membrane protein assembly prediction; secondary structure and domain assignment; structure-based function prediction; structural databases; structural genomics; structure prediction; structure representation; the role of geometry and energetics in protein structure and function Last, sponsors are still welcomed - see online information. Looking forward to meeting you at 3Dsig, 3Dsig organizing committee ~~~~~~~~~~~~~~~~~~~~~~ http://3Dsig.weizmann.ac.il/ 3Dsig@weizmann.ac.il --Boundary_(ID_dT4fYpwRZ+Q9Fja1OLNA7A) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_dT4fYpwRZ+Q9Fja1OLNA7A)-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: automatic bonding script? Date: Mon, 28 Jun 2004 23:18:58 +0100 (BST) To: Rasmol Mailing List Hi, I have the ID of various residues, and I would like to visualize their separation in space by bonding them (at the CA) and then drawing a wireframe between them. Given the residue ID, is there any way I can get the numeric atom ID required for the bond command? Any suggestions welcome! Cheers, Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: automatic bonding script? Date: Mon, 28 Jun 2004 18:50:39 -0400 To: rasmol@lists.umass.edu Dan Bolser sent (2004.06.28 at 11.18p [+0100gmt]) : > >Hi, I have the ID of various residues, and I would like to visualize >their separation in space by bonding them (at the CA) and then >drawing a wireframe between them. > >Given the residue ID, is there any way I can get the numeric atom ID >required for the bond command? > >Any suggestions welcome! > hi Dan, can you provide a little more info, please? Is this in RasMol or Chime or other software? how are you getting the group id, and how do you want to get the atom number? is javascript involved, or a rasmol scr/spt file? in rasmol, clicking on an atom will give you the atom id in the command line. Chime shows the id in the status bar at the bottom of the window, IIRC< and passes it thru the pickCallBack as well. regards, tim -- Timothy Driscoll molvisions - see, grasp, learn. usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: automatic bonding script? Date: Tue, 29 Jun 2004 00:32:14 +0100 (BST) To: rasmol@lists.umass.edu On Mon, 28 Jun 2004, timothy driscoll wrote: >Dan Bolser sent (2004.06.28 at 11.18p [+0100gmt]) : > >> >>Hi, I have the ID of various residues, and I would like to visualize >>their separation in space by bonding them (at the CA) and then >>drawing a wireframe between them. >> >>Given the residue ID, is there any way I can get the numeric atom ID >>required for the bond command? >> >>Any suggestions welcome! >> > > >hi Dan, > >can you provide a little more info, please? Is this in RasMol or Chime >or other software? how are you getting the group id, and how do you >want to get the atom number? is javascript involved, or a rasmol >scr/spt file? > >in rasmol, clicking on an atom will give you the atom id in the command >line. Chime shows the id in the status bar at the bottom of the window, >IIRC< and passes it thru the pickCallBack as well. > Hi, Cheers, I am using Rasmol, hopefully script file (or just copy and paste for the time being). I get a list of residue ID's from an internal database of residue-residue 'contacts' and I want to look at these in more detail. I only have the residue id details, and not the details of the atoms in question. From this DB I would like to generate a script which highlightes contacts as bonds between CA atoms. For example I could draw stronger bonds (not that I have that data) as thicker bonds. I find that the rasmol 'bond' command requires the numeric atom id and will accept nothing else. I guess I will have to do some data integration, and somehow query the CA atom id for my given residue id. I have been using the MSD API (in unrelated work), and I find this to be an overal exelent database. Cheers, Dan. > >regards, > >tim > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline User-Agent: KMail/1.6.1 X-Spam-Level: References: ++++------+------+------+------+------+------+------+------+------+------+ From: b g Subject: Re: automatic bonding script? Date: Tue, 29 Jun 2004 10:19:43 +0300 To: rasmol@lists.umass.edu Dan, Here is my suggestion: you can write a program (I used perl for pretty similar task) that takes the original PDB file and the ID's of the residues of interest. Then the program generates a perl script that draws the whole structure, colors and displays whatever you need, in whatever way you want, using rasmol commands like (select, wireframe color etc). If you want to, I'll send you my scripts privatly. On Tuesday 29 June 2004 02:32, Dan Bolser wrote: > On Mon, 28 Jun 2004, timothy driscoll wrote: > >Dan Bolser sent (2004.06.28 at 11.18p [+0100gmt]) : > >>Hi, I have the ID of various residues, and I would like to visualize > >>their separation in space by bonding them (at the CA) and then > >>drawing a wireframe between them. > >> > >>Given the residue ID, is there any way I can get the numeric atom ID > >>required for the bond command? > >> > >>Any suggestions welcome! > > > >hi Dan, > > > >can you provide a little more info, please? Is this in RasMol or Chime > >or other software? how are you getting the group id, and how do you > >want to get the atom number? is javascript involved, or a rasmol > >scr/spt file? > > > >in rasmol, clicking on an atom will give you the atom id in the command > >line. Chime shows the id in the status bar at the bottom of the window, > >IIRC< and passes it thru the pickCallBack as well. > > Hi, Cheers, > > I am using Rasmol, hopefully script file (or just copy and paste for the > time being). > > I get a list of residue ID's from an internal database of residue-residue > 'contacts' and I want to look at these in more detail. > > I only have the residue id details, and not the details of the atoms in > question. From this DB I would like to generate a script which highlightes > contacts as bonds between CA atoms. > > For example I could draw stronger bonds (not that I have that data) as > thicker bonds. > > I find that the rasmol 'bond' command requires the numeric atom id and > will accept nothing else. I guess I will have to do some data integration, > and somehow query the CA atom id for my given residue id. > > I have been using the MSD API (in unrelated work), and I find this to be > an overal exelent database. > > Cheers, > Dan. > > >regards, > > > >tim > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7) Gecko/20040616 X-Accept-Language: en-us, en X-Spam-Status: No, hits=-0.8 required=5.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,RCVD_IN_ORBS,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_MOZILLA_UA version=2.55 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) References: ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: automatic bonding script? Date: Tue, 29 Jun 2004 09:27:11 +0200 To: rasmol@lists.umass.edu Dan Bolser wrote: >On Mon, 28 Jun 2004, timothy driscoll wrote: > > > >>Dan Bolser sent (2004.06.28 at 11.18p [+0100gmt]) : >> >> >> >>>Hi, I have the ID of various residues, and I would like to visualize >>>their separation in space by bonding them (at the CA) and then >>>drawing a wireframe between them. >>> >>>Given the residue ID, is there any way I can get the numeric atom ID >>>required for the bond command? >>> >>>Any suggestions welcome! >>> >>> >>> >>hi Dan, >> >>can you provide a little more info, please? Is this in RasMol or Chime >>or other software? how are you getting the group id, and how do you >>want to get the atom number? is javascript involved, or a rasmol >>scr/spt file? >> >>in rasmol, clicking on an atom will give you the atom id in the command >>line. Chime shows the id in the status bar at the bottom of the window, >>IIRC< and passes it thru the pickCallBack as well. >> >> >> > >Hi, Cheers, > >I am using Rasmol, hopefully script file (or just copy and paste for the >time being). > >I get a list of residue ID's from an internal database of residue-residue >'contacts' and I want to look at these in more detail. > >I only have the residue id details, and not the details of the atoms in >question. From this DB I would like to generate a script which highlightes >contacts as bonds between CA atoms. > >For example I could draw stronger bonds (not that I have that data) as >thicker bonds. > >I find that the rasmol 'bond' command requires the numeric atom id and >will accept nothing else. > yes it would be very helpful, if RasMol would accept something like bond [T]1:D.O4 [T]1:D.C5M + in addition to bond 259 261 + at the moment, you need two passes with RasMol, first you had to start a script like that select [T]1:D.O4, [T]1:D.C5M show selected atoms with the rasmol executable (I missed the -nodisplay option in RasWin) and parse the output for a second script rasmol_8BIT64 -script selection.RAZ -nodisplay pdb1nfk.ent | perl -e 'if(/Atom:\s+\w+\s+(\d+)/){push @a,$1;}END{printf "bond %d %d +\n", @a;}' and send this to a second RasMol instance e.g. | rasmol_8BIT64 pdb1nfk.ent >I guess I will have t > >o do some data integration, >and somehow query the CA atom id for my given residue id. > > but if you want to walk along the backbone you may use backbone for bond and there you may apply the already implemented selection mechanism. Regards, Jan >I have been using the MSD API (in unrelated work), and I find this to be >an overal exelent database. > >Cheers, >Dan. > > > > > > >>regards, >> >>tim >> >> >> ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: automatic bonding script? Date: Tue, 29 Jun 2004 09:56:45 +0100 (BST) To: rasmol@lists.umass.edu Thanks for the reply! On Tue, 29 Jun 2004, Jan Reichert wrote: >Dan Bolser wrote: > >>On Mon, 28 Jun 2004, timothy driscoll wrote: >> >> >> >>>Dan Bolser sent (2004.06.28 at 11.18p [+0100gmt]) : >>> >>> >>> >>>>Hi, I have the ID of various residues, and I would like to visualize >>>>their separation in space by bonding them (at the CA) and then >>>>drawing a wireframe between them. >>>> >>>>Given the residue ID, is there any way I can get the numeric atom ID >>>>required for the bond command? >>>> >>>>Any suggestions welcome! >>>> >>>> >>>> >>>hi Dan, >>> >>>can you provide a little more info, please? Is this in RasMol or Chime >>>or other software? how are you getting the group id, and how do you >>>want to get the atom number? is javascript involved, or a rasmol >>>scr/spt file? >>> >>>in rasmol, clicking on an atom will give you the atom id in the command >>>line. Chime shows the id in the status bar at the bottom of the window, >>>IIRC< and passes it thru the pickCallBack as well. >>> >>> >>> >> >>Hi, Cheers, >> >>I am using Rasmol, hopefully script file (or just copy and paste for the >>time being). >> >>I get a list of residue ID's from an internal database of residue-residue >>'contacts' and I want to look at these in more detail. >> >>I only have the residue id details, and not the details of the atoms in >>question. From this DB I would like to generate a script which highlightes >>contacts as bonds between CA atoms. >> >>For example I could draw stronger bonds (not that I have that data) as >>thicker bonds. >> >>I find that the rasmol 'bond' command requires the numeric atom id and >>will accept nothing else. >> >yes it would be very helpful, if RasMol would accept something like > bond [T]1:D.O4 [T]1:D.C5M + >in addition to > bond 259 261 + I agree, and a bit more consistent too. >at the moment, you need two passes with RasMol, first you had to start a >script like that > select [T]1:D.O4, [T]1:D.C5M > show selected atoms >with the rasmol executable (I missed the -nodisplay option in RasWin) >and parse the output for a second script > rasmol_8BIT64 -script selection.RAZ -nodisplay pdb1nfk.ent | perl -e >'if(/Atom:\s+\w+\s+(\d+)/){push @a,$1;}END{printf "bond %d %d +\n", @a;}' >and send this to a second RasMol instance e.g. > | rasmol_8BIT64 pdb1nfk.ent Yikes! I like it! > >>I guess I will have t >> > >>o do some data integration, >>and somehow query the CA atom id for my given residue id. >> >> >but if you want to walk along the backbone you may use backbone for bond >and there you may apply the already implemented selection mechanism. >Regards, Jan :( No, usually non backbone 'bonds' which I want to visualize. Actually I am finding my task very hard, I want to look at a group of residues which are separated by a characteristic distance, and characterize them... It is hard man! Thanks again, Dan. >>I have been using the MSD API (in unrelated work), and I find this to be >>an overal exelent database. >> >>Cheers, >>Dan. >> >> >> >> >> >> >>>regards, >>> >>>tim >>> >>> >>> > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MSMail-Priority: High boundary="A5B3B_68528D_AB7_F_5_" ++++------+------+------+------+------+------+------+------+------+------+ From: "Admin" Subject: ADV: Attention All School Staff: Teachers, Students and Faculty Members: Date: Thu, 01 Jul 04 10:05:49 GMT To: nnor@bio.umass.edu This is a multi-part message in MIME format. --A5B3B_68528D_AB7_F_5_ Attention All School Staff: Teachers, Students and Faculty Members: You Must Respond By 5 P.M. Friday, July 2, 2004. Through a special arrangement, Avtech Direct is offering a limited allotment of BRAND NEW, top of-the-line, name-brand desktop computers at more than 50% off MSRP to all Teachers, Students,Faculty and Staff, who respond to this message before 5 P.M., Friday, July 2, 2004. All desktop are brand-new, packed in their original boxes, and come with a full manufacturer's warranty plus a 100% satisfaction guarantee. These professional grade Desktops are fully equipped with 2004 next generation technology, making these the best performing computers money can buy. Avtech Direct is offering these feature rich, top performing Desktop Computers with the latest Intel technology at an amazing price to all who call: 1-800-884-9510 by 5 P.M. Friday, July 2, 2004 The fast and powerful AT-2400 series Desktop features: * Intel 2.0Ghz Processor for amazing speed and performance * 128MB DDR RAM, --- Upgradeable to 1024 * 20 GB UDMA Hard Drive, --- Upgradeable to 80 GB * 52X CD-Rom Drive, --- Upgradeable to DVD/CDRW * 1.44 Floppy disk drive * Next Generation Technology * ATI Premium video and sound * Full Connectivity with Fax modem/Lan/IEE 1394/USB 2.0 * Soft Touch Keyboard and scroll mouse * Internet Ready * Network Ready * 1 Year parts and labor warranty * Priority customer service and tech support MSRP $699 ........................................ Your Cost $297 How to qualify: 1. You must be a Teacher, Student, Faculty or Staff Member: 2. All desktop computers will be available on a first come first serve basis. 3. You must call 1-800-884-9510 by 5 P.M. Friday, July 2, 2004 and we will hold the desktops you request on will call. 4. You are not obligated in any way. 5. 100% Satisfaction Guaranteed. Call Avtech Direct 1-800-884-9510 before 5 P.M. Friday, July 2, 2004 Visit our website at http://www.avtechdirect-education.com If you wish to unsubscribe from this list, please go to: http://www.computeradvice.org/unsubscribe.asp Avtech Direct 22647 Ventura Blvd., Suite 374 Woodland Hills, CA 91364 --A5B3B_68528D_AB7_F_5_-- ++++------+------+------+------+------+------+------+------+------+------+ From: Wayne Decatur Subject: genereate pdb file from dna sequence Date: Thu, 01 Jul 2004 13:56:57 -0700 (PDT) To: rasmol@lists.umass.edu In the past I used a site on the web to generate pdb files for theoretical B-form DNA and A-form RNA molecules with just a sequence of nucleotides in text form. The site I had listed is http://www.psc.edu/general/help/webtools.html. However this site no longer seems to offer this program. Is there some new (or correct) site that people know of or a convenient way of doing this? Thanks, Wayne Decatur UMASS Amherst __________________________________ Do you Yahoo!? Yahoo! Mail Address AutoComplete - You start. We finish. http://promotions.yahoo.com/new_mail ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Jim Perkins Subject: Re: genereate pdb file from dna sequence Date: Thu, 01 Jul 2004 17:22:04 -0500 To: rasmol@lists.umass.edu Try this site at The International Center for Genetic Engineering and Biotechnology in Trieste, Italy: http://hydra.icgeb.trieste.it/~kristian/dna/ Click on "model it" and the fill out the input form. Jim >In the past I used a site on the web to generate pdb >files for theoretical B-form DNA and A-form RNA >molecules with just a sequence of nucleotides in text >form. The site I had listed is >http://www.psc.edu/general/help/webtools.html. > >However this site no longer seems to offer this >program. Is there some new (or correct) site that >people know of or a convenient way of doing this? > >Thanks, >Wayne Decatur >UMASS Amherst ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: center and center selected Date: Fri, 02 Jul 2004 15:06:24 +0100 (BST) To: Rasmol Mailing List select carbon center center selected Why would the above two commands have different results? any way to dump the current center point? Ta, Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-pair-Authenticated: 209.197.6.81 References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: center and center selected Date: Fri, 02 Jul 2004 11:03:03 -0400 To: rasmol@lists.umass.edu Centre without arguments is the same as centre all, not centre selected. In RasMol 2.7.2.1.1, show center returns a non-zero centre. -- HJB At 3:06 PM +0100 7/2/04, Dan Bolser wrote: >select carbon > >center > >center selected > >Why would the above two commands have different results? > >any way to dump the current center point? > >Ta, > >Dan. > -- ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: -xyz glytch? Date: Fri, 02 Jul 2004 16:26:02 +0100 (BST) To: Rasmol Mailing List I get all kinds nonsense at the terminal when I select certain atoms in -xyz format. Like reading raw binary at the terminal... is this a know problem? Also, why does within() have a limit of 40 angstroms? ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal User-Agent: SquirrelMail/1.4.2 ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Subject: Re: center and center selected Date: Fri, 02 Jul 2004 17:05:16 +0200 (CEST) To: rasmol@lists.umass.edu Dan wrote: > select carbon > > center > > center selected > > Why would the above two commands have different results? My understanding is ... The center command takes an arbitrary expression as an argument. The center is set to the geometric average (unweighted center of gravity). If no argument is passed then it defaults to 'all'. The following are equivalent: center center * center all AND select all center selected There is nothing special about 'selected' ... it simply refers to the selected set. The following are equivalent: center carbon center *.c?? # this may not be exactly correct, but you get the idea center (carbon or oxygen) and !oxygen AND select carbon center selected > any way to dump the current center point? saying 'center' or 'center all' resets it to the default value that is used at startup. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: center and center selected Date: Fri, 02 Jul 2004 17:29:51 +0100 (BST) To: rasmol@lists.umass.edu Thanks both for clear responses. However, the problem persists (I didn't describe in enough detail). Attached is the file I am looking at in xyz format (domain1.xyz). It contains a bunch of CA atoms from one of the domains of pdb 1RYP. These are of type C. I have also included a N whose position is the geometrc average center of the CA atoms. If I type select all center selected I clearly see the molecule is rotating about the nitrogen... My calculated center = 40.18108780487804, -134.62689268292684, 69.39078048780488 rasmol show center [-266,-972,481] Hmmm... If I type center Same as select all \n center selected right? Wrong... I see the molecule clearly not rotating about the nitrogen. This structure also shows the garbled command line clicking most atoms, which is a real pain, so be warned. I have to look directly into a binary file and scroll down until my terminal is fixed. Maybe this is an xyz problem? Version 2.7.2.1.1 January 2004 Final experiment rasmol center all ... is wrong too, just like center on its own. In case you are wondering I am looking at bounding spheres, which is why I would like to select within(arbitary,nitrogen). Cheers, Dan. On Fri, 2 Jul 2004, Miguel wrote: > >Dan wrote: > >> select carbon >> >> center >> >> center selected >> >> Why would the above two commands have different results? > >My understanding is ... > >The center command takes an arbitrary expression as an argument. The >center is set to the geometric average (unweighted center of gravity). If >no argument is passed then it defaults to 'all'. > >The following are equivalent: > >center >center * >center all >AND >select all >center selected > >There is nothing special about 'selected' ... it simply refers to the >selected set. > >The following are equivalent: > >center carbon >center *.c?? # this may not be exactly correct, but you get the idea >center (carbon or oxygen) and !oxygen >AND >select carbon >center selected > > >> any way to dump the current center point? > >saying 'center' or 'center all' resets it to the default value that is >used at startup. > > >Miguel > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: center and center selected Date: Fri, 02 Jul 2004 17:31:03 +0100 (BST) To: rasmol@lists.umass.edu Any way to explicitly set the center? center set x, y, z ? On Fri, 2 Jul 2004, Herbert J. Bernstein wrote: >Centre without arguments is the same as centre all, not centre selected. >In RasMol 2.7.2.1.1, show center returns a non-zero centre. -- HJB > > >At 3:06 PM +0100 7/2/04, Dan Bolser wrote: >>select carbon >> >>center >> >>center selected >> >>Why would the above two commands have different results? >> >>any way to dump the current center point? >> >>Ta, >> >>Dan. >> > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: center and center selected Date: Fri, 02 Jul 2004 17:32:24 +0100 (BST) To: rasmol@lists.umass.edu This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. --Boundary_(ID_xrNrFoZPTALtzhbrMLHmTA) Sorry, here is the attachment (hopefully not too big) Dan. On Fri, 2 Jul 2004, Dan Bolser wrote: > >Thanks both for clear responses. However, the problem persists (I didn't >describe in enough detail). > >Attached is the file I am looking at in xyz format (domain1.xyz). > >It contains a bunch of CA atoms from one of the domains of pdb 1RYP. These >are of type C. I have also included a N whose position is the geometrc >average center of the CA atoms. > >If I type > >select all >center selected > >I clearly see the molecule is rotating about the nitrogen... > >My calculated center = > >40.18108780487804, >-134.62689268292684, >69.39078048780488 > >rasmol show center >[-266,-972,481] > >Hmmm... > >If I type > >center > >Same as select all \n center selected right? > >Wrong... > >I see the molecule clearly not rotating about the nitrogen. > >This structure also shows the garbled command line clicking most atoms, >which is a real pain, so be warned. I have to look directly into a binary >file and scroll down until my terminal is fixed. > >Maybe this is an xyz problem? > >Version 2.7.2.1.1 January 2004 > > >Final experiment > >rasmol center all ... is wrong too, just like center on its own. > > >In case you are wondering I am looking at bounding spheres, which is why I >would like to select within(arbitary,nitrogen). > >Cheers, >Dan. > > > >On Fri, 2 Jul 2004, Miguel wrote: > >> >>Dan wrote: >> >>> select carbon >>> >>> center >>> >>> center selected >>> >>> Why would the above two commands have different results? >> >>My understanding is ... >> >>The center command takes an arbitrary expression as an argument. The >>center is set to the geometric average (unweighted center of gravity). If >>no argument is passed then it defaults to 'all'. >> >>The following are equivalent: >> >>center >>center * >>center all >>AND >>select all >>center selected >> >>There is nothing special about 'selected' ... it simply refers to the >>selected set. >> >>The following are equivalent: >> >>center carbon >>center *.c?? # this may not be exactly correct, but you get the idea >>center (carbon or oxygen) and !oxygen >>AND >>select carbon >>center selected >> >> >>> any way to dump the current center point? >> >>saying 'center' or 'center all' resets it to the default value that is >>used at startup. >> >> >>Miguel >> >> >> >> > > > --Boundary_(ID_xrNrFoZPTALtzhbrMLHmTA) Content-id: * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_xrNrFoZPTALtzhbrMLHmTA)-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: center and center selected Date: Fri, 02 Jul 2004 18:38:53 +0100 (BST) To: rasmol@lists.umass.edu Should I send the file in an email? On Fri, 2 Jul 2004, Dan Bolser wrote: > >Sorry, here is the attachment (hopefully not too big) > >Dan. > >On Fri, 2 Jul 2004, Dan Bolser wrote: > >> >>Thanks both for clear responses. However, the problem persists (I didn't >>describe in enough detail). >> >>Attached is the file I am looking at in xyz format (domain1.xyz). >> >>It contains a bunch of CA atoms from one of the domains of pdb 1RYP. These >>are of type C. I have also included a N whose position is the geometrc >>average center of the CA atoms. >> >>If I type >> >>select all >>center selected >> >>I clearly see the molecule is rotating about the nitrogen... >> >>My calculated center = >> >>40.18108780487804, >>-134.62689268292684, >>69.39078048780488 >> >>rasmol show center >>[-266,-972,481] >> >>Hmmm... >> >>If I type >> >>center >> >>Same as select all \n center selected right? >> >>Wrong... >> >>I see the molecule clearly not rotating about the nitrogen. >> >>This structure also shows the garbled command line clicking most atoms, >>which is a real pain, so be warned. I have to look directly into a binary >>file and scroll down until my terminal is fixed. >> >>Maybe this is an xyz problem? >> >>Version 2.7.2.1.1 January 2004 >> >> >>Final experiment >> >>rasmol center all ... is wrong too, just like center on its own. >> >> >>In case you are wondering I am looking at bounding spheres, which is why I >>would like to select within(arbitary,nitrogen). >> >>Cheers, >>Dan. >> >> >> >>On Fri, 2 Jul 2004, Miguel wrote: >> >>> >>>Dan wrote: >>> >>>> select carbon >>>> >>>> center >>>> >>>> center selected >>>> >>>> Why would the above two commands have different results? >>> >>>My understanding is ... >>> >>>The center command takes an arbitrary expression as an argument. The >>>center is set to the geometric average (unweighted center of gravity). If >>>no argument is passed then it defaults to 'all'. >>> >>>The following are equivalent: >>> >>>center >>>center * >>>center all >>>AND >>>select all >>>center selected >>> >>>There is nothing special about 'selected' ... it simply refers to the >>>selected set. >>> >>>The following are equivalent: >>> >>>center carbon >>>center *.c?? # this may not be exactly correct, but you get the idea >>>center (carbon or oxygen) and !oxygen >>>AND >>>select carbon >>>center selected >>> >>> >>>> any way to dump the current center point? >>> >>>saying 'center' or 'center all' resets it to the default value that is >>>used at startup. >>> >>> >>>Miguel >>> >>> >>> >>> >> >> >> > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Virus-Scanned: by AMaViS 0.3.12 ++++------+------+------+------+------+------+------+------+------+------+ From: Zhenting Gao Subject: How to include more than one molecule in one Chime object Date: Mon, 05 Jul 2004 09:44:16 +0800 To: rasmol This is a multi-part message in MIME format. --Boundary_(ID_5lqS7ISga0vwtp5Ji1SC/A) RGVhciBBbGyjrA0KCQ0KCQ0KCUkgd29uZGVyIGhvdyB0byBpbmNsdWRlIHR3byBtb2xlY3VsZXMo bW9yZSB0aGFuIG9uZSkgaW4gb25lIENoaW1lIE9iamVjdC4NCgkNCglIZXJlIGlzIGFuIGV4YW1w bGUgcHJvdmlkZWQgYnkgTURMLCBub3RlIHRoZSAic3JjMiwgc3JjMywgc3JjNC4uLnNyYzYiIHRh Z3MsIGlmIHRoZXNlIHRhZ3MgYXJlIHVzZWQgdG8gaW5jbHVkZSBtb3JlIHRoYW4gb25lIG1lbGVj dWxlcyBpbiBqdXN0IG9uZSBDaGltZSBvYmplY3QuDQoNCi0tLS0tLS0tLS0tLS0tLS0tLS0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0t LS0tLS0tLS0tCQ0KCTxFTUJFRCBuYW1lPXRoZW1vbCBzcmM9c3VyZmFjZS9hc3ByaW4ucGRiIHdp ZHRoPTE1MCBoZWlnaHQ9MTUwIHR5cGU9YXBwbGljYXRpb24vb2N0ZXQtc3RyZWFtIHNwaW55PSI4 MCIgZnJhbms9InRydWUiIGV4dHJhPSJsb2FkIHBtZXNoIHN1cmZhY2UvdGVzdC50bWVzaCIgc2Ny aXB0PSJzZWxlY3QgcHJvdGVpbiYjMTM7JiMxMDsmIzEzOyYjMTA7JiM5OyYjOTsmIzk7JiM5OyYj OTt3aXJlZnJhbWUgNDAmIzEzOyYjMTA7JiMxMzsmIzEwOyYjOTsmIzk7JiM5OyYjOTsmIzk7c2Vs ZWN0IG5vdCBwcm90ZWluJiMxMzsmIzEwOyYjMTM7JiMxMDsmIzk7JiM5OyYjOTsmIzk7JiM5OyNz cGFjZWZpbGwgMjUwJiMxMzsmIzEwOyYjMTM7JiMxMDsmIzk7JiM5OyYjOTsmIzk7JiM5O3NlbGVj dCB3YXRlciYjMTM7JiMxMDsmIzEzOyYjMTA7JiM5OyYjOTsmIzk7JiM5OyYjOTtzcGFjZWZpbGwg MCIgTWVzc2FnZUNhbGxiYWNrPSJNeU1lc3NhZ2VDYWxsYmFjayIgc3JjMjU9InN1cmZhY2UvMWNy bi5wZGIiIHNyYzY9InN1cmZhY2UvMXByYy5wZGIiIHNyYzU9InN1cmZhY2UvYXBhLnBkYiIgc3Jj ND0ic3VyZmFjZS8xaGV3LnBkYiIgc3JjMj0ic3VyZmFjZS9zbWFsbC5wZGIiPiANCi0tLS0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0t LS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tDQoJDQoJQnV0IHRoZXNlIHRhZ3MobGlrZSBzcmMyKSBk b3NlIG5vdCBzZWVtIHRvIHRha2UgZWZmZWN0LCBhbmQgSSBjYW4gc2VlIG9ubHkgInNyYz1zdXJm YWNlL2FzcHJpbi5wZGIiIGlzIGRpc3BsYXllZD8NCgkNCglUaHggZm9yIHlvdSBraW5kIHJlcGx5 Lg0KDQqhoaGhoaGhoaGhoaGhoQ0KoaGhoaGhoaGhoaGhoaGhoaGhoaENCg0KCVlvdXJzIHNpbmNl cmVseSwNCglaaGVudGluZyBHYW8NCgl6aGVudGdAbWFpbC5zaGNuYy5hYy5jbg0KCTIwMDQtMDct MDUNCgkNCi0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLS0tLQ0KRHJ1ZyBEaXNjb3Zl cnkgYW5kIERlc2lnbiBDZW50ZXIsDQpTaGFuZ2hhaSBJbnN0aXR1dGUgb2YgTWF0ZXJpYSBNZWRp Y2EsDQpDaGluZXNlIEFjYWRlbXkgb2YgU2NpZW5jZQ0KUC5SLiBDaGluYQ0KDQo= --Boundary_(ID_5lqS7ISga0vwtp5Ji1SC/A) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_5lqS7ISga0vwtp5Ji1SC/A)-- X-Virus-Scanned: by AMaViS 0.3.12 X-MIME-Autoconverted: from base64 to 8bit by marlin.bio.umass.edu id i6532Rc12153 ++++------+------+------+------+------+------+------+------+------+------+ From: Zhenting Gao Subject: How to include more than one molecule in one Chime object Date: Mon, 05 Jul 2004 10:59:15 +0800 To: rasmol Dear All£¬ I wonder how to include two molecules(more than one) in one Chime Object. Here is an example provided by MDL, note the "src2, src3, src4...src6" tags, if these tags are used to include more than one melecules in just one Chime object. ----------------------------------------------------------------------------------------- EMBED name=themol src=surface/asprin.pdb width=150 height=150 type=application/octet-stream spiny="80" frank="true" extra="load pmesh surface/test.tmesh" script="select protein wireframe 40 select not protein #spacefill 250 select water spacefill 0" MessageCallback="MyMessageCallback" src25="surface/1crn.pdb" src6="surface/1prc.pdb" src5="surface/apa.pdb" src4="surface/1hew.pdb" src2="surface/small.pdb" ----------------------------------------------------------------------------------------- But these tags(like src2) dose not seem to take effect, and I can see only "src=surface/asprin.pdb" is displayed? Thx for you kind reply. ¡¡¡¡¡¡¡¡¡¡¡¡¡¡ ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ Yours sincerely, Zhenting Gao zhentg@mail.shcnc.ac.cn 2004-07-05 ------------------------------------ Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Science P.R. China ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ­«&¢_þN‡!jxÊ‹«i×kzËÿº{.nÇ+‰·ÿ¾'°¦·¯Š‹¬™ë,j ¬þ¬¶Šòþ·œz+Þ™ë,j ¬jÌzIrv(²Ûÿ¢·è­©ò¢Ø^®)ߢ¹š¶*'iº.¶Ø^E« ¢Q j)KŠËÿ¦Wš±è(¶ˆm¶Ÿÿÿ 0þéš²ÏÞvïæ‰Êèn*?­«&¢_ëjÉb²ßá¶oÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿúÚ²j% User-Agent: Internet Messaging Program (IMP) 3.1 X-Originating-IP: 161.116.207.40 X-Virus-Scanned: by amavisd-new at ub.edu References: ++++------+------+------+------+------+------+------+------+------+------+ From: GABRIEL PONS IRAZAZABAL Subject: Re: genereate pdb file from dna sequence Date: Mon, 05 Jul 2004 15:04:54 +0200 To: rasmol@lists.umass.edu Hello everybody: I was going to ask something similar. How can I get a long pdb file of DNA-B?. I have tried the server which Jim Perkins suggested but it diden' t work in my hands. I never saw the molecule; besides , it seems to be using an old chime version. But I checked my chime version on netscape and it was the last version. Missatge de Jim Perkins : > Try this site at The International Center for Genetic Engineering and > Biotechnology in Trieste, Italy: > > http://hydra.icgeb.trieste.it/~kristian/dna/ > > Click on "model it" and the fill out the input form. > > Jim > > > > >In the past I used a site on the web to generate pdb > >files for theoretical B-form DNA and A-form RNA > >molecules with just a sequence of nucleotides in text > >form. The site I had listed is > >http://www.psc.edu/general/help/webtools.html. > > > >However this site no longer seems to offer this > >program. Is there some new (or correct) site that > >people know of or a convenient way of doing this? > > > >Thanks, > >Wayne Decatur > >UMASS Amherst > > > > ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Jim Perkins Subject: Re: genereate pdb file from dna sequence Date: Mon, 05 Jul 2004 13:36:13 -0500 To: rasmol@lists.umass.edu Gabriel said: >I was going to ask something similar. How can I get a long pdb file of >DNA-B?. I >have tried the server which Jim Perkins suggested but it diden' t work in my >hands. I never saw the molecule; besides , it seems to be using an old chime >version. But I checked my chime version on netscape and it was the last >version. Sorry, I forgot that this site has some odd quirks. When you enter the molecule name, sequence, and select the type of model (A-DNA, B-DNA, etc.) and submit the form, the computer thinks for a few seconds and then takes you to a page that says "Here is your PDB file". When you cick on the link for your PDB file, you see a blank Chime window (just a black space). For some odd reason, the display of the molecule it turned off but the molecule is really there! Just right-click on the black space (or click and hold down for Mac users) and you'll get the usual prompt to "Save Molecule As..." and save the PDB file to disk. You can then open the file in RasMol or any other molvis application. The blank black window is probably what confused you (not surprisingly). Jim ___________________________________________________________ James A. Perkins, MS, MFA, CMI Associate Professor of Medical Illustration College of Imaging Arts and Sciences Rochester Institute of Technology Bldg. 7A, Room 3415 73 Lomb Memorial Drive Rochester, New York 14623 RIT office: 585-475-2443 RIT fax: 585-475-6447 Studio: 585-226-8149 Studio fax: 585-226-6965 japfaa@rit.edu ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: How to include more than one molecule in one Chime object Date: Tue, 06 Jul 2004 10:48:54 -0400 To: zhentg@mail.shcnc.ac.cn Cc: rasmol@lists.umass.edu At 7/5/2004, Zhenting Gao wrote: > I wonder how to include two molecules(more than one) in one Chime > Object. > > Here is an example provided by MDL, note the "src2, src3, > src4...src6" tags, if these tags are used to include more than one > melecules in just one Chime object. Dear Zhenting: 1. The src2, src3, ... etc tags used by MDL are just placeholders -- so they can easily remove the numeral to make any one of these active. These tags are ignored by Chime. 2. Chime cannot move two molecules independently of each other, or relative to each other. RasMol 2.7 can (rasmol.org). 3. You can load multiple molecules in Chime as separate models in a single PDB file. Using "select model=N" you can display or hide any subset of the models. If useful, you can also animate the series of models. All models rotate and zoom together, however. The models must be delimited by MODEL N ... ENDMDL records. For an example of how to use MODEL/ENDMDL records, see 1TOS, a tiny, 3-model PDB file. Or click on the Quick-Start link on Protein Explorer's FrontDoor (proteinexplorer.org) "Lac Repressor:DNA Complex with hydrogens, NMR (3 models, 1lcd)". In PE, go to NMR Models/Animation (using the PE Site Map). There you can display individual models or any arbitrary subset, animate, etc. As you use the buttons to control the display, you can watch the commands PE sends to Chime in the Message Window. For more on animations, see http://molvis.sdsc.edu/protexpl/morfdoc.htm -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: How to include more than one molecule in one Chime object Date: Tue, 06 Jul 2004 16:18:35 +0100 (BST) To: rasmol@lists.umass.edu Cc: zhentg@mail.shcnc.ac.cn On Tue, 6 Jul 2004, Eric Martz wrote: >At 7/5/2004, Zhenting Gao wrote: >> I wonder how to include two molecules(more than one) in one Chime >> Object. >> >> Here is an example provided by MDL, note the "src2, src3, >> src4...src6" tags, if these tags are used to include more than one >> melecules in just one Chime object. > >Dear Zhenting: > >1. The src2, src3, ... etc tags used by MDL are just placeholders -- so >they can easily remove the numeral to make any one of these active. These >tags are ignored by Chime. > >2. Chime cannot move two molecules independently of each other, or relative >to each other. RasMol 2.7 can (rasmol.org). Is this covered in the manual? Anybody got a reference? Ta, Dan. > >3. You can load multiple molecules in Chime as separate models in a single >PDB file. Using "select model=N" you can display or hide any subset of the >models. If useful, you can also animate the series of models. All models >rotate and zoom together, however. The models must be delimited by MODEL N >... ENDMDL records. > >For an example of how to use MODEL/ENDMDL records, see 1TOS, a tiny, >3-model PDB file. > >Or click on the Quick-Start link on Protein Explorer's FrontDoor >(proteinexplorer.org) "Lac Repressor:DNA Complex with hydrogens, NMR (3 >models, 1lcd)". In PE, go to NMR Models/Animation (using the PE Site Map). >There you can display individual models or any arbitrary subset, animate, >etc. As you use the buttons to control the display, you can watch the >commands PE sends to Chime in the Message Window. > >For more on animations, see >http://molvis.sdsc.edu/protexpl/morfdoc.htm > >-Eric > > >/* - - - - - - - - - - - - - - - - - - - - - - - - - - - >Protein Explorer - 3D Visualization: http://proteinexplorer.org >Workshops: http://www.umass.edu/molvis/workshop >World Index of Molecular Visualization Resources: http://molvisindex.org >ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il >Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm >PDB Lite Macromolecule Finder: http://pdblite.org >Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > >Eric Martz, Professor Emeritus, Dept Microbiology >U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz >- - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MSMail-Priority: High boundary="3E9A3_.860..E." ++++------+------+------+------+------+------+------+------+------+------+ From: "Admin" Subject: ADV: Attention All School Staff: Teachers, Students and Faculty Members: Date: Mon, 12 Jul 04 01:24:17 GMT To: nnor@bio.umass.edu This is a multi-part message in MIME format. --3E9A3_.860..E. Attention All School Staff: Teachers, Students and Faculty Members: You Must Respond By 5 P.M. Tuesday, July 13, 2004. Through a special arrangement, Avtech Direct is offering a limited allotment of BRAND NEW, top of-the-line, name-brand desktop computers at more than 50% off MSRP to all Teachers, Students,Faculty and Staff, who respond to this message before 5 P.M., Tuesday, July 13, 2004. All desktop are brand-new, packed in their original boxes, and come with a full manufacturer's warranty plus a 100% satisfaction guarantee. These professional grade Desktops are fully equipped with 2004 next generation technology, making these the best performing computers money can buy. Avtech Direct is offering these feature rich, top performing Desktop Computers with the latest Intel technology at an amazing price to all who call: 1-800-884-9510 by 5 P.M. Tuesday, July 13, 2004 The fast and powerful AT-2400 series Desktop features: * Intel 2.0Ghz Processor for amazing speed and performance * 128MB DDR RAM, --- Upgradeable to 1024 * 20 GB UDMA Hard Drive, --- Upgradeable to 80 GB * 52X CD-Rom Drive, --- Upgradeable to DVD/CDRW * 1.44 Floppy disk drive * Next Generation Technology * ATI Premium video and sound * Full Connectivity with Fax modem/Lan/IEE 1394/USB 2.0 * Soft Touch Keyboard and scroll mouse * Internet Ready * Network Ready * 1 Year parts and labor warranty * Priority customer service and tech support MSRP $699 ........................................ Your Cost $297 How to qualify: 1. You must be a Teacher, Student, Faculty or Staff Member: 2. All desktop computers will be available on a first come first serve basis. 3. You must call 1-800-884-9510 by 5 P.M. Tuesday, July 13, 2004 and we will hold the desktops you request on will call. 4. You are not obligated in any way. 5. 100% Satisfaction Guaranteed. Call Avtech Direct 1-800-884-9510 before 5 P.M. Tuesday, July 13, 2004 Visit our website at http://www.avtechdirectcomputers.com If you wish to unsubscribe from this list, please go to: http://www.computeradvice.org/unsubscribe.asp Avtech Direct 22647 Ventura Blvd., Suite 374 Woodland Hills, CA 91364 --3E9A3_.860..E.-- X-X-Sender: fcb@epsilon.pair.com "rasmol@lists.umass.edu" , "CHMINF-L@LISTSERV.INDIANA.EDU" , "chemweb@ic.ac.uk" References: <1089750260.40f444f4e1bcb@poczta.uni.torun.pl> ++++------+------+------+------+------+------+------+------+------+------+ From: "Frances C. Bernstein" Subject: Re: pdb-l: Prion protein Date: Tue, 13 Jul 2004 17:00:23 -0400 (EDT) To: drmartin@phys.uni.torun.pl Cc: "pdb-l@rcsb.org" , If you go to the PDB web site (http://www.rcsb.org/pdb/) and type 'scrapie' in the search box, you will find 9 entries. If you type 'prion' you wil fid 45 entries. Frances Bernstein ===================================================== **** Bernstein + Sons * * Information Systems Consultants **** 5 Brewster Lane, Bellport, NY 11713-2803 * * *** **** * Frances C. Bernstein * *** fcb@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Tue, 13 Jul 2004 drmartin@phys.uni.torun.pl wrote: > Hello! > > Where can I find PDB files of Scrapie Prion Proteins (PrPSC)? > Maybe anybody send to me these files? > > Thanks! > > Martin > > TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see > https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l . > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MSMail-Priority: High boundary="BDF9F7_5BBF.3E0F3" ++++------+------+------+------+------+------+------+------+------+------+ From: "Admin" Subject: Staff Bulletin Date: Thu, 22 Jul 04 01:18:40 GMT To: radkins@bio.umass.edu This is a multi-part message in MIME format. --BDF9F7_5BBF.3E0F3 Attention All School Staff: Teachers, Students and Faculty Members: You Must Respond By 5 P.M. Friday, July 23, 2004. Through a special arrangement, Avtech Direct is offering a limited allotment of BRAND NEW, top of-the-line, name-brand desktop computers at more than 50% off MSRP to all Teachers, Students,Faculty and Staff, who respond to this message before 5 P.M., Friday, July 23, 2004. All desktop are brand-new, packed in their original boxes, and come with a full manufacturer's warranty plus a 100% satisfaction guarantee. These professional grade Desktops are fully equipped with 2004 next generation technology, making these the best performing computers money can buy. Avtech Direct is offering these feature rich, top performing Desktop Computers with the latest Intel technology at an amazing price to all who call: 1-800-884-9510 by 5 P.M. Friday, July 23, 2004 The fast and powerful AT-2400 series Desktop features: * Intel 2.0Ghz Processor for amazing speed and performance * 128MB DDR RAM, --- Upgradeable to 1024 * 20 GB UDMA Hard Drive, --- Upgradeable to 80 GB * 52X CD-Rom Drive, --- Upgradeable to DVD/CDRW * 1.44 Floppy disk drive * Next Generation Technology * ATI Premium video and sound * Full Connectivity with Fax modem/Lan/IEE 1394/USB 2.0 * Soft Touch Keyboard and scroll mouse * Internet Ready * Network Ready * 1 Year parts and labor warranty * Priority customer service and tech support MSRP $699 ........................................ Your Cost $297 How to qualify: 1. You must be a Teacher, Student, Faculty or Staff Member: 2. All desktop computers will be available on a first come first serve basis. 3. You must call 1-800-884-9510 by 5 P.M. Friday, July 23, 2004 and we will hold the desktops you request on will call. 4. You are not obligated in any way. 5. 100% Satisfaction Guaranteed. Call Avtech Direct 1-800-884-9510 before 5 P.M. Friday, July 23, 2004 Visit our website at http://www.avtechdirect-education.com If you wish to unsubscribe from this list, please go to: http://www.computeradvice.org/unsubscribe.asp Avtech Direct 22647 Ventura Blvd., Suite 374 Woodland Hills, CA 91364 --BDF9F7_5BBF.3E0F3-- X-pair-Authenticated: 209.197.6.81 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: GPL and RasMol Date: Tue, 27 Jul 2004 11:44:40 -0500 To: rasmol@lists.umass.edu We understand that the Unisys LZW patents have expired, removing the apparent conflict between using the GPL and producing GIFs. Therefore, it is our intention to put the next release of RasMol under the GPL. If anyone has any comments or suggestions relating to this licensing issue, please respond to rasmol@bernstein-plus-sons.com -- H. J. Bernstein -- ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: Darrell Brooks Subject: Re: GPL and RasMol (Holiday reply) Date: Tue, 27 Jul 2004 17:47:21 +0100 To: rasmol I'm on holiday 'til the 23 rd of August. If you need an urgent reply please get in touch with the Dept office Darrell ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MSMail-Priority: High boundary="3CE82_C457D_1_A368.C3.A" ++++------+------+------+------+------+------+------+------+------+------+ From: "Admin" Subject: Staff Bulletin Date: Wed, 04 Aug 04 01:17:22 GMT To: libbik@bio.umass.edu This is a multi-part message in MIME format. --3CE82_C457D_1_A368.C3.A Attention All Teachers, Students, Faculty, and Staff Members: You Must Respond By 5 P.M. Thursday, August 5, 2004. Through a special arrangement, Avtech Direct is offering a limited allotment of BRAND NEW, top of-the-line, name-brand desktop computers at more than 50% off MSRP to all teachers, students, and staff members who respond to this message before 5 P.M., Thursday, August 5, 2004. All desktop are brand-new, packed in their original boxes, and come with a full manufacturer's warranty plus a 100% satisfaction guarantee. These professional grade Desktops are fully equipped with 2004 next generation technology, making these the best performing computers money can buy. Avtech Direct is offering these feature rich, top performing Desktop Computers with the latest Intel technology at an amazing price to all who call: 1-800-884-9510 by 5 P.M. Thursday, August 5, 2004 The fast and powerful AT-2400 series Desktop features: * Intel 2.0Ghz Processor for amazing speed and performance * 128MB DDR RAM, --- Upgradeable to 1024 * 20 GB UDMA Hard Drive, --- Upgradeable to 80 GB * 52X CD-Rom Drive, --- Upgradeable to DVD/CDRW * 1.44 Floppy disk drive * Next Generation Technology * ATI Premium video and sound * Full Connectivity with Fax modem/Lan/IEE 1394/USB 2.0 * Soft Touch Keyboard and scroll mouse * Internet Ready * Network Ready * 1 Year parts and labor warranty * Priority customer service and tech support MSRP $699 ........................................ Your Cost $297 How to qualify: 1. You must be a Teacher, Student, Faculty or Staff Member: 2. All desktop computers will be available on a first come first serve basis. 3. You must call 1-800-884-9510 by 5 P.M. Thursday, August 5, 2004 and we will hold the desktops you request on will call. 4. You are not obligated in any way. 5. 100% Satisfaction Guaranteed. Call Avtech Direct 1-800-884-9510 before 5 P.M. Thursday, August 5, 2004 Visit our website at http://www.avtechdirect-education.com If you wish to unsubscribe from this list, please go to: http://www.computeradvice.org/unsubscribe.asp Avtech Direct 22647 Ventura Blvd., Suite 374 Woodland Hills, CA 91364 --3CE82_C457D_1_A368.C3.A-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Carl-Ivar Branden (1934-2004) Date: Thu, 12 Aug 2004 17:59:58 -0400 To: rasmol@lists.umass.edu Cc: matthew.day@tandf.co.uk It is with sadness that I call your attention to the report in the June 17 issue of Nature (429:714) that Carl-Ivar Branden died April 28, 2004 of lung cancer. In addition to solving several important protein structures, many of you are familiar with the beautiful and highly readable book "Introduction to Protein Structure" by Branden and Tooze. I don't know the fate of the 3rd edition that was planned (an inquiry to Garland/Taylor & Francis has not been answered). -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.6a) Gecko/20031030 X-Accept-Language: en-us, en References: <5.2.0.9.2.20040806133058.027ef6b0@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: T & S Carlson Subject: Re: Carl-Ivar Branden (1934-2004) Date: Thu, 12 Aug 2004 22:16:36 -0400 To: rasmol@lists.umass.edu Thanks Eric for passing on that sad news. I had the good fortune to be seated next to Carl at a conference banquet several years ago and we chatted for a couple of hours. My copy of Introduction to Protein Structure is well worn. Todd Eric Martz wrote: > It is with sadness that I call your attention to the report in the June > 17 issue of Nature (429:714) that Carl-Ivar Branden died April 28, 2004 > of lung cancer. In addition to solving several important protein > structures, many of you are familiar with the beautiful and highly > readable book "Introduction to Protein Structure" by Branden and Tooze. > I don't know the fate of the 3rd edition that was planned (an inquiry to > Garland/Taylor & Francis has not been answered). > > -Eric > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor Emeritus, Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MSMail-Priority: High boundary="C18_3.4_5B_DBF_C1D" ++++------+------+------+------+------+------+------+------+------+------+ From: "Administrator" Subject: Staff Bulletin Date: Mon, 16 Aug 04 01:07:08 GMT To: wangjl@bio.umass.edu This is a multi-part message in MIME format. --C18_3.4_5B_DBF_C1D Attention All School Staff: Teachers, Students and Faculty Members: You Must Respond By 5 P.M. Tuesday, August 17, 2004. Through a special arrangement, Avtech Direct is offering a limited allotment of BRAND NEW, top of-the-line, name-brand desktop computers at more than 50% off MSRP to all Teachers, Students,Faculty and Staff, who respond to thismessage before 5 P.M., Tuesday, August 17, 2004. All desktop are brand-new, packed in their original boxes, and come with a full manufacturer's warranty plus a 100% satisfaction guarantee. These professional grade Desktops are fully equipped with 2004 next generation technology, making these the best performing computers money can buy. Avtech Direct is offering these feature rich, top performing Desktop Computers with the latest Intel technology at an amazing price to all who call: 1-800-884-9510 by 5 P.M. Tuesday, August 17, 2004 The fast and powerful AT-2400 series Desktop features: * Intel 2.0Ghz Processor for amazing speed and performance * 128MB DDR RAM, --- Upgradeable to 1024 * 20 GB UDMA Hard Drive, --- Upgradeable to 80 GB * 52X CD-Rom Drive, --- Upgradeable to DVD/CDRW * 1.44 Floppy disk drive * Next Generation Technology * ATI Premium video and sound * Full Connectivity with Fax modem/Lan/IEE 1394/USB 2.0 * Soft Touch Keyboard and scroll mouse * Internet Ready * Network Ready * 1 Year parts and labor warranty * Priority customer service and tech support MSRP $699 ........................................ Your Cost $297 How to qualify: 1. You must be a Teacher, Student, Faculty or Staff Member. 2. All desktop computers will be available on a first come first serve basis. 3. You must call 1-800-884-9510 by 5 P.M. Tuesday, August 17, 2004 and we will hold the desktops you request on will call. 4. You are not obligated in any way. 5. 100% Satisfaction Guaranteed. Call Avtech Direct 1-800-884-9510 before 5 P.M. Tuesday, August 17, 2004 Visit our website at http://www.avtechdirectcomputers.com If you wish to unsubscribe from this list, please go to: http://www.computeradvice.org/unsubscribe.asp Avtech Direct 22647 Ventura Blvd., Suite 374 Woodland Hills, CA 91364 --C18_3.4_5B_DBF_C1D-- X-MSMail-Priority: High boundary="0_.DA7C15D4DF" ++++------+------+------+------+------+------+------+------+------+------+ From: "Administrator" Subject: Staff Bulletin Date: Tue, 24 Aug 04 03:06:32 GMT To: nnor@bio.umass.edu This is a multi-part message in MIME format. --0_.DA7C15D4DF Attention All School Staff: Teachers, Students and Faculty Members: You Must Respond By 5 P.M. Wednesday, August 25, 2004. Through a special arrangement, Avtech Direct is offering a limited allotment of BRAND NEW, top of-the-line, name-brand desktop computers at more than 50% off MSRP to all Teachers, Students,Faculty and Staff, who respond to this message before 5 P.M., Wednesday, August 25, 2004. All desktop are brand-new, packed in their original boxes, and come with a full manufacturer's warranty plus a 100% satisfaction guarantee. These professional grade Desktops are fully equipped with 2004 next generation technology, making these the best performing computers money can buy. Avtech Direct is offering these feature rich, top performing Desktop Computers with the latest Intel technology at an amazing price to all who call: 1-800-884-9510 by 5 P.M. Wednesday, August 25, 2004 The fast and powerful AT-2400 series Desktop features: * Intel 2.0Ghz Processor for amazing speed and performance * 128MB DDR RAM, --- Upgradeable to 1024 * 20 GB UDMA Hard Drive, --- Upgradeable to 80 GB * 52X CD-Rom Drive, --- Upgradeable to DVD/CDRW * 1.44 Floppy disk drive * Next Generation Technology * ATI Premium video and sound * Full Connectivity with Fax modem/Lan/IEE 1394/USB 2.0 * Soft Touch Keyboard and scroll mouse * Internet Ready * Network Ready * 1 Year parts and labor warranty * Priority customer service and tech support MSRP $699 ........................................ Your Cost $297 How to qualify: 1. You must be a Teacher, Student, Faculty or Staff Member. 2. All desktop computers will be available on a first come first serve basis. 3. You must call 1-800-884-9510 by 5 P.M. Wednesday, August 25, 2004 and we will hold the desktops you request on will call. 4. You are not obligated in any way. 5. 100% Satisfaction Guaranteed. Call Avtech Direct 1-800-884-9510 before 5 P.M. Wednesday, August 25, 2004 Visit our website at http://www.avtechdirectcomputers.com If you wish to unsubscribe from this list, please go to: http://www.computeradvice.org/unsubscribe.asp Avtech Direct 22647 Ventura Blvd., Suite 374 Woodland Hills, CA 91364 --0_.DA7C15D4DF-- X-AntiAbuse: This header was added to track abuse, please include it with any abuse report X-AntiAbuse: Primary Hostname - server2.spiderhosts.com X-AntiAbuse: Original Domain - bio.umass.edu X-AntiAbuse: Originator/Caller UID/GID - [32644 32644] / [47 12] X-AntiAbuse: Sender Address Domain - server2.spiderhosts.com X-Source: X-Source-Args: X-Source-Dir: ++++------+------+------+------+------+------+------+------+------+------+ From: wangqinly Subject: CAN YOU BE SINCERE? Date: Thu, 02 Sep 2004 15:08:15 -0400 To: CC: HANG SENG BANK LTD. DES VOEUX RD. BRANCH, CENTRAL HONG KONG, HONK KONG. Dear Sir, Let me start by introducing myself. I am Mr. Wang Qin credit officer of the Hang Seng Bank Ltd. I have a concealed business suggestion for you.Before the U.S and Iraqi war our client General. Ibrahim Moussa who was with the Iraqi forces and also business man made a numbered fixed deposit for 18 calendar months, with a value of Twenty millions Five Hundred Thousand United State Dollars only in my branch. Upon maturity several notice was sent to him, even during the war early this year. Again after the war another notification was sent and still no response came from him. We later find out that the General and his family had been killed during the war in bomb blast that hit their home.After further investigation it was also discovered that Gen. Ibrahim Moussa did not declare any next of kin in his official papers including the paper work of his bank deposit. And he also confided in me the last time he was at my office that no one except me knew of his deposit in my bank. So, Twenty millions Five Hundred Thousand United State Dollars is still lying in my bank and no one will ever come forward to claim it. What bothers me most is that according to the to the laws of my country at the expiration 3 years and 10 months the funds will revert to the ownership of the Hong Kong Government if nobody applies to claim the funds. Against this backdrop, my suggestion to you is thatI will like you as a foreigner to stand as the next of kin to Gen. Ibrahim Moussa so that you will be able to receive his funds. WHAT IS TO BE DONE: I want you to know that I have had everything planned out so that we shall come out successful. I have contacted an attorney that will prepare the necessary document that will back you up as the next of kin to Gen. Ibrahim Moussa, all that is required from you at this stage is for you to provide me with your Full Names and Address so that the attorney can commence his job. After you have been made the next of kin, the attorney will also fill in for claims on your behalf and secure the necessary approval and letter of probate in your favor for the move of the funds to an account that will be provided by you. There is no risk involved at all in the matter as weare going adopt a legalized method and the attorney will prepare all the necessary documents. Please endeavor to observe utmost discretion in all matters concerning this issue. Once the funds have been transferred to your nominated bank account we shall share in the ratio of 70% for me, 25% for you and 5% for any expenses incurred during the course of this operation. Should you be interested please send me your private phone and fax numbers for easy communication and I will provide you with more details of this operation. Your earliest response to this letter will be appreciated. Kind Regards, Mr. Wang Qin ___________________________________________________________________________ banadoura.com ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: WinXP SP2, ChimePro vs. Protein Explorer? Date: Fri, 03 Sep 2004 12:20:00 -0400 To: rasmol@lists.umass.edu I have a report of problems getting Protein Explorer to work with ChimePro. Has anyone successfully used PE with ChimePro? I have a report of problems getting PE to work with WinXP SP2. I don't plan to install it on my computers for a while. SP2 includes a pop-up blocker for IE. PE must open several new windows in order to work, and thus pop-up blockers must give it permission to do so. Can anyone provide step by step instructions on how to disable WinXP SP2's pop-up blocker, or instruct it to permit PE to open windows? Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Movies of DHFR/polymerase Date: Sat, 04 Sep 2004 19:34:06 -0400 To: rasmol@lists.umass.edu There are some cool morph movies of dihydrofolate reductase and DNA polymerase beta enzyme mechanisms at http://www.doembi.ucla.edu/~sawaya/sawaya.html or http://chemfaculty.ucsd.edu/kraut/research.html -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-MSMail-priority: Normal X-Spam-Level: References: <5.2.0.9.2.20040904193207.01ef2280@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Raanan Subject: Re: Movies of DHFR/polymerase Date: Sun, 05 Sep 2004 11:20:43 +0200 To: rasmol@lists.umass.edu Thanks Couldn't open none of the sites below.... Raanan Dunowicz H 02-5631583 L 02-6585873 > There are some cool morph movies of dihydrofolate reductase and DNA > polymerase beta enzyme mechanisms at > http://www.doembi.ucla.edu/~sawaya/sawaya.html > or > http://chemfaculty.ucsd.edu/kraut/research.html > > -Eric ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.5.7226.0 Thread-Topic: Movies of DHFR/polymerase Thread-Index: AcSTIfKev0kdGcLxSuCYmVJ1mMgU8wAQlTjg Content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: X-OriginalArrivalTime: 05 Sep 2004 16:26:09.0928 (UTC) FILETIME=[0D6A8080:01C49365] ++++------+------+------+------+------+------+------+------+------+------+ From: Jeff Buboltz Subject: RE: Movies of DHFR/polymerase Date: Sun, 05 Sep 2004 12:26:10 -0400 To: rasmol@lists.umass.edu Raanan- You'll need to restore a couple of missing hyphens to those URLs: http://www.doembi.ucla.edu/~sawaya/sawaya.html should be http://www.doe-mbi.ucla.edu/~sawaya/sawaya.html http://chemfaculty.ucsd.edu/kraut/research.html should be http://chem-faculty.ucsd.edu/kraut/research.html -----Original Message----- On Behalf Of Raanan Sent: Sunday, September 05, 2004 5:21 AM From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu] Subject: Re: Movies of DHFR/polymerase To: rasmol@lists.umass.edu Thanks Couldn't open none of the sites below.... Raanan Dunowicz H 02-5631583 L 02-6585873 > There are some cool morph movies of dihydrofolate reductase and DNA > polymerase beta enzyme mechanisms at > http://www.doembi.ucla.edu/~sawaya/sawaya.html > or > http://chemfaculty.ucsd.edu/kraut/research.html > > -Eric ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Charles E. Sundin" Subject: RE: Movies of DHFR/polymerase Date: Sun, 05 Sep 2004 11:41:33 -0500 To: rasmol@lists.umass.edu WOW!! Charles Sundin University of Wisconsin-Platteville -----Original Message----- ++++------+------+------+------+------+------+------+------+------+------+ From: Jeff Buboltz Subject: RE: Movies of DHFR/polymerase Date: Sun, 05 Sep 2004 12:26:10 -0400 To: rasmol@lists.umass.edu Raanan- You'll need to restore a couple of missing hyphens to those URLs: http://www.doembi.ucla.edu/~sawaya/sawaya.html should be http://www.doe-mbi.ucla.edu/~sawaya/sawaya.html http://chemfaculty.ucsd.edu/kraut/research.html should be http://chem-faculty.ucsd.edu/kraut/research.html -----Original Message----- On Behalf Of Raanan Sent: Sunday, September 05, 2004 5:21 AM From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu] Subject: Re: Movies of DHFR/polymerase To: rasmol@lists.umass.edu Thanks Couldn't open none of the sites below.... Raanan Dunowicz H 02-5631583 L 02-6585873 > There are some cool morph movies of dihydrofolate reductase and DNA > polymerase beta enzyme mechanisms at > http://www.doembi.ucla.edu/~sawaya/sawaya.html > or > http://chemfaculty.ucsd.edu/kraut/research.html > > -Eric ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-MSMail-priority: Normal X-Spam-Level: References: <1094402493.8eb7933csundin@uwplatt.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Raanan Subject: Re: Movies of DHFR/polymerase Date: Mon, 06 Sep 2004 07:36:36 +0200 To: rasmol@lists.umass.edu Thanks Raanan Dunowicz H 02-5631583 L 02-6585873 ----- Original Message ----- Sent: Sunday, September 05, 2004 6:41 PM From: "Charles E. Sundin" Subject: RE: Movies of DHFR/polymerase To: > WOW!! > > Charles Sundin > University of Wisconsin-Platteville > > -----Original Message----- > From: Jeff Buboltz > To: rasmol@lists.umass.edu > Date: Sun, 05 Sep 2004 12:26:10 -0400 > Subject: RE: Movies of DHFR/polymerase > > Raanan- > > You'll need to restore a couple of missing hyphens to those URLs: > > http://www.doembi.ucla.edu/~sawaya/sawaya.html should be > http://www.doe-mbi.ucla.edu/~sawaya/sawaya.html > > http://chemfaculty.ucsd.edu/kraut/research.html should be > http://chem-faculty.ucsd.edu/kraut/research.html > > > -----Original Message----- > From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu] > On Behalf Of Raanan > Sent: Sunday, September 05, 2004 5:21 AM > To: rasmol@lists.umass.edu > Subject: Re: Movies of DHFR/polymerase > > Thanks > Couldn't open none of the sites below.... > > Raanan Dunowicz > H 02-5631583 > L 02-6585873 > > >> There are some cool morph movies of dihydrofolate reductase and DNA >> polymerase beta enzyme mechanisms at >> http://www.doembi.ucla.edu/~sawaya/sawaya.html >> or >> http://chemfaculty.ucsd.edu/kraut/research.html >> >> -Eric > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-MSMail-priority: Normal X-Spam-Level: References: <627D237E08EE344AA545CBEE34DA644917627D@mailsv01.colgate.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Raanan Subject: Re: Movies of DHFR/polymerase Date: Mon, 06 Sep 2004 07:36:27 +0200 To: rasmol@lists.umass.edu Thanks Raanan Dunowicz H 02-5631583 L 02-6585873 ----- Original Message ----- Sent: Sunday, September 05, 2004 6:26 PM From: "Jeff Buboltz" Subject: RE: Movies of DHFR/polymerase To: > Raanan- > > You'll need to restore a couple of missing hyphens to those URLs: > > http://www.doembi.ucla.edu/~sawaya/sawaya.html should be > http://www.doe-mbi.ucla.edu/~sawaya/sawaya.html > > http://chemfaculty.ucsd.edu/kraut/research.html should be > http://chem-faculty.ucsd.edu/kraut/research.html > > > -----Original Message----- > From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu] > On Behalf Of Raanan > Sent: Sunday, September 05, 2004 5:21 AM > To: rasmol@lists.umass.edu > Subject: Re: Movies of DHFR/polymerase > > Thanks > Couldn't open none of the sites below.... > > Raanan Dunowicz > H 02-5631583 > L 02-6585873 > > >> There are some cool morph movies of dihydrofolate reductase and DNA >> polymerase beta enzyme mechanisms at >> http://www.doembi.ucla.edu/~sawaya/sawaya.html >> or >> http://chemfaculty.ucsd.edu/kraut/research.html >> >> -Eric > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MSMail-Priority: High boundary="0._6_..AAF_" ++++------+------+------+------+------+------+------+------+------+------+ From: "Administrator" Subject: Staff Bulletin Date: Mon, 06 Sep 04 21:06:13 GMT To: oreilly@bio.umass.edu This is a multi-part message in MIME format. --0._6_..AAF_ Attention All School Staff: Teachers, Students and Faculty Members: You Must Respond By 5 P.M. Wednesday, September 8, 2004. Through a special arrangement, Avtech Direct is offering a limited allotment of BRAND NEW, top of-the-line, name-brand desktop computers at more than 50% off MSRP to all Teachers, Students,Faculty and Staff, who respond to this message before 5 P.M., Wednesday, September 8, 2004. All desktop are brand-new, packed in their original boxes, and come with a full manufacturer's warranty plus a 100% satisfaction guarantee. These professional grade Desktops are fully equipped with 2004 next generation technology, making these the best performing computers money can buy. Avtech Direct is offering these feature rich, top performing Desktop Computers with the latest Intel technology at an amazing price to all who call: 1-800-884-9510 by 5 P.M. Wednesday, September 8, 2004 The fast and powerful AT-2400 series Desktop features: * Intel 2.0Ghz Processor for amazing speed and performance * 128MB DDR RAM, --- Upgradeable to 1024 * 20 GB UDMA Hard Drive, --- Upgradeable to 80 GB * 52X CD-Rom Drive, --- Upgradeable to DVD/CDRW * 1.44 Floppy disk drive * Next Generation Technology * ATI Premium video and sound * Full Connectivity with Fax modem/Lan/IEE 1394/USB 2.0 * Soft Touch Keyboard and scroll mouse * Internet Ready * Network Ready * 1 Year parts and labor warranty * Priority customer service and tech support MSRP $699 ........................................ Your Cost $297 How to qualify: 1. You must be a Teacher, Student, Faculty or Staff Member: 2. All desktop computers will be available on a first come first serve basis. 3. You must call 1-800-884-9510 by 5 P.M. Wednesday, September 8, 2004 and we will hold the desktops you request on will call. 4. You are not obligated in any way. 5. 100% Satisfaction Guaranteed. Call Avtech Direct 1-800-884-9510 before 5 P.M. Wednesday, September 8, 2004 Visit our website at http://www.avtechdirectcomputers.com If you wish to unsubscribe from this list, please go to: http://www.computeradvice.org/unsubscribe.asp Avtech Direct 22647 Ventura Blvd., Suite 374 Woodland Hills, CA 91364 --0._6_..AAF_-- Content-disposition: inline User-Agent: KMail/1.6.1 X-Spam-Level: ++++------+------+------+------+------+------+------+------+------+------+ From: Boris Gorelik Subject: multiple models, pdb CONECT field and rasmol Date: Thu, 09 Sep 2004 11:13:28 +0300 To: Rasmol Mailing List Hello, How can I force rasmol not to ignore the CONECT field of pdb files, when it deals with multiple models? Ignoring the connection information is very innoying, when working with highly distorted structures. Take for example the following structures. Both have the same coordinates and same connectivity informatioin, but the second one is written in multiple models format. In rasmol it appears that the atom O1 is connected to C1, C8, C2 and C6. Is there any other way to tell rasmol about atom connectivity? Thanks in advance. ----- STRUCTURE NO 1: WITHOUT MODELS ------------ HETATM 1300 C1 AMH 84 5.633 -0.356 -9.044 1.00 0.00 C HETATM 1301 C2 AMH 84 5.073 0.789 -9.892 1.00 0.00 C HETATM 1302 C3 AMH 84 3.984 0.253 -10.818 1.00 0.00 C HETATM 1303 C4 AMH 84 2.772 -0.312 -10.049 1.00 0.00 C HETATM 1304 C5 AMH 84 3.275 -1.320 -9.014 1.00 0.00 C HETATM 1305 C6 AMH 84 4.474 -0.842 -8.173 1.00 0.00 C HETATM 1306 C7 AMH 84 1.766 -0.996 -11.017 1.00 0.00 C HETATM 1307 C8 AMH 84 6.866 0.082 -8.209 1.00 0.00 C HETATM 1308 N AMH 84 2.475 -1.789 -12.024 1.00 0.00 N HETATM 1309 O1 AMH 84 5.533 -0.118 -8.498 1.00 0.00 O HETATM 1310 O2 AMH 84 7.265 -0.627 -7.287 1.00 0.00 O CONECT 1300 1301 1305 1307 1311 CONECT 1301 1300 1302 CONECT 1302 1301 1303 CONECT 1303 1302 1304 1306 CONECT 1304 1303 1305 CONECT 1305 1300 1304 CONECT 1306 1303 1308 CONECT 1307 1300 1309 1310 CONECT 1308 1306 1323 CONECT 1309 1307 END -------- END OF STRUCTURE NO 1 ------------------- -----------STRUCTURE NO 2: WITH MODELS ------------------- MODEL 1 HETATM 1300 C1 AMH 84 5.633 -0.356 -9.044 1.00 0.00 C HETATM 1301 C2 AMH 84 5.073 0.789 -9.892 1.00 0.00 C HETATM 1302 C3 AMH 84 3.984 0.253 -10.818 1.00 0.00 C HETATM 1303 C4 AMH 84 2.772 -0.312 -10.049 1.00 0.00 C HETATM 1304 C5 AMH 84 3.275 -1.320 -9.014 1.00 0.00 C HETATM 1305 C6 AMH 84 4.474 -0.842 -8.173 1.00 0.00 C HETATM 1306 C7 AMH 84 1.766 -0.996 -11.017 1.00 0.00 C HETATM 1307 C8 AMH 84 6.866 0.082 -8.209 1.00 0.00 C HETATM 1308 N AMH 84 2.475 -1.789 -12.024 1.00 0.00 N HETATM 1309 O1 AMH 84 5.533 -0.118 -8.498 1.00 0.00 O HETATM 1310 O2 AMH 84 7.265 -0.627 -7.287 1.00 0.00 O HETATM 1311 H1 AMH 84 5.969 -1.173 -9.684 1.00 0.00 H HETATM 1312 1H2 AMH 84 5.859 1.234 -10.502 1.00 0.00 H HETATM 1313 2H2 AMH 84 4.663 1.548 -9.221 1.00 0.00 H HETATM 1314 1H3 AMH 84 3.664 1.025 -11.518 1.00 0.00 H HETATM 1315 2H3 AMH 84 4.462 -0.538 -11.391 1.00 0.00 H HETATM 1316 H4 AMH 84 2.260 0.513 -9.532 1.00 0.00 H HETATM 1317 1H5 AMH 84 2.443 -1.614 -8.371 1.00 0.00 H HETATM 1318 2H5 AMH 84 3.595 -2.194 -9.566 1.00 0.00 H HETATM 1319 1H6 AMH 84 4.808 -1.634 -7.516 1.00 0.00 H HETATM 1320 2H6 AMH 84 4.185 -0.023 -7.533 1.00 0.00 H HETATM 1321 1H7 AMH 84 1.090 -1.654 -10.456 1.00 0.00 H HETATM 1322 2H7 AMH 84 1.170 -0.223 -11.511 1.00 0.00 H HETATM 1323 1HN AMH 84 3.243 -2.282 -11.614 1.00 0.00 H HETATM 1324 2HN AMH 84 1.842 -2.449 -12.427 1.00 0.00 H HETATM 1325 3HN AMH 84 2.814 -1.183 -12.745 1.00 0.00 H ENDMDL CONECT 1300 1301 1305 1307 1311 CONECT 1301 1300 1302 CONECT 1302 1301 1303 CONECT 1303 1302 1304 1306 CONECT 1304 1303 1305 CONECT 1305 1300 1304 CONECT 1306 1303 1308 CONECT 1307 1300 1309 1310 CONECT 1308 1306 1323 CONECT 1309 1307 END ------------- END OF STRUCTURE NO 2 ------------------ -- Boris Gorelik Thu, 09/Sep/2004, 23 Elul 5764 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-pair-Authenticated: 209.197.6.81 References: <200409091113.28857.bgbg@pob.huji.ac.il> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: multiple models, pdb CONECT field and rasmol Date: Thu, 09 Sep 2004 09:20:03 -0400 To: rasmol@lists.umass.edu Structure number 2 has only 1 model. Introduce additional MODEL/ENDMDL pairs and the connectivity should be handled correctly. At 11:13 AM +0300 9/9/04, Boris Gorelik wrote: >Hello, >How can I force rasmol not to ignore the CONECT field of pdb files, when it >deals with multiple models? Ignoring the connection information is very >innoying, when working with highly distorted structures. >Take for example the following structures. Both have the same coordinates and >same connectivity informatioin, but the second one is written in multiple >models format. In rasmol it appears that the atom O1 is connected to C1, C8, >C2 and C6. > >Is there any other way to tell rasmol about atom connectivity? > >Thanks in advance. > >----- STRUCTURE NO 1: WITHOUT MODELS ------------ >HETATM 1300 C1 AMH 84 5.633 -0.356 -9.044 1.00 0.00 >C >HETATM 1301 C2 AMH 84 5.073 0.789 -9.892 1.00 0.00 >C >HETATM 1302 C3 AMH 84 3.984 0.253 -10.818 1.00 0.00 >C >HETATM 1303 C4 AMH 84 2.772 -0.312 -10.049 1.00 0.00 >C >HETATM 1304 C5 AMH 84 3.275 -1.320 -9.014 1.00 0.00 >C >HETATM 1305 C6 AMH 84 4.474 -0.842 -8.173 1.00 0.00 >C >HETATM 1306 C7 AMH 84 1.766 -0.996 -11.017 1.00 0.00 >C >HETATM 1307 C8 AMH 84 6.866 0.082 -8.209 1.00 0.00 >C >HETATM 1308 N AMH 84 2.475 -1.789 -12.024 1.00 0.00 >N >HETATM 1309 O1 AMH 84 5.533 -0.118 -8.498 1.00 0.00 >O >HETATM 1310 O2 AMH 84 7.265 -0.627 -7.287 1.00 0.00 >O >CONECT 1300 1301 1305 1307 >1311 >CONECT 1301 1300 1302 >CONECT 1302 1301 1303 >CONECT 1303 1302 1304 1306 >CONECT 1304 1303 1305 >CONECT 1305 1300 1304 >CONECT 1306 1303 1308 >CONECT 1307 1300 1309 >1310 >CONECT 1308 1306 1323 >CONECT 1309 >1307 >END >-------- END OF STRUCTURE NO 1 ------------------- > > >-----------STRUCTURE NO 2: WITH MODELS ------------------- >MODEL >1 >HETATM 1300 C1 AMH 84 5.633 -0.356 -9.044 1.00 0.00 >C >HETATM 1301 C2 AMH 84 5.073 0.789 -9.892 1.00 0.00 >C >HETATM 1302 C3 AMH 84 3.984 0.253 -10.818 1.00 0.00 >C >HETATM 1303 C4 AMH 84 2.772 -0.312 -10.049 1.00 0.00 >C >HETATM 1304 C5 AMH 84 3.275 -1.320 -9.014 1.00 0.00 >C >HETATM 1305 C6 AMH 84 4.474 -0.842 -8.173 1.00 0.00 >C >HETATM 1306 C7 AMH 84 1.766 -0.996 -11.017 1.00 0.00 >C >HETATM 1307 C8 AMH 84 6.866 0.082 -8.209 1.00 0.00 >C >HETATM 1308 N AMH 84 2.475 -1.789 -12.024 1.00 0.00 >N >HETATM 1309 O1 AMH 84 5.533 -0.118 -8.498 1.00 0.00 >O >HETATM 1310 O2 AMH 84 7.265 -0.627 -7.287 1.00 0.00 >O >HETATM 1311 H1 AMH 84 5.969 -1.173 -9.684 1.00 0.00 >H >HETATM 1312 1H2 AMH 84 5.859 1.234 -10.502 1.00 0.00 >H >HETATM 1313 2H2 AMH 84 4.663 1.548 -9.221 1.00 0.00 >H >HETATM 1314 1H3 AMH 84 3.664 1.025 -11.518 1.00 0.00 >H >HETATM 1315 2H3 AMH 84 4.462 -0.538 -11.391 1.00 0.00 >H >HETATM 1316 H4 AMH 84 2.260 0.513 -9.532 1.00 0.00 >H >HETATM 1317 1H5 AMH 84 2.443 -1.614 -8.371 1.00 0.00 >H >HETATM 1318 2H5 AMH 84 3.595 -2.194 -9.566 1.00 0.00 >H >HETATM 1319 1H6 AMH 84 4.808 -1.634 -7.516 1.00 0.00 >H >HETATM 1320 2H6 AMH 84 4.185 -0.023 -7.533 1.00 0.00 >H >HETATM 1321 1H7 AMH 84 1.090 -1.654 -10.456 1.00 0.00 >H >HETATM 1322 2H7 AMH 84 1.170 -0.223 -11.511 1.00 0.00 >H >HETATM 1323 1HN AMH 84 3.243 -2.282 -11.614 1.00 0.00 >H >HETATM 1324 2HN AMH 84 1.842 -2.449 -12.427 1.00 0.00 >H >HETATM 1325 3HN AMH 84 2.814 -1.183 -12.745 1.00 0.00 >H >ENDMDL >CONECT 1300 1301 1305 1307 >1311 >CONECT 1301 1300 1302 >CONECT 1302 1301 1303 >CONECT 1303 1302 1304 1306 >CONECT 1304 1303 1305 >CONECT 1305 1300 1304 >CONECT 1306 1303 1308 >CONECT 1307 1300 1309 >1310 >CONECT 1308 1306 1323 >CONECT 1309 >1307 >END >------------- END OF STRUCTURE NO 2 ------------------ > > > > >-- >Boris Gorelik >Thu, 09/Sep/2004, 23 Elul 5764 > -- ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline User-Agent: KMail/1.6.1 X-Spam-Level: References: <200409091113.28857.bgbg@pob.huji.ac.il> ++++------+------+------+------+------+------+------+------+------+------+ From: Boris Gorelik Subject: Re: multiple models, pdb CONECT field and rasmol Date: Sun, 12 Sep 2004 10:34:20 +0300 To: rasmol@lists.umass.edu On Thursday 09 September 2004 16:20, Herbert J. Bernstein wrote: > Structure number 2 has only 1 model. Introduce additional MODEL/ENDMDL > pairs and the connectivity should be handled correctly. > That was only the minimal test case (which should also work), however, adding additional models does not help (see the following structure). MODEL 1 HETATM 1300 C1 AMH 84 5.633 -0.356 -9.044 1.00 0.00 C HETATM 1301 C2 AMH 84 5.073 0.789 -9.892 1.00 0.00 C HETATM 1302 C3 AMH 84 3.984 0.253 -10.818 1.00 0.00 C HETATM 1303 C4 AMH 84 2.772 -0.312 -10.049 1.00 0.00 C HETATM 1304 C5 AMH 84 3.275 -1.320 -9.014 1.00 0.00 C HETATM 1305 C6 AMH 84 4.474 -0.842 -8.173 1.00 0.00 C HETATM 1306 C7 AMH 84 1.766 -0.996 -11.017 1.00 0.00 C HETATM 1307 C8 AMH 84 6.866 0.082 -8.209 1.00 0.00 C HETATM 1308 N AMH 84 2.475 -1.789 -12.024 1.00 0.00 N HETATM 1309 O1 AMH 84 5.533 -0.118 -8.498 1.00 0.00 O HETATM 1310 O2 AMH 84 7.265 -0.627 -7.287 1.00 0.00 O ENDMDL MODEL 2 HETATM 1300 C1 AMH 84 5.033 -0.356 -9.044 1.00 0.00 C HETATM 1301 C2 AMH 84 5.073 0.789 -9.892 1.00 0.00 C HETATM 1302 C3 AMH 84 3.984 0.253 -10.818 1.00 0.00 C HETATM 1303 C4 AMH 84 2.772 -0.312 -10.049 1.00 0.00 C HETATM 1304 C5 AMH 84 3.275 -1.320 -9.014 1.00 0.00 C HETATM 1305 C6 AMH 84 4.474 -0.842 -8.173 1.00 0.00 C HETATM 1306 C7 AMH 84 1.766 -0.996 -11.017 1.00 0.00 C HETATM 1307 C8 AMH 84 6.866 0.082 -8.209 1.00 0.00 C HETATM 1308 N AMH 84 2.475 -1.789 -12.024 1.00 0.00 N HETATM 1309 O1 AMH 84 5.533 -0.118 -8.498 1.00 0.00 O HETATM 1310 O2 AMH 84 7.265 -0.627 -7.287 1.00 0.00 O ENDMDL CONECT 1300 1301 1305 1307 1311 CONECT 1301 1300 1302 CONECT 1302 1301 1303 CONECT 1303 1302 1304 1306 CONECT 1304 1303 1305 CONECT 1305 1300 1304 CONECT 1306 1303 1308 CONECT 1307 1300 1309 1310 CONECT 1308 1306 1323 CONECT 1309 1307 END ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-pair-Authenticated: 209.197.6.81 References: <200409091113.28857.bgbg@pob.huji.ac.il> <200409121034.20476.bgbg@pob.huji.ac.il> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: multiple models, pdb CONECT field and rasmol Date: Sun, 12 Sep 2004 08:46:16 -0400 To: rasmol@lists.umass.edu If you don't make the structure into mutiple models with distinct atom serial numbers it is difficult to control the bonding. However, if you make multiple models, and give each atom its own atom serial number, then you can use the unbond command to edit your bonds within each model, over-riding the short-distance-generated bonds caused by the distortions in the structure. -- HJB At 10:34 AM +0300 9/12/04, Boris Gorelik wrote: >On Thursday 09 September 2004 16:20, Herbert J. Bernstein wrote: >> Structure number 2 has only 1 model. Introduce additional MODEL/ENDMDL >> pairs and the connectivity should be handled correctly. >> >That was only the minimal test case (which should also work), however, adding >additional models does not help (see the following structure). >MODEL 1 >HETATM 1300 C1 AMH 84 5.633 -0.356 -9.044 1.00 0.00 >C >HETATM 1301 C2 AMH 84 5.073 0.789 -9.892 1.00 0.00 >C >HETATM 1302 C3 AMH 84 3.984 0.253 -10.818 1.00 0.00 >C >HETATM 1303 C4 AMH 84 2.772 -0.312 -10.049 1.00 0.00 >C >HETATM 1304 C5 AMH 84 3.275 -1.320 -9.014 1.00 0.00 >C >HETATM 1305 C6 AMH 84 4.474 -0.842 -8.173 1.00 0.00 >C >HETATM 1306 C7 AMH 84 1.766 -0.996 -11.017 1.00 0.00 >C >HETATM 1307 C8 AMH 84 6.866 0.082 -8.209 1.00 0.00 >C >HETATM 1308 N AMH 84 2.475 -1.789 -12.024 1.00 0.00 >N >HETATM 1309 O1 AMH 84 5.533 -0.118 -8.498 1.00 0.00 >O >HETATM 1310 O2 AMH 84 7.265 -0.627 -7.287 1.00 0.00 >O >ENDMDL >MODEL 2 >HETATM 1300 C1 AMH 84 5.033 -0.356 -9.044 1.00 0.00 >C >HETATM 1301 C2 AMH 84 5.073 0.789 -9.892 1.00 0.00 >C >HETATM 1302 C3 AMH 84 3.984 0.253 -10.818 1.00 0.00 >C >HETATM 1303 C4 AMH 84 2.772 -0.312 -10.049 1.00 0.00 >C >HETATM 1304 C5 AMH 84 3.275 -1.320 -9.014 1.00 0.00 >C >HETATM 1305 C6 AMH 84 4.474 -0.842 -8.173 1.00 0.00 >C >HETATM 1306 C7 AMH 84 1.766 -0.996 -11.017 1.00 0.00 >C >HETATM 1307 C8 AMH 84 6.866 0.082 -8.209 1.00 0.00 >C >HETATM 1308 N AMH 84 2.475 -1.789 -12.024 1.00 0.00 >N >HETATM 1309 O1 AMH 84 5.533 -0.118 -8.498 1.00 0.00 >O >HETATM 1310 O2 AMH 84 7.265 -0.627 -7.287 1.00 0.00 >O >ENDMDL >CONECT 1300 1301 1305 1307 >1311 >CONECT 1301 1300 1302 >CONECT 1302 1301 1303 >CONECT 1303 1302 1304 1306 >CONECT 1304 1303 1305 >CONECT 1305 1300 1304 >CONECT 1306 1303 1308 >CONECT 1307 1300 1309 >1310 >CONECT 1308 1306 1323 >CONECT 1309 >1307 >END > -- ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 X-MSMail-priority: Normal References: <200409091113.28857.bgbg@pob.huji.ac.il> <200409121034.20476.bgbg@pob.huji.ac.il> ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: multiple models, pdb CONECT field and rasmol Date: Sun, 12 Sep 2004 14:57:04 +0100 To: rasmol@lists.umass.edu The structures both in Model 1 and 2 are very irreal (close contacts and bad angles). The numbering is also faulty: the CONECT records refer to atoms 1311 and 1323, which are outside the MODELs, it is a mistake. Dr. Tamas E. Gunda Dept. of Pharmaceutical Chemistry University of Debrecen POBox 36 H-4010 Debrecen, Hungary tgunda (AT) puma.unideb.hu ----- Original Message ----- Sent: Sunday, September 12, 2004 8:34 AM From: "Boris Gorelik" Subject: Re: multiple models, pdb CONECT field and rasmol To: > On Thursday 09 September 2004 16:20, Herbert J. Bernstein wrote: > > Structure number 2 has only 1 model. Introduce additional MODEL/ENDMDL > > pairs and the connectivity should be handled correctly. > > > That was only the minimal test case (which should also work), however, adding > additional models does not help (see the following structure). > MODEL 1 > HETATM 1300 C1 AMH 84 5.633 -0.356 -9.044 1.00 0.00 C > HETATM 1301 C2 AMH 84 5.073 0.789 -9.892 1.00 0.00 C > HETATM 1302 C3 AMH 84 3.984 0.253 -10.818 1.00 0.00 C > HETATM 1303 C4 AMH 84 2.772 -0.312 -10.049 1.00 0.00 C > HETATM 1304 C5 AMH 84 3.275 -1.320 -9.014 1.00 0.00 C > HETATM 1305 C6 AMH 84 4.474 -0.842 -8.173 1.00 0.00 C > HETATM 1306 C7 AMH 84 1.766 -0.996 -11.017 1.00 0.00 C > HETATM 1307 C8 AMH 84 6.866 0.082 -8.209 1.00 0.00 C > HETATM 1308 N AMH 84 2.475 -1.789 -12.024 1.00 0.00 N > HETATM 1309 O1 AMH 84 5.533 -0.118 -8.498 1.00 0.00 O > HETATM 1310 O2 AMH 84 7.265 -0.627 -7.287 1.00 0.00 O > ENDMDL > MODEL 2 > HETATM 1300 C1 AMH 84 5.033 -0.356 -9.044 1.00 0.00 C > HETATM 1301 C2 AMH 84 5.073 0.789 -9.892 1.00 0.00 C > HETATM 1302 C3 AMH 84 3.984 0.253 -10.818 1.00 0.00 C > HETATM 1303 C4 AMH 84 2.772 -0.312 -10.049 1.00 0.00 C > HETATM 1304 C5 AMH 84 3.275 -1.320 -9.014 1.00 0.00 C > HETATM 1305 C6 AMH 84 4.474 -0.842 -8.173 1.00 0.00 C > HETATM 1306 C7 AMH 84 1.766 -0.996 -11.017 1.00 0.00 C > HETATM 1307 C8 AMH 84 6.866 0.082 -8.209 1.00 0.00 C > HETATM 1308 N AMH 84 2.475 -1.789 -12.024 1.00 0.00 N > HETATM 1309 O1 AMH 84 5.533 -0.118 -8.498 1.00 0.00 O > HETATM 1310 O2 AMH 84 7.265 -0.627 -7.287 1.00 0.00 O > ENDMDL > CONECT 1300 1301 1305 1307 1311 > CONECT 1301 1300 1302 > CONECT 1302 1301 1303 > CONECT 1303 1302 1304 1306 > CONECT 1304 1303 1305 > CONECT 1305 1300 1304 > CONECT 1306 1303 1308 > CONECT 1307 1300 1309 1310 > CONECT 1308 1306 1323 > CONECT 1309 1307 > END > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Water, 10 molecules forming droplet Date: Sun, 12 Sep 2004 17:36:21 -0400 To: rasmol@lists.umass.edu For educational purposes, I have made a morph and animations of a theoretical simulation of 10 water molecules falling into a droplet, assembling into a hydrogen-bonded network. I used MDL Sculpt for energy minimization. I also provided 10 questions about the final compact conformation, suitable for students. Please see http://molvis.sdsc.edu/atlas/morphs/water10/index.htm This page is linked - From Protein Explorer's FrontDoor (click on Morphs) - From Protein Explorer's Atlas, under Lipid Bilayers and Water - From my MolVis resources page (http://www.umass.edu/microbio/chime/) - From the World Index of MolVis Resources, in both the Biochemical Tutorials and Inorganic Tutorials categories, under Water. The simulation is not yet included in the downloadable version of Protein Explorer, but will be soon. Meanwhile, the morph PDB file can be saved directly from Chime, and the animations that use it, from Netscape (File, Save As). -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: RE: Water, 10 molecules forming droplet Date: Sun, 12 Sep 2004 23:52:41 +0200 To: rasmol@lists.umass.edu Super good! I am sure you will want to fix the little typo in question number two: "How do the donor-to-accepor... " PLEASE MORE OF THIS SORT. Resources for secondary education are still too slim. Lewis Edgel -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Eric Martz Sent: den 12 september 2004 23:36 From: owner-rasmol@lists.umass.edu Subject: Water, 10 molecules forming droplet To: rasmol@lists.umass.edu For educational purposes, I have made a morph and animations of a theoretical simulation of 10 water molecules falling into a droplet, assembling into a hydrogen-bonded network. I used MDL Sculpt for energy minimization. I also provided 10 questions about the final compact conformation, suitable for students. Please see http://molvis.sdsc.edu/atlas/morphs/water10/index.htm This page is linked - From Protein Explorer's FrontDoor (click on Morphs) - From Protein Explorer's Atlas, under Lipid Bilayers and Water - From my MolVis resources page (http://www.umass.edu/microbio/chime/) - From the World Index of MolVis Resources, in both the Biochemical Tutorials and Inorganic Tutorials categories, under Water. The simulation is not yet included in the downloadable version of Protein Explorer, but will be soon. Meanwhile, the morph PDB file can be saved directly from Chime, and the animations that use it, from Netscape (File, Save As). -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: Water, 10 molecules forming droplet Date: Mon, 13 Sep 2004 10:21:23 +0100 (BST) To: rasmol@lists.umass.edu On Sun, 12 Sep 2004, Eric Martz wrote: >For educational purposes, I have made a morph and animations of a >theoretical simulation of 10 water molecules falling into a droplet, >assembling into a hydrogen-bonded network. I used MDL Sculpt for energy >minimization. I also provided 10 questions about the final compact >conformation, suitable for students. Please see That is really excellent! I found (just now) that you can get the chime exe without so much fuss from wget http://www.mdl.com/downloads/public/chime/2.6.SP6/winnt4-2000-xp/MDLChimeSP6.exe For some reason I couldn't download it via the 'DOWNLOAD NOW' button using mozilla. > >http://molvis.sdsc.edu/atlas/morphs/water10/index.htm > >This page is linked > > - From Protein Explorer's FrontDoor (click on Morphs) > - From Protein Explorer's Atlas, under Lipid Bilayers and Water > - From my MolVis resources page (http://www.umass.edu/microbio/chime/) > - From the World Index of MolVis Resources, in both the Biochemical >Tutorials and Inorganic Tutorials categories, under Water. > >The simulation is not yet included in the downloadable version of Protein >Explorer, but will be soon. Meanwhile, the morph PDB file can be saved >directly from Chime, and the animations that use it, from Netscape (File, >Save As). > >-Eric > > > >/* - - - - - - - - - - - - - - - - - - - - - - - - - - - >Protein Explorer - 3D Visualization: http://proteinexplorer.org >Workshops: http://www.umass.edu/molvis/workshop >World Index of Molecular Visualization Resources: http://molvisindex.org >ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il >Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm >PDB Lite Macromolecule Finder: http://pdblite.org >Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > >Eric Martz, Professor Emeritus, Dept Microbiology >U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz >- - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_JqLkcWY4s+6RAKB1opaHLA)" References: <5.2.0.9.2.20040912161924.016b5e20@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Herve Bizot Subject: MDLChime / ChimePro version Date: Mon, 13 Sep 2004 13:03:32 +0200 To: rasmol@lists.umass.edu --Boundary_(ID_JqLkcWY4s+6RAKB1opaHLA) > >Following this : >I found (just now) that you can get the chime exe without so much fuss >from > >wget >http://www.mdl.com/downloads/public/chime/2.6.SP6/winnt4-2000-xp/MDLChimeSP6.exe is this version worth upgrading ? mine is 3.46 Mb big ( how to identify the current version on one's PC) *************************************************Moreover ******************** In your (can we say ?) Opensource community what can you advise concerning Coarse grained MD ? Any package available ? any thing similar to QM/MM such as CoarseMD/ ClassicalMD available or being developped --Boundary_(ID_JqLkcWY4s+6RAKB1opaHLA) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_JqLkcWY4s+6RAKB1opaHLA)-- References: <5.2.0.9.2.20040912161924.016b5e20@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: MDLChime / ChimePro version Date: Mon, 13 Sep 2004 18:12:52 -0400 To: rasmol@lists.umass.edu At 9/13/2004, Herve Bizot wrote: >>http://www.mdl.com/downloads/public/chime/2.6.SP6/winnt4-2000-xp/MDLChimeSP6.exe >is this version worth upgrading ? >mine is 3.46 Mb big ( how to identify the current version on one's PC) Changes in recent SP#'s of Chime are detailed here http://www.umass.edu/microbio/chime/chimvers.htm To find Chime's version number, go to http://www.umass.edu/microbio/chime/atp.pdb which should display the ATP molecule in Chime. (If you get an error about ChimeShim Library Object, you need to upgrade Chime to SP6 for sure!) Click on MDL at the lower right, then on Chime's pop-up menu, About. Alternatively, in Netscape, Help, About Plugins. -Eric ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Status of PE vs. pop-up blocker in WinXP SP2 Date: Fri, 17 Sep 2004 15:40:38 -0400 To: rasmol@lists.umass.edu On August 10, I released some changes in Protein Explorer (version 2.411) that make it easier to configure Windows XP SP2's pop-up blocker to permit PE to work. Also PE now displays explicit instructions on how to do that when needed. We think that PE on-line is now working well with WinXP SP2. However, there are still problems with getting SP2 to enable downloaded copies of PE to open new windows. We haven't found any way to totally disable SP2's pop-up blocker (for all sites) that actually seems to work. Any suggestions are welcome! We are also working on getting PE's demo movies to work in WinXP SP2. We hope to devise solutions for these issues soon. Meanwhile, PE 2.41 remains downloadable, but not yet 2.411. The demo movies are not downloadable either yet pending a few fixes. For those who use PE in Windows XP and have not yet upgraded to SP2, we suggest that you postpone that upgrade for awhile! -Eric Martz & Frieda Reichsman /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Status of PE vs. pop-up blocker in WinXP SP2 Date: Fri, 17 Sep 2004 16:35:28 -0400 To: rasmol@lists.umass.edu In my previous message, I wrote: "On August 10, I released some changes in Protein Explorer (version 2.411) ..." Oops, make that September 10. Whew, has school started already :-) -Eric ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MSMail-Priority: High boundary="8C_._B53D6._01D_.__5B07_" ++++------+------+------+------+------+------+------+------+------+------+ From: "Admin" Subject: ADV: Announcement To All Staff Date: Tue, 21 Sep 04 01:39:42 GMT To: kadterry@bio.umass.edu This is a multi-part message in MIME format. --8C_._B53D6._01D_.__5B07_ Attention All School Staff: Teachers, Students and Faculty Members: You Must Respond By 5 P.M. Wednesday, September 22, 2004. Through a special arrangement, Avtech Direct is offering a limited allotment of BRAND NEW, top of-the-line, name-brand desktop computers at more than 50% off MSRP to all Teachers, Students,Faculty and Staff, who respond to this message before 5 P.M., Wednesday, September 22, 2004. All desktop are brand-new, packed in their original boxes, and come with a full manufacturer's warranty plus a 100% satisfaction guarantee. These professional grade Desktops are fully equipped with 2004 next generation technology, making these the best performing computers money can buy. Avtech Direct is offering these feature rich, top performing Desktop Computers with the latest Intel technology at an amazing price to all who call: 1-800-884-9510 by 5 P.M. Wednesday, September 22, 2004 The fast and powerful AT-2400 series Desktop features: * Intel 2.0Ghz Processor for amazing speed and performance * 128MB DDR RAM, --- Upgradeable to 1024 * 20 GB UDMA Hard Drive, --- Upgradeable to 80 GB * 52X CD-Rom Drive, --- Upgradeable to DVD/CDRW * 1.44 Floppy disk drive * Next Generation Technology * ATI Premium video and sound * Full Connectivity with Fax modem/Lan/IEE 1394/USB 2.0 * Soft Touch Keyboard and scroll mouse * Internet Ready * Network Ready * 1 Year parts and labor warranty * Priority customer service and tech support MSRP $699 ........................................ Your Cost $297 How to qualify: 1. You must be a Teacher, Student, Faculty or Staff Member: 2. All desktop computers will be available on a first come first serve basis. 3. You must call 1-800-884-9510 by 5 P.M. Wednesday, September 22, 2004 and we will hold the desktops you request on will call. 4. You are not obligated in any way. 5. 100% Satisfaction Guaranteed. Call Avtech Direct 1-800-884-9510 before 5 P.M. Wednesday, September 22, 2= 004 Visit our website at http://www.avtechdirectcomputers.com If you wish to unsubscribe from this list, please go to: http://www.computeradvice.org/unsubscribe.asp Avtech Direct 22647 Ventura Blvd., Suite 374 Woodland Hills, CA 91364 --8C_._B53D6._01D_.__5B07_-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Roberts, Rebecca" Subject: Oklahoma City Bioinformatics Workshop Announcement Date: Thu, 23 Sep 2004 08:25:22 -0400 To: rasmol@lists.umass.edu ----Original Message----- Sent: Wednesday, September 22, 2004 3:48 PM rroberts@ursinus.edu; eversea@beloit.edu From: Sue Risseeuw [mailto:risseeuw@beloit.edu] Subject: Oklahoma City Bioinformatics Workshop Announcement To: risseeuw@beloit.edu Cc: sdonovan@pitt.edu; weisstae@truman.edu; stanleye@beloit.edu; We are writing this note to inform you of the faculty development workshop, "Bioinformatics in Biology Education: Working with Sequence, Structure and Function" which will be held at Oklahoma City Community College in Oklahoma City, Oklahoma on January 6 - 8, 2005. This is part of an NSF funded bioinformatics education project titled BEDROCK that focuses on helping faculty develop strategies for incorporating bioinformatics into their courses. The workshop will begin on Thursday and run through Saturday. The bulk of the workshop will involve a mixture of focused presentations on the conceptual basis for bioinformatics analyses and hands-on group problem solving activities around rich biological contexts. This workshop is appropriate for faculty who have beginning or intermediate experience with sequence analysis. Participants will be responsible for the cost of their travel and lodging but there are no fees for the workshop itself or the materials provided. Some meals will also be provided. We do have some resources available to provide lodging for faculty who are employed by one of the Oklahoma INBRE undergraduate campuses (Langston University, Northeastern State University, Southwestern Oklahoma State University, Oklahoma City Community College, University of Central Oklahoma, Cameron University, Redlands Community College, and Comanche Nation College). Please email if this applies to you. There is additional information about the workshop on the web page at . Please feel free to share this announcement with other interested faculty. Please feel free to contact Sue Risseeuw (risseeuw@beloit.edu, 608-363-2012) with any questions you have. Sincerely, -John and Sam John R. Jungck Sam Donovan BioQUEST Curriculum Consortium Department of Biology Beloit College ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MSMail-Priority: High boundary="F39EE3D58DE.0._38ED" ++++------+------+------+------+------+------+------+------+------+------+ From: "Admin" Subject: ADV: Announcement To All Staff Date: Wed, 29 Sep 04 05:37:19 GMT To: fletcher@bio.umass.edu This is a multi-part message in MIME format. --F39EE3D58DE.0._38ED Attention All School Staff: Teachers, Students and Faculty Members: You Must Respond By 5 P.M. Thursday, September 30, 2004. Through a special arrangement, Avtech Direct is offering a limited allotment of BRAND NEW, top of-the-line, name-brand desktop computers at more than 50% off MSRP to all Teachers, Students,Faculty and Staff, who respond to this message before 5 P.M., Thursday, September 30, 2004. All desktop are brand-new, packed in their original boxes, and come with a full manufacturer's warranty plus a 100% satisfaction guarantee. These professional grade Desktops are fully equipped with 2004 next generation technology, making these the best performing computers money can buy. Avtech Direct is offering these feature rich, top performing Desktop Computers with the latest Intel technology at an amazing price to all who call: 1-800-884-9510 by 5 P.M. Thursday, September 30, 2004 The fast and powerful AT-2400 series Desktop features: * Intel 2.0Ghz Processor for amazing speed and performance * 128MB DDR RAM, --- Upgradeable to 1024 * 20 GB UDMA Hard Drive, --- Upgradeable to 80 GB * 52X CD-Rom Drive, --- Upgradeable to DVD/CDRW * 1.44 Floppy disk drive * Next Generation Technology * ATI Premium video and sound * Full Connectivity with Fax modem/Lan/IEE 1394/USB 2.0 * Soft Touch Keyboard and scroll mouse * Internet Ready * Network Ready * 1 Year parts and labor warranty * Priority customer service and tech support MSRP $699 ........................................ Your Cost $297 How to qualify: 1. You must be a Teacher, Student, Faculty or Staff Member. 2. All desktop computers will be available on a first come first serve basis. 3. You must call 1-800-884-9510 by 5 P.M. Thursday, September 30, 2004 and we will hold the desktops you request on will call. 4. You are not obligated in any way. 5. 100% Satisfaction Guaranteed. Call Avtech Direct 1-800-884-9510 before 5 P.M. Thursday, September 30, 20= 04 Visit our website at http://www.avtechdirectcomputers.com If you wish to unsubscribe from this list, please go to: http://www.computeradvice.org/unsubscribe.asp Avtech Direct 22647 Ventura Blvd., Suite 374 Woodland Hills, CA 91364 --F39EE3D58DE.0._38ED-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Announcing molviz.org Date: Thu, 30 Sep 2004 17:32:53 -0400 To: rasmol@lists.umass.edu Announcing http://MolViz.Org (same as http://molviz.org, http://www.molviz.org) The name of the main page for Chime-based tutorials and educational resources that I've authored over the years has been changed to a new domain, http://molviz.org, to make it easy to remember. (molvis.org was already taken by the journal of molecular vision, about the biochemistry of sight.) -EricM /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.6603.0 Thread-Topic: Invitation to submit to BioMoleculesAlive Thread-Index: AcSo7Yp9mKBSoRiISAyA7F720GcOtg== Content-Class: urn:content-classes:message X-MS-Has-Attach: yes X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: Paul A Craig Subject: Invitation to submit to BioMoleculesAlive Date: Sat, 02 Oct 2004 22:06:06 -0400 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_bPVS1Uotq0zpVbqiulpbxA) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_bPVS1Uotq0zpVbqiulpbxA)-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.6603.0 boundary="Boundary_(ID_E8wvB967hl9MByDvpgNPOw)" Thread-Topic: Invitation to submit to BioMoleculesAlive Thread-Index: AcSpPjqmw69wjx/zT1eGcT7GVT8Vkw== Content-Class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: Paul A Craig Subject: Invitation to submit to BioMoleculesAlive Date: Sun, 03 Oct 2004 07:43:42 -0400 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_E8wvB967hl9MByDvpgNPOw) Dear Rasmol List Member, I would like to invite you to submit any molecular visualizations, structure images, Flash animations, software or curriculum resources you have developed to BioMoleculesAlive (http://www.biomoleculesalive.org ), a searchable collection of peer-reviewed digital resources sponsored by the ASBMB. The digital library provides an electronically accessible repository of high quality instructional materials and learning objects that can be used primarily by educators at the undergraduate, graduate and medical school levels to augment classroom, laboratory and independent learning. The digital library is part of a larger effort called the "BEN Collaborative" (www.BioScieEdNet.org ) managed by The American Association for the Advancement of Science (AAAS). Materials found in BioMoleculesAlive fall into four categories: Software, Visual Resources, Curriculum Resources, Articles & Reviews, from the ASBMB managed journal Biochemistry and Molecular Biology Education (BAMBED). Submission and Review on BioMoleculesAlive is modeled after the Journal of Biological Chemistry model. The review process will include technical review (for operating system, browser, plug-in requirements) as well as evaluation of style and content by a board of associate editors and a group of peer reviewers. The abstracts of all resources that are accepted by BioMoleculesAlive will be published in Biochemistry and Molecular Biology Education. This will allow you to give a citation from a peer-reviewed journal for an electronic resource you have developed.This should support you in review processes for tenure and promotion. Submission is easy. Just go to http://www.biomoleculesalive.org and click on "submit a resource". Before submitting, please register. Hope to hear from you. Paul Paul A. Craig Professor of Chemistry Rochester Institute of Technology 85 Lomb Memorial Drive Rochester NY 14623-5603 Phone: 585-475-6145 FAX: 585-475-7800 email: paul.craig@rit.edu --Boundary_(ID_E8wvB967hl9MByDvpgNPOw) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_E8wvB967hl9MByDvpgNPOw)-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.6603.0 Thread-Topic: Invitation to submit to BioMoleculesAlive Thread-Index: AcSpPmoJRTriFTeMTce6+BqoZsMlNQ== Content-Class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: Paul A Craig Subject: Invitation to submit to BioMoleculesAlive Date: Sun, 03 Oct 2004 07:45:02 -0400 To: rasmol@lists.umass.edu Dear Rasmol List Member, I would like to invite you to submit any molecular visualizations, structure images, Flash animations, software or curriculum resources you have developed to BioMoleculesAlive (http://www.biomoleculesalive.org), a searchable collection of peer-reviewed digital resources sponsored by the ASBMB. The digital library provides an electronically accessible repository of high quality instructional materials and learning objects that can be used primarily by educators at the undergraduate, graduate and medical school levels to augment classroom, laboratory and independent learning. The digital library is part of a larger effort called the "BEN Collaborative" (www.BioScieEdNet.org) managed by The American Association for the Advancement of Science (AAAS). Materials found in BioMoleculesAlive fall into four categories: Software, Visual Resources, Curriculum Resources, Articles & Reviews, from the ASBMB managed journal Biochemistry and Molecular Biology Education (BAMBED). Submission and Review on BioMoleculesAlive is modeled after the Journal of Biological Chemistry model. The review process will include technical review (for operating system, browser, plug-in requirements) as well as evaluation of style and content by a board of associate editors and a group of peer reviewers. The abstracts of all resources that are accepted by BioMoleculesAlive will be published in Biochemistry and Molecular Biology Education. This will allow you to give a citation from a peer-reviewed journal for an electronic resource you have developed.This should support you in review processes for tenure and promotion. Submission is easy. Just go to http://www.biomoleculesalive.org and click on "submit a resource". Before submitting, please register. Hope to hear from you. Paul Paul A. Craig Professor of Chemistry Rochester Institute of Technology 85 Lomb Memorial Drive Rochester NY 14623-5603 Phone: 585-475-6145 FAX: 585-475-7800 email: paul.craig@rit.edu Paul A. Craig Professor of Chemistry Rochester Institute of Technology 85 Lomb Memorial Drive Rochester NY 14623-5603 Phone: 585-475-6145 FAX: 585-475-7800 email: paul.craig@rit.edu PLEASE NOTE: My email address has changed. Please use the new address for all future emails. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Morph of lac repressor bending DNA operon Date: Sun, 03 Oct 2004 15:34:32 -0400 To: rasmol@lists.umass.edu I have created a morph of the lac repressor bending the DNA operon as it changes from nonspecific to specific binding. http://molvis.sdsc.edu/atlas/morphs/lacrep/index.htm Click the above link to see animated multi-GIF's (small, and large, suitable for pasting into Powerpoint) that don't require Chime. Anyone is welcome to copy these or other portions into their websites or presentations, provided proteinexplorer.org is cited as the source. I provided 9 questions for students. Suggestions for additional questions are welcome, as are comments on my questions or answers. I have included several animations saved from Protein Explorer (requiring Chime) that highlight different features, including one that shows 5 hydrogen bonds forming in the major and minor grooves. This was possible because of the July 2004 publication of an NMR solution for the nonspecific binding by Kalodimos et al. in Science. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15256668 The new morphs and animations are available - From Protein Explorer's FrontDoor (click on Morphs) - From Protein Explorer's Atlas, under Proteins Complexed to Nucleic Acids - From http://MolviZ.Org - and (shortly) from the World Index of MolVis Resources, in the Biochemical Tutorials category. The simulation is not yet included in the downloadable version of Protein Explorer, but will be soon. Meanwhile, the morph PDB file can be saved directly from Chime, and the animations that use it, from IE or Netscape (File, Save As). -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop Biochem Structure Tutorials http://MolviZ.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Bcc: X-Accept-Language: en,es-ES ++++------+------+------+------+------+------+------+------+------+------+ From: shalpine@earthlink.net Subject: J. Chem. Ed. cover story on visualization Date: Mon, 04 Oct 2004 18:44:26 -0700 Dear MolVis colleagues: The article, Introducing Molecular Visualization to Primary Schools in California: The STArt! teaching Science Through Art Program, is featured on the cover of the October "National Chemistry Week" issue of the Journal of Chemical Education. For more information please visit: In addition to the classroom work with Elementary Schools described in the JCE paper, I also developed an informal science-and-technology after-school program for Middle School students. Their digital animations and "Power Molecule" T-shirt designs are posted on the Web: Sincerely, Susana Susana Maria Halpine Founding Director STArt! teaching Science Through Art 239 Sunridge Street Playa del Rey, CA 90293 (310) 306-8399 shalpine@earthlink.net http://home.earthlink.net/~shalpine Executive Committee Member and Women Chemists Committee Chair, SoCal Section of the American Chemical Society Steering Committee Member, http://BioMoleculesAlive.org ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-MSMail-priority: Normal References: <4161FC6E.5257E8DA@earthlink.net> ++++------+------+------+------+------+------+------+------+------+------+ From: Robert Bateman Subject: Re: J. Chem. Ed. cover story on visualization Date: Mon, 04 Oct 2004 22:23:18 -0500 To: rasmol@lists.umass.edu Nicely done, Susana! ----- Original Message ----- Sent: Monday, October 04, 2004 8:44 PM From: Subject: J. Chem. Ed. cover story on visualization > Dear MolVis colleagues: > > The article, Introducing Molecular Visualization to Primary Schools in > California: The STArt! teaching Science Through Art Program, is featured > on the cover of the October "National Chemistry Week" issue of the > Journal of Chemical Education. > > For more information please visit: > > > In addition to the classroom work with Elementary Schools described in > the JCE paper, I also developed an informal science-and-technology > after-school program for Middle School students. Their digital > animations and "Power Molecule" T-shirt designs are posted on the Web: > > > Sincerely, > > Susana > > Susana Maria Halpine > Founding Director > STArt! teaching Science Through Art > 239 Sunridge Street > Playa del Rey, CA 90293 > (310) 306-8399 > shalpine@earthlink.net > http://home.earthlink.net/~shalpine > > Executive Committee Member and Women Chemists Committee Chair, SoCal > Section of the American Chemical Society > Steering Committee Member, http://BioMoleculesAlive.org > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Slides to demonstrate conservation of protein structure? Date: Fri, 08 Oct 2004 11:13:32 +0100 (BST) To: Rasmol Mailing List Cc: Sequence Search Mailing List Hi, I would like to demonstrate the well known principal that protein structure is more conserved than protein sequence in evolutionary time. I am presenting to a group of structural biologists, so I want to emphasize the bioinformatic perspective. My idea for a series of slides is this 1) show two clearly structurally similar (same topology) protein domains. 1.1) show that the two sequences are very different, and result in a 'bad' sequence alignment (somehow visually). 2) Show a nieve (and hopefully bad) structural alignment of the two domains based (nievely) on the sequence alignment. 3) Show a pure (and simple) structural alignment of the two domains. 3.1) Show the sequence alignment based on the good structural alignment. My idea is to convey the importance of structure in recognizing distant homology between domains. I want to use a real example using real tools, but I am not sure how / which tools to use.Any suggetions? Good demo / bad demo? Naturally I need this done by yesterday, so the simpler the tools the better. I will be happy to post the slides somewhere appropriate to share this work with the world. All the best, Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Virus-Scanned: by amavisd-milter (http://www.amavis.org/) References: X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id i98BNwH26325 ++++------+------+------+------+------+------+------+------+------+------+ From: Annemarie Honegger Subject: Re: Slides to demonstrate conservation of protein structure? Date: Fri, 08 Oct 2004 13:22:30 +0200 To: rasmol@lists.umass.edu Hi Dan I've used the example of the different immunoglobulin domains within an antibody molecule to demonstrate this see http://www.biochem.unizh.ch/antibody/Introduction/Institutsseminar97/ source/slide4.htm Hi Dan On http://www.biochem.unizh.ch/antibody/macros you also find some excel macros which allow to import sequences into excel and, for example, color code them for similarity to a reference sequence or to import the coordinates of the c-alpha atoms of multiple 3D-aligned structures and color code the sequence alignment according to the deviation from the average structure Annemarie On Oct 8, 2004, at 12:13 PM, Dan Bolser wrote: > > Hi, > > I would like to demonstrate the well known principal that protein > structure is more conserved than protein sequence in evolutionary > time. I am presenting to a group of structural biologists, so I > want to emphasize the bioinformatic perspective. > > My idea for a series of slides is this > > 1) show two clearly structurally similar (same topology) protein > domains. > 1.1) show that the two sequences are very different, and result in > a 'bad' sequence alignment (somehow visually). > > 2) Show a nieve (and hopefully bad) structural alignment of the two > domains based (nievely) on the sequence alignment. > > 3) Show a pure (and simple) structural alignment of the two domains. > 3.1) Show the sequence alignment based on the good structural > alignment. > > > My idea is to convey the importance of structure in recognizing distant > homology between domains. > > I want to use a real example using real tools, but I am not sure how / > which tools to use.Any suggetions? Good demo / bad demo? Naturally I > need > this done by yesterday, so the simpler the tools the better. > > I will be happy to post the slides somewhere appropriate to share this > work with the world. > > All the best, > Dan. > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > > ________________________________________________________ Dr. Annemarie Honegger, Ph.D. Zürich University, Dept. of Biochemistry Winterthurerstr.190 CH-8057 Zürich Switzerland e-mail: honegger@bioc.unizh.ch Tel. 41-44-635 55 62 Fax 41-44-635 57 12 www: http://www.biochem.unizh.ch/antibody _______________________________________________________ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-MSMail-priority: Normal References: <57C95F5E-191C-11D9-A561-000A95A789BA@bioc.unizh.ch> ++++------+------+------+------+------+------+------+------+------+------+ From: Edward Werner Cook Subject: Best hardware configuration for molecular modeling Date: Fri, 08 Oct 2004 08:34:16 -0400 To: rasmol@lists.umass.edu What is the best computer hardware configuration for molecular modeling? It is now time for us to upgrade our computers in the Science Department at our College and we are thinking of reserving several computers for molecular modeling. While most configurations would doubtless work, we thought that, beyond obvious minimum speed and memory requirements, some video cards could be better suited to modeling than others. Some display configurations could also be preferable.Perhaps more. And, while our IT folk would prefer Windows XP, they would have to go along with any version (2000?) or OS (Linux in which version or flavour?) we found necessary. Does anybody have preferences and why? Edward Werner Cook Chair, Department of Life and Physical Sciences Tunxis Community College Farmington, Connecticut ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Ids: 164 X-Greylist: Sender IP whitelisted, not delayed by milter-greylist-1.5.8 (shiva.jussieu.fr [134.157.0.164]); Fri, 08 Oct 2004 18:48:45 +0200 (CEST) X-Miltered: at shiva.jussieu.fr with ID 4166C4ED.000 by Joe's j-chkmail (http://j-chkmail.ensmp.fr)! X-Antivirus: scanned by sophie at shiva.jussieu.fr ++++------+------+------+------+------+------+------+------+------+------+ From: Christian Simon Subject: Re: Best hardware configuration for molecular modeling Date: Fri, 08 Oct 2004 18:48:44 +0200 To: rasmol@lists.umass.edu Dear Edward, Being in charge of computer management in a modeling lab, and being a user too, I would say there is no unique answer. The main questions are: 1- what are the teaching goals ? (what do you expect the students to learn) 2- to achieve this, what software do you plan to use ? Just graphics or also computationally demanding soft ? 3- how much resources the IT people can devote to these machines and how should these machine interact with the rest of IT resources for students ? (should the students be able to save their results on a shared filesystem they can access from elsewhere ? Do you want them to produce results to be imported in reports written with MSWord ?) If you plan to teach them modeling + a bit of programming, the best choice is probably not the same as if you just want to introduce them to crystallography (for example). If you expect them to build small web pages to present projects, the answer maybe another... From my point of view, aside WindowsXP and Linux, I would add MacOSX : you can have software from both worlds (both MS and UNIX) on this platform, (check first). It is easy for users, can provide a good working environment, for programming/developing, computing, modeling, writing, producing movies or other communication stuffs. If you want the students to start with a beginner level, you can. If you plan to let them study on these machines several years, they can also go deep inside system knowledge. (while Linux would request a minimum knowledge: hard for beginners; Windows would limit necessary proficiencies: frustrating for experienced students) It is open and compatible with other systems (can handle SMB or NFS files, can use directories systems like LDAP etc...). From the IT people point of view, it should be easy to manage a pool of identical computers, and to keep them up to date, and this is a secure system. It is not that expensive. MacOSX can even provide you a way to do simple parallel computing... And if you plan to teach bioinformatics, Apple deliver small clusters with all tools preconfigured. If you want, tell me which softs you plan to use, and I will tell you if they are available on a Mac. It's all about what you want to teach. If you do not know for the moment, MacOSX does not force you to choose right now, and preserves all options. Once more, it's all about what you want to teach, there is no unique answer. Sincerely, -- Dr. Christian SIMON, Maitre de Conferences Laboratoire LI2C-UMR7612 Bat. F74, piece 757 Universite Pierre et Marie Curie Tel:+33.1.44.27.32.65 Case 51 Fax:+33.1.44.27.32.28 4 Place Jussieu 75252 Paris Cedex 05 FRANCE/Europe ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline User-Agent: Mutt/1.4i References: <57C95F5E-191C-11D9-A561-000A95A789BA@bioc.unizh.ch> <012a01c4ad33$31ea1be0$1f7bfea9@ibmaptiva> ++++------+------+------+------+------+------+------+------+------+------+ From: Eugen Leitl Subject: Re: Best hardware configuration for molecular modeling Date: Fri, 08 Oct 2004 20:06:31 +0200 To: rasmol@lists.umass.edu On Fri, Oct 08, 2004 at 08:34:16AM -0400, Edward Werner Cook wrote: > What is the best computer hardware configuration for molecular modeling? The visualization aspect, or the crunch aspect? Either way, AMD (Opteron and Athlon64) are better than Intel. You should use at least 1 GByte of (DDR, not yet DDR2) memory for the workstation, preferrably more (2-4 should be enough). > It is now time for us to upgrade our computers in the Science Department at > our College and we are thinking of reserving several computers for molecular > modeling. While most configurations would doubtless work, we thought that, > beyond obvious minimum speed and memory requirements, some video cards could What is your budget? Are some machines to be more powerful than others? How much noise and power dissipation can you tolerate? > be better suited to modeling than others. Some display configurations could > also be preferable.Perhaps more. > And, while our IT folk would prefer Windows XP, they would have to go along Right now Windows drivers have an edge in performance, at least on the gamer platform (buying a silent (water-cooled) gamer machine might be actually cost-effective). Of course, chemical visualization is different, so there might not that much difference between both Linux/Windows and ATI/nVidia. > with any version (2000?) or OS (Linux in which version or flavour?) we found If you say Linux, you say ATI or nVidia. Right now you should go with an nVidia card (dual-DVI?), but ATI has tentatively announced much better driver support. One warning: will not be trivial to configure your workstation with acceleration on Linux. OS X is nice, but Apple's 3d accelerators are typically vintage. I.e. not high-performance hardware. On the other hand, it might be enough. Check out G5 based systems, both G5 Tower and the G5 iMac. > necessary. > Does anybody have preferences and why? The query is too broad as stated. Perhaps you can refine? -- Eugen* Leitl leitl ______________________________________________________________ ICBM: 48.07078, 11.61144 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE http://moleculardevices.org http://nanomachines.net ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Slides to demonstrate conservation of protein structure? Date: Fri, 08 Oct 2004 17:40:02 -0400 To: rasmol@lists.umass.edu At 10/8/04, Dan Bolser wrote: >Hi, > >I would like to demonstrate the well known principal that protein >structure is more conserved than protein sequence in evolutionary >time. I am presenting to a group of structural biologists, so I >want to emphasize the bioinformatic perspective. > >My idea for a series of slides is this > >1) show two clearly structurally similar (same topology) protein domains. One example pointed out to me years ago by Gabe McCool is the bacterial cell division protein FtsZ. A structure-based search turns up tubulin, but the sequence identity is only 16% (if I recall). This paper by Friedberg, Kaplan and Margalit http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11152139 assesses "the accuracy of PSI-BLAST alignments on a stringent database of 123 structurally similar, sequence-dissimilar pairs of proteins, by comparing them to the alignments defined on a structural basis." I will be quite interested in your slides when they become available! Please keep us posted. -Eric Martz >1.1) show that the two sequences are very different, and result in > a 'bad' sequence alignment (somehow visually). > >2) Show a nieve (and hopefully bad) structural alignment of the two > domains based (nievely) on the sequence alignment. > >3) Show a pure (and simple) structural alignment of the two domains. >3.1) Show the sequence alignment based on the good structural alignment. > > >My idea is to convey the importance of structure in recognizing distant >homology between domains. > >I want to use a real example using real tools, but I am not sure how / >which tools to use.Any suggetions? Good demo / bad demo? Naturally I need >this done by yesterday, so the simpler the tools the better. > >I will be happy to post the slides somewhere appropriate to share this >work with the world. > >All the best, >Dan. > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop Biochem Structure Tutorials http://MolviZ.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Microsoft-Entourage/11.0.0.040405 ++++------+------+------+------+------+------+------+------+------+------+ From: Gabe McCool Subject: Re: Slides to demonstrate conservation of protein structure? Date: Sat, 09 Oct 2004 00:56:14 -0400 To: rasmol@lists.umass.edu Dan- Sounds great...looking forward to seeing your slides at some point. Further to Eric Martz's FtsZ suggestion, the presentation at http://www.umass.edu/microbio/chime/pipe/ftsz/present/index.htm tries to point out FtsZ's close structural alignment with tubulin contrasted with the low seq identity (<20%) between aligned FtsZ + tubulin aa sequences. Hope its helpful in some regard. Gabe McCool > From: Eric Martz > Reply-To: > Date: Fri, 08 Oct 2004 17:40:02 -0400 > To: > Subject: Re: Slides to demonstrate conservation of protein structure? > > At 10/8/04, Dan Bolser wrote: > >> Hi, >> >> I would like to demonstrate the well known principal that protein >> structure is more conserved than protein sequence in evolutionary >> time. I am presenting to a group of structural biologists, so I >> want to emphasize the bioinformatic perspective. >> >> My idea for a series of slides is this >> >> 1) show two clearly structurally similar (same topology) protein domains. > > One example pointed out to me years ago by Gabe McCool is the bacterial > cell division protein FtsZ. A structure-based search turns up tubulin, but > the sequence identity is only 16% (if I recall). > > This paper by Friedberg, Kaplan and Margalit > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abst > ract&list_uids=11152139 > assesses > "the accuracy of PSI-BLAST alignments on a stringent database of 123 > structurally similar, sequence-dissimilar pairs of proteins, by comparing > them to the alignments defined on a structural basis." > > I will be quite interested in your slides when they become available! > Please keep us posted. > -Eric Martz > >> 1.1) show that the two sequences are very different, and result in >> a 'bad' sequence alignment (somehow visually). >> >> 2) Show a nieve (and hopefully bad) structural alignment of the two >> domains based (nievely) on the sequence alignment. >> >> 3) Show a pure (and simple) structural alignment of the two domains. >> 3.1) Show the sequence alignment based on the good structural alignment. >> >> >> My idea is to convey the importance of structure in recognizing distant >> homology between domains. >> >> I want to use a real example using real tools, but I am not sure how / >> which tools to use.Any suggetions? Good demo / bad demo? Naturally I need >> this done by yesterday, so the simpler the tools the better. >> >> I will be happy to post the slides somewhere appropriate to share this >> work with the world. >> >> All the best, >> Dan. >> > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > Biochem Structure Tutorials http://MolviZ.org > World Index of Molecular Visualization Resources: http://molvisindex.org > ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il > Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor Emeritus, Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Toni Pomar Subject: Embed chime object in ppt Date: Sun, 10 Oct 2004 20:06:07 +0200 (CEST) To: rasmol@lists.umass.edu Hi!!! Can I embed a pdb file in a powerpoint document. Regards. ______________________________________________ Renovamos el Correo Yahoo!: ¡100 MB GRATIS! Nuevos servicios, más seguridad http://correo.yahoo.es ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MSMail-Priority: High boundary="FC.5F2_3F31D_.AE_DA4C4_" ++++------+------+------+------+------+------+------+------+------+------+ From: "Administrator" Subject: ADV: Staff Annoucement Date: Sun, 10 Oct 04 14:30:43 GMT To: rasmol-digest@bio.umass.edu This is a multi-part message in MIME format. --FC.5F2_3F31D_.AE_DA4C4_ Attention All School Staff: Teachers, Students and Faculty Members: You Must Respond By 5 P.M. Tuesday, October 12, 2004. Through a special arrangement, Avtech Direct is offering a limited allotment of BRAND NEW, top of-the-line, name-brand desktop computers at more than 50% off MSRP to all Teachers, Students,Faculty and Staff, who respond to this message before 5 P.M., Tuesday, October 12, 2004 All desktop computers are brand-new packed in their original boxes, and come with a full manufacturer's warranty plus a 100% satisfaction guarantee. These professional grade Desktops are fully equipped with 2005 next generation technology, making these the best performing computers money can buy. Avtech Direct is offering these feature rich, top performing Desktops with the latest technology at an amazing price to all who call: 1-800-795-8466 by 5 P.M. 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Ask for Department C. Call Avtech Direct 1-800-795-8466 before 5 P.M. Tuesday, October 12, 2004 Visit our website at http://www.avtechdirectcomputers.com If you wish to unsubscribe from this list, please go to http://www.computeradvice.org/unsubscribelink.asp Avtech Direct 22647 Ventura Blvd. Suite 374 Woodland Hills, CA 91364 --FC.5F2_3F31D_.AE_DA4C4_-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 boundary="Boundary_(ID_dYx+wTIQBgya3rQ2pafyvA)" X-MSMail-priority: Normal X-Virus-Scanned: Yes References: <20041010180607.40554.qmail@web51110.mail.yahoo.com> ++++------+------+------+------+------+------+------+------+------+------+ From: Duane Sears Subject: Re: Embed chime object in ppt Date: Sun, 10 Oct 2004 23:32:07 -0700 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_dYx+wTIQBgya3rQ2pafyvA) Toni, =20 I've experimented around with a few different ways to embed web pages = with Chime images into PowerPoint slides and I find that the free = LiveWeb Add-In for PowerPoint (http://www.mvps.org/skp/liveweb.htm ) = gives the best result and is easy to manage once you figure out the = logic of the Add-In. This Add-In exploits the functionality of the = Visual Basic WebBrowser function which launches an Internet Explorer = browser embedded in a slide or a Visual Basic UserForm. I know it works = with Windows operating systems 98, 2000, and XP. I don't know about = other operating systems. =20 =20 If you want to see an example, you can find a "zipped" sample PowerPoint = presentation on my web site at=20 http://tutor.lscf.ucsb.edu/instdev/sears/biochemistry/DWSEARS2004-Ppt-Emb= eddedChimeWebpages.zip=20 =20 EMBEDDED WEB BROWSERS WITH CHIME IMAGES In a nutshell, this is how LiveWeb works. Install LiveWeb and then = configure PowerPoint for the Add-In by selecting LiveWeb from the = Standard Toolbar option -- "Tools/Add-Ins/Install New." Now select the = "Insert/Web Pages" drop-down option found on the PowerPoint Standard = Toolbar. This option activates a LiveWeb wizard for embedding a = WebBrowser Visual Basic function into a slide. The wizard presents a = dialog box for you to enter the URL of the web page you want to view on = the slide. With a second drop-down LiveWeb menu option -- "Insert/Edit = Page Property" - the WebBrowser associated URL can also easily be = modified at a later time. This option (which is not particularly well = documented and took me a while to discover) is very useful because you = can easily update a link if it changes, or change the associated URL for = a copied slide so it's WebBrowser is associated with a new web page. =20 = =20 A few additional points to note:=20 =20 After a web page has been embedded in a slide, the resizable area you = see reserved for the WebBrowser function will always appear on top = during Show Mode, even if you have text or a figure pasted over the = embedded browser as it appears in the Slide Edit mode. =20 =20 Also, web pages sometimes don't load into the embedded WebBrowser = function the first time they are encountered in Show Mode. I don't know = why this is, but to partially alleviate this problem, I found a Visual = Basic Subroutine that I add to the embedded WebBrowser function's Visual = Basic code. This subroutine is designed to trigger web page loading the = first time the slide with the WebBrowser function is encountered during = the Show Mode. To add the following Subroutine VB code to the = WebBrowser function code, DOUBLE CLICK on the WebBrowser you see mapped = on the slide in the edit mode. The following Visual Basic text appears = initially: --------------------------------------------------- Private Sub WebBrowser1_StatusTextChange(ByVal Text As String) =20 End Sub --------------------------------------------------- APPEND the following Subroutine to this text and change the URL = accordingly. ------------------------------- Sub WebBrowser1_DocumentComplete(ByVal pDisp As Object, URL As Variant) Dim varURL As Variant =20 'Check to see if this is the first time this 'control has been run, if so, load the page. =20 If URL =3D "" Then varURL =3D = "http://tutor.lscf.ucsb.edu/instdev/sears/biochemistry/"=20 'INSERT YOUR OWN URL HERE =20 WebBrowser1.Navigate varURL End If =20 End Sub --------------------------------------- =20 POPUP WEB BROWSERS WITH CHIME IMAGES I've also found a way to create pop-up web pages that float over the = PowerPoint slides without completely hiding the slide being viewed in = Show mode. For this application, the WebBrowser function is added to a = Visual Basic UserForm after opening the Visual Basic Editor from the = Standard Toolbar option -- "Tools/Macro/Visual Basic Editor." With the = VB Editor open, the first step is to select "Insert/UserForm" and the = second step is to drag the WebBrowser function on to the UserForm from = the "Toolbox. " The first time you do this, the "Microsoft Web Browser" = function will probably be located in "Additional Functions" and can be = found after right clicking on the ToolBox panel and searching through = the list; however, the "WebBrowser" will remain visible on the Toolbox = thereafter. =20 Now, do the following: 1.. Open the "Project" and "Properties" windows in the VB Editor, if = not already open. 2.. Re-size the "Height" and "Width" of both the UserForm and = WebBrowser to the same dimensions, and set "Top" and "Left" to zero for = both the UserForm and the WebBrowser. Also, select the = "StartUpPosition" option you desire for the Userform. 3.. From the "Properties" window, change the "Name" option from = "UserForm" to an informative new name without spaces, e.g. "AminoAcids" 4.. From the "Properties" window, change the name WebBrower1 to = something like WebBrower20 (a unique number); you will need a new = WebBrowerXX for every URL projected as a popup browser. 5.. After double clicking on WebBrowser20 (which is superimposed on = the UserForm in the VB Editor window), the following VB code appears: ------------------------------------ Private Sub WebBrowser20_StatusTextChange(ByVal Text As String) End Sub ------------------------------------ 6.. ADD the following code and change the URL to what you want. ----------------------------------------------- Private Sub UserForm_Activate() WebBrowser20.Navigate = "http://tutor.lscf.ucsb.edu/instdev/sears/biochemistry/tw-amn/aaschargedp= olar-frames.htm" End Sub ------------------------------------------ 7.. With the VB Editor select "Insert/Module" 8.. Add the following macro to the Module (e.g., Modul111) with the = designation before the period (say "AminoAcids" in "AminoAcids.Show") = exactly matching the name of the UserForm the macro refers to (i.e., = "AminoAcids") ----------------------------------------- Sub Slide20browse() ' ' Macro created 10/10/04 by Duane W. Sears ' AminoAcids.Show End Sub -------------------------------------- 9.. Close out of the Visual Basic Editor and insert an Action Button = on the slide. 10.. Format the Action Settings of the button by selecting "Run macro" = and selecting "Slide20browse" for the macro. 11.. Now, when you click on the button, WebBrowser20 will pop up over = the slide, and it can be moved around with the mouse if desired. Note = that you have to close the WebBrowser before being able to continue with = the Slide Show. 12.. NOTE: When PowerPoint is first installed, it usually defaults to = the "Highest Security" setting for macros. You have to change this to = "Medium Security" ("Tools/Options/Security/Macro Security/Medium") in = order to be able to activate the popup menu Active X components = associated with the action buttons and WebBrowser functions. After = changing the setting, it is necessary to close out of PowerPoint and = re-open the file before the new security setting remains active (until = you change it). I hope this helps. Good luck. =20 Duane =20 __________________________________ Duane W. Sears Department of Molecular, Cellular, and Developmental Biology University of California Santa Barbara, CA 93106-9610 Office (voice): 805-893-3499 Fax: 805-893-5081 Lab: 805-893-4272 ----- Original Message -----=20 Sent: Sunday, October 10, 2004 11:06 AM From: "Toni Pomar" Subject: Embed chime object in ppt To: > Hi!!! > Can I embed a pdb file in a powerpoint document. > Regards. >=20 >=20 >=20 > ______________________________________________ > Renovamos el Correo Yahoo!: =A1100 MB GRATIS! > Nuevos servicios, m=E1s seguridad > http://correo.yahoo.es >=20 > = > --Boundary_(ID_dYx+wTIQBgya3rQ2pafyvA) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_dYx+wTIQBgya3rQ2pafyvA)-- User-Agent: Internet Messaging Program (IMP) 3.1 X-Originating-IP: 80.28.71.168 X-Virus-Scanned: by amavisd-new at ub.edu References: <5.2.0.9.2.20041008173417.02e682f0@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: GABRIEL PONS IRAZAZABAL Subject: Re: Slides to demonstrate conservation of protein structure? Date: Mon, 11 Oct 2004 11:51:11 +0200 To: rasmol@lists.umass.edu This message is in MIME format. --Boundary_(ID_2Ps9ot4FXHhpoMed8kZr1Q) Hello Dan: I remember that proteins which transport or fix oxygen like myoglobin, hemoglobin or others could be a good exemple. They have low sequence homology but great 3D conservation. For instance, chain alfa and beta of human hemoglobin only share 24 out 141 AA positions with mioglobin, however if you take a look to the image enclosed (mioglobin left, beta chain of hemoglobin right) the conservation of the shape is outstanding Regards, Gabriel Pons > > ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ --Boundary_(ID_2Ps9ot4FXHhpoMed8kZr1Q) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_2Ps9ot4FXHhpoMed8kZr1Q)-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.6) Gecko/20040113 X-Accept-Language: en-us, en References: <20041010180607.40554.qmail@web51110.mail.yahoo.com> ++++------+------+------+------+------+------+------+------+------+------+ From: "Joseph J. Grabowski" Subject: Re: Embed chime object in ppt Date: Mon, 11 Oct 2004 08:30:16 -0400 To: rasmol@lists.umass.edu > Subject: Embed chime object in ppt > Date: Sun, 10 Oct 2004 20:06:07 +0200 (CEST) > From: Toni Pomar > Reply-To: rasmol@lists.umass.edu > To: rasmol@lists.umass.edu > > Hi!!! > Can I embed a pdb file in a powerpoint document. > Regards. One answer is YES, if you use a Windows machine and use Accelrys' Active X control. http://www.accelrys.com/dstudio/ds_viewer/ (freeware last time I downloaded it). When using this control, I find that first converting pdb files to the native format of Accelrys' products (i.e., .msv) to be more reliable however. Also, when using a powerpoint file containing embedded files relying on this Active X control, launch it by double clicking on the .ppt file itself rather than using the "Open" command under the file menu. This seems to obviate the problem of the program not being able to "remember" where the actual molecule structure files are located. Cheers, Joe G. -- Joseph J. Grabowski Associate Professor, Department of Chemistry Director of Undergraduate Research, Arts & Sciences University of Pittsburgh Pittsburgh, PA 15260 Home Page: http://chemed.chem.pitt.edu/joeg Phone: 412-624-8632 Fax: 412-624-8611 ---------------------------------------------------------- Success is relative. It is what we can make of the mess we have made of things. -- T. S. Eliot ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- displaying chime objects X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-MSMail-priority: Normal X-Virus-Scanned: Yes ++++------+------+------+------+------+------+------+------+------+------+ From: Duane Sears Subject: Creating PowerPoint slides with embedded and popup web pages Date: Mon, 11 Oct 2004 11:47:01 -0700 To: rasmol@lists.umass.edu Dear Colleagues, It has come to my attention that the message below, which I sent to the RasMol list server last night in response to Toni Pomar's question about embedding Chime objects in PowerPoint slides, was not received by at least some of you, probably because I failed to format it in plain text, Thus, I am re-sending the message in the appropriate format, and I apologize for the e-mail clutter. Duane W. Sears Department of Molecular, Cellular, and Developmental Biology University of California Santa Barbara, CA 93106-9610 Office (voice): 805-893-3499 Fax: 805-893-5081 Lab: 805-893-4272 ================================================================================= Toni, I've experimented around with a few different ways to embed web pages with Chime images into PowerPoint slides and I find that the free LiveWeb Add-In for PowerPoint (http://www.mvps.org/skp/liveweb.htm ) gives the best result and is easy to manage once you figure out the logic of the Add-In. This Add-In exploits the functionality of the Visual Basic WebBrowser function which launches an Internet Explorer browser embedded in a slide or a Visual Basic UserForm. I know it works with Windows operating systems 98, 2000, and XP. I don't know about other operating systems. If you want to see an example of PowerPoint slide show with such features, you can download a "zipped" sample PowerPoint presentation from my web site at http://tutor.lscf.ucsb.edu/instdev/sears/biochemistry/DWSEARS2004-Ppt-EmbeddedChimeWebpages.zip EMBEDDED WEB BROWSERS WITH CHIME IMAGES In a nutshell, this is how LiveWeb works. Install LiveWeb and then configure PowerPoint for the Add-In by selecting LiveWeb from the Standard Toolbar option -- "Tools/Add-Ins/Install New." Now select the "Insert/Web Pages" drop-down option found on the PowerPoint Standard Toolbar. This option activates a LiveWeb wizard for embedding a WebBrowser Visual Basic function into a slide. The wizard presents a dialog box for you to enter the URL of the web page you want to view on the slide. With a second drop-down LiveWeb menu option -- "Insert/Edit Page Property" - the WebBrowser associated URL can also easily be modified at a later time. This option (which is not particularly well documented and took me a while to discover) is very useful because you can easily update a link if it changes, or change the associated URL for a copied slide so it's WebBrowser is associated with a new web page. A few additional points to note: After a web page has been embedded in a slide, the resizable area you see reserved for the WebBrowser function will always appear on top during Show Mode, even if you have text or a figure pasted over the embedded browser as it appears in the Slide Edit mode. Also, web pages sometimes don't load into the embedded WebBrowser function the first time they are encountered in Show Mode. I don't know why this is, but to partially alleviate this problem, I found a Visual Basic Subroutine that I add to the embedded WebBrowser function's Visual Basic code. This subroutine is designed to trigger web page loading the first time the slide with the WebBrowser function is encountered during the Show Mode. To add the following Subroutine VB code to the WebBrowser function code, DOUBLE CLICK on the WebBrowser you see mapped on the slide in the edit mode. The following Visual Basic text appears initially: --------------------------------------------------- Private Sub WebBrowser1_StatusTextChange(ByVal Text As String) End Sub --------------------------------------------------- Now, APPEND the following Subroutine to this text and change the URL accordingly. ------------------------------- Sub WebBrowser1_DocumentComplete(ByVal pDisp As Object, URL As Variant) Dim varURL As Variant 'Check to see if this is the first time this 'control has been run, if so, load the page. If URL = "" Then varURL = "http://tutor.lscf.ucsb.edu/instdev/sears/biochemistry/" 'INSERT YOUR OWN URL HERE WebBrowser1.Navigate varURL End If End Sub --------------------------------------- POPUP WEB BROWSERS WITH CHIME IMAGES I've also found a way to create pop-up web pages that float over the PowerPoint slides without completely hiding the slide being viewed in Show mode. For this application, the WebBrowser function is added to a Visual Basic UserForm after opening the Visual Basic Editor from the Standard Toolbar option -- "Tools/Macro/Visual Basic Editor." With the VB Editor open, the first step is to select "Insert/UserForm" and the second step is to drag the WebBrowser function on to the UserForm from the "Toolbox. " The first time you do this, the "Microsoft Web Browser" function will probably be located in "Additional Functions" and can be found after right clicking on the ToolBox panel and searching through the list; however, the "WebBrowser" will remain visible on the Toolbox thereafter. Now, do the following: 1. Open the "Project" and "Properties" windows in the VB Editor, if not already open. 2. Re-size the "Height" and "Width" of both the UserForm and WebBrowser to the same dimensions, and set "Top" and "Left" to zero for both the UserForm and the WebBrowser. Also, select the "StartUpPosition" option you desire for the UserForm. 3. From the "Properties" window, change the "Name" option from "UserForm" to an informative new name without spaces, e.g. "AminoAcids" 4. From the "Properties" window, change the name WebBrower1 to something like WebBrower20 (a unique number). You will need a new WebBrowerXX number for every different URL projected as a popup browser. 5. After double clicking on WebBrowser20 (which is superimposed on the UserForm in the VB Editor window), the following VB code appears: ------------------------------------ Private Sub WebBrowser20_StatusTextChange(ByVal Text As String) End Sub ------------------------------------ 6. Now, APPEND the following code and change the URL to what you want. ----------------------------------------------- Private Sub UserForm_Activate() WebBrowser20.Navigate "http://tutor.lscf.ucsb.edu/instdev/sears/biochemistry/tw-amn/aaschargedpolar-frames.htm" End Sub ------------------------------------------ 7. With the VB Editor select "Insert/Module" 8. Add the following macro to the Module (e.g., Modul111) with the designation before the period (say "AminoAcids" in "AminoAcids.Show") exactly matching the name of the UserForm the macro refers to (i.e., "AminoAcids") ----------------------------------------- Sub Slide20browse() ' ' Macro created 10/10/04 by Duane W. Sears ' AminoAcids.Show End Sub -------------------------------------- 9. Close out of the Visual Basic Editor and insert an Action Button on the slide. 10. Format the Action Settings of the button by selecting "Run macro" and selecting "Slide20browse" for the macro. 11. Now, when you click on the button, WebBrowser20 will pop up over the slide, and it can be moved around with the mouse if desired. Note that you have to close the WebBrowser before being able to continue with the Slide Show. 12. NOTE: When PowerPoint is first installed, it usually defaults to the "Highest Security" setting for macros. You have to change this to at least "Medium Security" ("Tools/Options/Security/Macro Security/Medium") in order to be able to activate the popup menu Active X components associated with the action buttons and WebBrowser functions. After changing the setting, it is necessary to close out of PowerPoint and re-open the file before the new security setting remains active (until you change it). I hope this helps. Good luck. Duane __________________________________ Duane W. Sears Department of Molecular, Cellular, and Developmental Biology University of California Santa Barbara, CA 93106-9610 Office (voice): 805-893-3499 Fax: 805-893-5081 Lab: 805-893-4272 ----- Original Message ----- Sent: Sunday, October 10, 2004 11:06 AM From: "Toni Pomar" Subject: Embed chime object in ppt To: > Hi!!! > Can I embed a pdb file in a powerpoint document. > Regards. > > > > ______________________________________________ > Renovamos el Correo Yahoo!: ¡100 MB GRATIS! > Nuevos servicios, más seguridad > http://correo.yahoo.es > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Sequence Search Mailing List X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: [ssml] Re: Slides to demonstrate conservation of protein structure? Date: Tue, 12 Oct 2004 17:54:24 +0100 (BST) Cc: Rasmol Mailing List , Thanks all for the suggestions! I made some slides but they are not really what I hoped for... Anyway, I can provide them for anyone on request. Now I have another question - What is the original reference for the 'well known fact' that protein structure is more conserved than sequence? It was pointed out by Max Perutz when the first protein structures were solved in parrallel with John Kendrew (heamaglobin / myoglobin from horse / whale although I forget which from which). They didn't see sequence identity, but found structural identity (by conincidence?). Also the protein was all alpha, just after Linus Pauling predicted that would be a stable form of protein. I was thinking that the original RMSD / sequence identity relationship by Chothiea and Lesk, but that dosen't really show the fact that the structure is conserved as sequence diverges. Or does it? Is there a reprint of the latter article? Cheers, Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id i9CKj6H19442 ++++------+------+------+------+------+------+------+------+------+------+ From: Craig Marshall Subject: Re: [ssml] Re: Slides to demonstrate conservation of protein structure? Date: Wed, 13 Oct 2004 09:44:03 +1300 To: rasmol@lists.umass.edu Dan, This may not be quite what you asked for but may be of interest given your question. Axe, D.D. (2000). “Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors.” Journal of Molecular Biology 301, 585-595. Regards, Craig On 13/10/2004, at 5:54 AM, Dan Bolser wrote: > > Thanks all for the suggestions! I made some slides but they are not > really > what I hoped for... > > Anyway, I can provide them for anyone on request. -- Craig Marshall craig.marshall@otago.ac.nz Biochemistry http://biochem.otago.ac.nz/staff/marshall/cmarshall.htm University of Otago Phone +64 3 479 7570 Fax +64 3 479 7866 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Edinburgh-Scanned: at lawnmarket.ucs.ed.ac.uk with MIMEDefang 2.33, Sophie 3.04rc1, Sophos Anti-Virus 3.86 X-Scanned-By: MIMEDefang 2.33 (www . roaringpenguin . com / mimedefang) References: <007101c4ad4b$4608a2a0$d418a580@bfoley> ++++------+------+------+------+------+------+------+------+------+------+ From: Andrew Coulson Subject: Re: [ssml] Re: Slides to demonstrate conservation of protein structure? Date: Wed, 13 Oct 2004 10:57:00 +0100 To: rasmol@lists.umass.edu Dan --- >Now I have another question - What is the original reference for the 'well >known fact' that protein structure is more conserved than sequence? I'm glad you've put this question again, because it gives me a chance once again to clamber onto my oldest and most battered pedantic hobby-horse. This 'well-known fact' does not have a respectable provenance, because it is a meaningless assertion. Sequence conservation can be measured, say, by %identity; less intuitively, structure conservation may be measured by RMS deviation. These are qualitatively different scales, and asking whether a pair of sequences is more conserved than a pair of structures is like asking whether Frost is 'closer' to Larkin than Boston is to Hull. 'You can't add apples to oranges', as Mr Ellenger said on Day 1 of Algebra at my (English) prep school. The study by Chothia and Lesk which you refer to showed empirically that there is a (non-linear) mapping between the two measures (see for example Fig 5.6 on p181 of Lesk' 'Introduction to Protein Architecture'). But the whole point of such a mapping is to allow distances on one scale to be converted to distances on the other (or rather, to make approximate estimates of the conversion) -- so that the underlying 'evolutionary distance' between two proteins comes out the same whichever way you look at it. It would be a meaningful -- and true -- assertion to say that evolutionary conservation may often be more easily recognised by comparing structures than by comparing sequences, but the inverse argument does not necessarily hold. If a pair of structures are recognisably similar, but the sequences are not, this may be because of convergent evolution. There are three types of evidence which argue for divergent evolution: 1) (much the strongest) is where you can establish a chain of pairwise sequence similarities, each individually strong, but the ends of the chain have no sequence similarity -- for example, leghemoglobin and the oxygen-carrying globins. 2) (a much used shortcut) is to use similarity of function, and perhaps conservation of active site residues, etc. This argument has been used, for example, to suggest that several TIM-barrels, whose function is saccharide hydrolysis, are evolutionarily related. Both of these arguments depend on evidence outside the naked structure; 3) is to argue that so many features of the structures which might have been different are the same that chance and convergent evolution are improbable. These arguments can be problematic because of the uncertainties involved in 'which might have been different'. Many years ago, Rossmann argued that subtilisin had a common ancestor with the Rossmann-fold dehydrogenases because, inter alia, the handedness of the beta-alpha-beta connections was the same throughout. It was quickly realised that this handedness is energetically favourable. Finally, can I make a pair of mischievous suggestions? One is that since we know (from Kabsch & Sander, initially) that identical subsequences may have differing structures, isn't it possible that occasionally 'sequence is more conserved than structure'? And the second is to wonder whether structure-based alignments are always a more reliable guide to evolution than sequence-based ones. Isn't it conceivable, for example, that a beta-strand might migrate through a sequence (steps of two-at-a-time, perhaps) after the insertion or deletion of loop residues? In such a case, structurally-aligned residues would not have a common ancestor. Andrew Coulson ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Harm van Heerikhuizen Subject: Re: [ssml] Re: Slides to demonstrate conservation of protein structure? Date: Wed, 13 Oct 2004 12:12:46 +0200 To: rasmol@lists.umass.edu >Thanks all for the suggestions! I made some slides but they are not really >what I hoped for... > >Anyway, I can provide them for anyone on request. Hi Dan, Although the slides may not have turned out the way you hoped, I nevertheless would be interested in receiving them. Thanks! Cheers, Harm -- *************************************************************************** Harm van Heerikhuizen, PhD Dept. of Biochemistry and Molecular Biology Vrije Universiteit De Boelelaan 1083 1081 HV Amsterdam The Netherlands tel: + 31 - 20 - 444 7573 (office) tel: + 31 - 20 - 444 7555 (secretary) fax: + 31 - 20 - 444 7553 e-mail: vheerik@chem.vu.nl *************************************************************************** ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <007101c4ad4b$4608a2a0$d418a580@bfoley> ++++------+------+------+------+------+------+------+------+------+------+ From: James Milner-White Subject: Re: [ssml] Re: Slides to demonstrate conservation of protein structure? Date: Wed, 13 Oct 2004 12:29:55 +0100 (BST) To: rasmol@lists.umass.edu Andrew, This is a really interesting point. I shall change my lectures this year because of it. Its an important issue and would make a good short letter to Nature or elsewhere, James >Dan --- > > >>Now I have another question - What is the original reference for the 'well >>known fact' that protein structure is more conserved than sequence? > I'm glad you've put this question again, because it gives me a >chance once again to clamber onto my oldest and most battered pedantic >hobby-horse. >This 'well-known fact' does not have a respectable provenance, because it >is a meaningless assertion. Sequence conservation can be measured, say, by >%identity; less intuitively, structure conservation may be measured by RMS >deviation. These are qualitatively different scales, and asking whether a >pair of sequences is more conserved than a pair of structures is like >asking whether Frost is 'closer' to Larkin than Boston is to Hull. 'You >can't add apples to oranges', as Mr Ellenger said on Day 1 of Algebra at my >(English) prep school. >The study by Chothia and Lesk which you refer to showed empirically that >there is a (non-linear) mapping between the two measures (see for example >Fig 5.6 on p181 of Lesk' 'Introduction to Protein Architecture'). But the >whole point of such a mapping is to allow distances on one scale to be >converted to distances on the other (or rather, to make approximate >estimates of the conversion) -- so that the underlying 'evolutionary >distance' between two proteins comes out the same whichever way you look >at it. > It would be a meaningful -- and true -- assertion to say that >evolutionary conservation may often be more easily recognised by comparing >structures than by comparing sequences, but the inverse argument does not >necessarily hold. If a pair of structures are recognisably similar, but the >sequences are not, this may be because of convergent evolution. There are >three types of evidence which argue for divergent evolution: >1) (much the strongest) is where you can establish a chain of pairwise >sequence similarities, each individually strong, but the ends of the chain >have no sequence similarity -- for example, leghemoglobin and the >oxygen-carrying globins. >2) (a much used shortcut) is to use similarity of function, and perhaps >conservation of active site residues, etc. This argument has been used, for >example, to suggest that several TIM-barrels, whose function is saccharide >hydrolysis, are evolutionarily related. >Both of these arguments depend on evidence outside the naked structure; >3) is to argue that so many features of the structures which might have >been different are the same that chance and convergent evolution are >improbable. These arguments can be problematic because of the uncertainties >involved in 'which might have been different'. Many years ago, Rossmann >argued that subtilisin had a common ancestor with the Rossmann-fold >dehydrogenases because, inter alia, the handedness of the beta-alpha-beta >connections was the same throughout. It was quickly realised that this >handedness is energetically favourable. > Finally, can I make a pair of mischievous suggestions? >One is that since we know (from Kabsch & Sander, initially) that identical >subsequences may have differing structures, isn't it possible that >occasionally 'sequence is more conserved than structure'? >And the second is to wonder whether structure-based alignments are always a >more reliable guide to evolution than sequence-based ones. Isn't it >conceivable, for example, that a beta-strand might migrate through a >sequence (steps of two-at-a-time, perhaps) after the insertion or deletion >of loop residues? In such a case, structurally-aligned residues would not >have a common ancestor. > >Andrew Coulson ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Edinburgh-Scanned: at lawnmarket.ucs.ed.ac.uk with MIMEDefang 2.33, Sophie 3.04rc1, Sophos Anti-Virus 3.86 X-Scanned-By: MIMEDefang 2.33 (www . roaringpenguin . com / mimedefang) References: <007101c4ad4b$4608a2a0$d418a580@bfoley> ++++------+------+------+------+------+------+------+------+------+------+ From: Andrew Coulson Subject: Re: [ssml] Re: Slides to demonstrate conservation of protein structure? Date: Wed, 13 Oct 2004 12:42:53 +0100 To: rasmol@lists.umass.edu Which point in particular? The one about structures migrating? I can't remember when this occurred to me, or what triggered it -- may just have been me slipping into Devils Advocate mode in face of some triumphalist crystallographer...... Is there any way we could get any evidence for its plausibility? ac Or the whole thing? Yes, I've sometimes thought about planting a squib somewhere -- wouldnt have thought it was up to Nature's august heights though.... At 12:29 13/10/2004, you wrote: >Andrew, >This is a really interesting point. I shall change my lectures this year >because of it. Its an important issue and would make a good short letter >to Nature or elsewhere, >James > > >Dan --- > > > > > >>Now I have another question - What is the original reference for the 'well > >>known fact' that protein structure is more conserved than sequence? > > I'm glad you've put this question again, because it gives me a > >chance once again to clamber onto my oldest and most battered pedantic > >hobby-horse. > >This 'well-known fact' does not have a respectable provenance, because it > >is a meaningless assertion. Sequence conservation can be measured, say, by > >%identity; less intuitively, structure conservation may be measured by RMS > >deviation. These are qualitatively different scales, and asking whether a > >pair of sequences is more conserved than a pair of structures is like > >asking whether Frost is 'closer' to Larkin than Boston is to Hull. 'You > >can't add apples to oranges', as Mr Ellenger said on Day 1 of Algebra at my > >(English) prep school. > >The study by Chothia and Lesk which you refer to showed empirically that > >there is a (non-linear) mapping between the two measures (see for example > >Fig 5.6 on p181 of Lesk' 'Introduction to Protein Architecture'). But the > >whole point of such a mapping is to allow distances on one scale to be > >converted to distances on the other (or rather, to make approximate > >estimates of the conversion) -- so that the underlying 'evolutionary > >distance' between two proteins comes out the same whichever way you look > >at it. > > It would be a meaningful -- and true -- assertion to say that > >evolutionary conservation may often be more easily recognised by comparing > >structures than by comparing sequences, but the inverse argument does not > >necessarily hold. If a pair of structures are recognisably similar, but the > >sequences are not, this may be because of convergent evolution. There are > >three types of evidence which argue for divergent evolution: > >1) (much the strongest) is where you can establish a chain of pairwise > >sequence similarities, each individually strong, but the ends of the chain > >have no sequence similarity -- for example, leghemoglobin and the > >oxygen-carrying globins. > >2) (a much used shortcut) is to use similarity of function, and perhaps > >conservation of active site residues, etc. This argument has been used, for > >example, to suggest that several TIM-barrels, whose function is saccharide > >hydrolysis, are evolutionarily related. > >Both of these arguments depend on evidence outside the naked structure; > >3) is to argue that so many features of the structures which might have > >been different are the same that chance and convergent evolution are > >improbable. These arguments can be problematic because of the uncertainties > >involved in 'which might have been different'. Many years ago, Rossmann > >argued that subtilisin had a common ancestor with the Rossmann-fold > >dehydrogenases because, inter alia, the handedness of the beta-alpha-beta > >connections was the same throughout. It was quickly realised that this > >handedness is energetically favourable. > > Finally, can I make a pair of mischievous suggestions? > >One is that since we know (from Kabsch & Sander, initially) that identical > >subsequences may have differing structures, isn't it possible that > >occasionally 'sequence is more conserved than structure'? > >And the second is to wonder whether structure-based alignments are always a > >more reliable guide to evolution than sequence-based ones. Isn't it > >conceivable, for example, that a beta-strand might migrate through a > >sequence (steps of two-at-a-time, perhaps) after the insertion or deletion > >of loop residues? In such a case, structurally-aligned residues would not > >have a common ancestor. > > > >Andrew Coulson > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Edinburgh-Scanned: at lawnmarket.ucs.ed.ac.uk with MIMEDefang 2.33, Sophie 3.04rc1, Sophos Anti-Virus 3.86 X-Scanned-By: MIMEDefang 2.33 (www . roaringpenguin . com / mimedefang) ++++------+------+------+------+------+------+------+------+------+------+ From: Andrew Coulson Subject: Apologies.... Date: Wed, 13 Oct 2004 12:50:14 +0100 To: rasmol@lists.umass.edu Middle-aged flying-finger trouble caused me not to notice that R was going to result in my sending what was intended to be a quick note to James Milner-White to this list as a whole. I am very, very sorry and promise to be more careful in future. Andrew Coulson ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: [ssml] Re: Slides to demonstrate conservation of protein structure? Date: Wed, 13 Oct 2004 13:12:23 +0100 (BST) To: rasmol@lists.umass.edu Cc: Sequence Search Mailing List On Wed, 13 Oct 2004, Andrew Coulson wrote: >Which point in particular? The one about structures migrating? I can't >remember when this occurred to me, or what triggered it -- may just have >been me slipping into Devils Advocate mode in face of some triumphalist >crystallographer...... Is there any way we could get any evidence for its >plausibility? I think the 'transitive' alignments you describe would be a good way to test the idea. You could carefully align a succession of sequences and show while the sequence alignments can cope with certain geometric alterations, traditional structural alignments cannot. Any clear examples of conformational change in evolutionary time? I was once hoping to study (search for) this type of thing, as I don't know of any clear rules that can be give for when / if this happens. I never looked into it though. However, I think structure alignments based on fragments, and allowing flexible regions (energy minimizing one alignment onto another) could counter these problems with the existing techniques. It is a good point you make though - our concepts are based on the tools used to investigate the data. Of course nature doesn't give a damn about conserving anything in particular, just increasing reproductive potential within the given physical laws of the universe. P.S. Can you send the Kabsch & Sander refernce? Cheers, Dan. >ac >Or the whole thing? Yes, I've sometimes thought about planting a squib >somewhere -- wouldnt have thought it was up to Nature's august heights >though.... > >At 12:29 13/10/2004, you wrote: >>Andrew, >>This is a really interesting point. I shall change my lectures this year >>because of it. Its an important issue and would make a good short letter >>to Nature or elsewhere, >>James >> >> >Dan --- >> > >> > >> >>Now I have another question - What is the original reference for the 'well >> >>known fact' that protein structure is more conserved than sequence? >> > I'm glad you've put this question again, because it gives me a >> >chance once again to clamber onto my oldest and most battered pedantic >> >hobby-horse. >> >This 'well-known fact' does not have a respectable provenance, because it >> >is a meaningless assertion. Sequence conservation can be measured, say, by >> >%identity; less intuitively, structure conservation may be measured by RMS >> >deviation. These are qualitatively different scales, and asking whether a >> >pair of sequences is more conserved than a pair of structures is like >> >asking whether Frost is 'closer' to Larkin than Boston is to Hull. 'You >> >can't add apples to oranges', as Mr Ellenger said on Day 1 of Algebra at my >> >(English) prep school. >> >The study by Chothia and Lesk which you refer to showed empirically that >> >there is a (non-linear) mapping between the two measures (see for example >> >Fig 5.6 on p181 of Lesk' 'Introduction to Protein Architecture'). But the >> >whole point of such a mapping is to allow distances on one scale to be >> >converted to distances on the other (or rather, to make approximate >> >estimates of the conversion) -- so that the underlying 'evolutionary >> >distance' between two proteins comes out the same whichever way you look >> >at it. >> > It would be a meaningful -- and true -- assertion to say that >> >evolutionary conservation may often be more easily recognised by comparing >> >structures than by comparing sequences, but the inverse argument does not >> >necessarily hold. If a pair of structures are recognisably similar, but the >> >sequences are not, this may be because of convergent evolution. There are >> >three types of evidence which argue for divergent evolution: >> >1) (much the strongest) is where you can establish a chain of pairwise >> >sequence similarities, each individually strong, but the ends of the chain >> >have no sequence similarity -- for example, leghemoglobin and the >> >oxygen-carrying globins. >> >2) (a much used shortcut) is to use similarity of function, and perhaps >> >conservation of active site residues, etc. This argument has been used, for >> >example, to suggest that several TIM-barrels, whose function is saccharide >> >hydrolysis, are evolutionarily related. >> >Both of these arguments depend on evidence outside the naked structure; >> >3) is to argue that so many features of the structures which might have >> >been different are the same that chance and convergent evolution are >> >improbable. These arguments can be problematic because of the uncertainties >> >involved in 'which might have been different'. Many years ago, Rossmann >> >argued that subtilisin had a common ancestor with the Rossmann-fold >> >dehydrogenases because, inter alia, the handedness of the beta-alpha-beta >> >connections was the same throughout. It was quickly realised that this >> >handedness is energetically favourable. >> > Finally, can I make a pair of mischievous suggestions? >> >One is that since we know (from Kabsch & Sander, initially) that identical >> >subsequences may have differing structures, isn't it possible that >> >occasionally 'sequence is more conserved than structure'? >> >And the second is to wonder whether structure-based alignments are always a >> >more reliable guide to evolution than sequence-based ones. Isn't it >> >conceivable, for example, that a beta-strand might migrate through a >> >sequence (steps of two-at-a-time, perhaps) after the insertion or deletion >> >of loop residues? In such a case, structurally-aligned residues would not >> >have a common ancestor. >> > >> >Andrew Coulson >> >> > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: Slides to demonstrate conservation of protein structure? Date: Wed, 13 Oct 2004 16:08:06 +0100 (BST) To: rasmol@lists.umass.edu Cheers! Dan. On Sat, 9 Oct 2004, Gabe McCool wrote: >Dan- > >Sounds great...looking forward to seeing your slides at some point. Further >to Eric Martz's FtsZ suggestion, the presentation at > >http://www.umass.edu/microbio/chime/pipe/ftsz/present/index.htm > >tries to point out FtsZ's close structural alignment with tubulin contrasted >with the low seq identity (<20%) between aligned FtsZ + tubulin aa >sequences. Hope its helpful in some regard. > > >Gabe McCool > > > > >> From: Eric Martz >> Reply-To: >> Date: Fri, 08 Oct 2004 17:40:02 -0400 >> To: >> Subject: Re: Slides to demonstrate conservation of protein structure? >> >> At 10/8/04, Dan Bolser wrote: >> >>> Hi, >>> >>> I would like to demonstrate the well known principal that protein >>> structure is more conserved than protein sequence in evolutionary >>> time. I am presenting to a group of structural biologists, so I >>> want to emphasize the bioinformatic perspective. >>> >>> My idea for a series of slides is this >>> >>> 1) show two clearly structurally similar (same topology) protein domains. >> >> One example pointed out to me years ago by Gabe McCool is the bacterial >> cell division protein FtsZ. A structure-based search turns up tubulin, but >> the sequence identity is only 16% (if I recall). >> >> This paper by Friedberg, Kaplan and Margalit >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abst >> ract&list_uids=11152139 >> assesses >> "the accuracy of PSI-BLAST alignments on a stringent database of 123 >> structurally similar, sequence-dissimilar pairs of proteins, by comparing >> them to the alignments defined on a structural basis." >> >> I will be quite interested in your slides when they become available! >> Please keep us posted. >> -Eric Martz >> >>> 1.1) show that the two sequences are very different, and result in >>> a 'bad' sequence alignment (somehow visually). >>> >>> 2) Show a nieve (and hopefully bad) structural alignment of the two >>> domains based (nievely) on the sequence alignment. >>> >>> 3) Show a pure (and simple) structural alignment of the two domains. >>> 3.1) Show the sequence alignment based on the good structural alignment. >>> >>> >>> My idea is to convey the importance of structure in recognizing distant >>> homology between domains. >>> >>> I want to use a real example using real tools, but I am not sure how / >>> which tools to use.Any suggetions? Good demo / bad demo? Naturally I need >>> this done by yesterday, so the simpler the tools the better. >>> >>> I will be happy to post the slides somewhere appropriate to share this >>> work with the world. >>> >>> All the best, >>> Dan. >>> >> >> /* - - - - - - - - - - - - - - - - - - - - - - - - - - - >> Protein Explorer - 3D Visualization: http://proteinexplorer.org >> Workshops: http://www.umass.edu/molvis/workshop >> Biochem Structure Tutorials http://MolviZ.org >> World Index of Molecular Visualization Resources: http://molvisindex.org >> ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il >> Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm >> PDB Lite Macromolecule Finder: http://pdblite.org >> Molecular Visualization EMail List: >> http://www.umass.edu/microbio/rasmol/raslist.htm >> >> Eric Martz, Professor Emeritus, Dept Microbiology >> U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 >> http://www.umass.edu/molvis/martz >> - - - - - - - - - - - - - - - - - - - - - - - - - - - */ >> >> > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Internet Messaging Program (IMP) 3.1 X-Originating-IP: 161.116.207.40 X-Virus-Scanned: by amavisd-new at ub.edu References: ++++------+------+------+------+------+------+------+------+------+------+ From: GABRIEL PONS IRAZAZABAL Subject: Re: not folded protein Date: Thu, 14 Oct 2004 14:50:33 +0200 To: rasmol@lists.umass.edu To illustrate the principles of protein folding I am trying to get a pdb file with a relatively long stretch of a chain completely unfolded (50-100 residues). Anybody knows where can I get it or how to generate it by easy modelling? Thanks ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Virus-Scanned: Symantec AntiVirus Scan Engine References: <1097758233.416e7619d1d6c@webmail3.ub.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Re: not folded protein Date: Thu, 14 Oct 2004 10:52:53 -0400 To: rasmol@lists.umass.edu Hi, Gabriel! DeepView (aka SwissPdbViewer) loads a FASTA file of sequence and automatically produces coordinates of the polypeptide as an alpha helix. Open the FASTA file with the menu command SwissModel:Load Raw Sequence to Model. Save the coordinates with File:Save:Layer. Reload the saved file. Using the command Tools:Reset Omega/Phi/Psi, or using the interactive Ramachandran diagram, you can alter the chain conformation to suit yourself. For more information about DeepView, see these sites: http://www.usm.maine.edu/spdbv/text/mirror.htm for the DeepView server nearest you. http://www.usm.maine.edu/~rhodes/SPVTut/index.html for a full tutorial on the program. Hope this helps. Cheers! On Oct 14, 2004, at 8:50 AM, GABRIEL PONS IRAZAZABAL wrote: > To illustrate the principles of protein folding I am trying to get a > pdb file > with a relatively long stretch of a chain completely unfolded (50-100 > residues). > Anybody knows where can I get it or how to generate it by easy > modelling? > > Thanks > > ------------------------------------------------- > This mail sent through IMP: http://horde.org/imp/ > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > > Gale Rhodes, Professor of Chemistry University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 http://www.usm.maine.edu/~rhodes ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <1097758233.416e7619d1d6c@webmail3.ub.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "James W. Caras" Subject: Re: not folded protein Date: Thu, 14 Oct 2004 09:55:56 -0500 To: rasmol@lists.umass.edu You could easily model it using Swiss PDB viewer. Jamie ======+======+======+======+====== James Caras, Ph.D. Principal Science Technologies 4214 Avenue D Austin, TX 78751 jcaras@sciencetechnologies.com http://www.sciencetechnologies.com AIM: jamiescience (512) 323-6565 Work (512) 467-8842 Home (512) 585-3281 Mobile On Oct 14, 2004, at 7:50 AM, GABRIEL PONS IRAZAZABAL wrote: > To illustrate the principles of protein folding I am trying to get a > pdb file > with a relatively long stretch of a chain completely unfolded (50-100 > residues). > Anybody knows where can I get it or how to generate it by easy > modelling? > > Thanks > > ------------------------------------------------- > This mail sent through IMP: http://horde.org/imp/ > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal User-Agent: SquirrelMail/1.4.3a X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <1097758233.416e7619d1d6c@webmail3.ub.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: dmb@mrc-dunn.cam.ac.uk Subject: Re: not folded protein Date: Thu, 14 Oct 2004 15:57:33 +0100 (BST) To: rasmol@lists.umass.edu Cc: rasmol@lists.umass.edu > Hi, Gabriel! > > DeepView (aka SwissPdbViewer) loads a FASTA file of sequence and > automatically produces coordinates of the polypeptide as an alpha > helix. Open the FASTA file with the menu command SwissModel:Load Raw > Sequence to Model. Save the coordinates with File:Save:Layer. > > Reload the saved file. Using the command Tools:Reset Omega/Phi/Psi, or > using the interactive Ramachandran diagram, you can alter the chain > conformation to suit yourself. > > For more information about DeepView, see these sites: > > http://www.usm.maine.edu/spdbv/text/mirror.htm for the DeepView server > nearest you. > > http://www.usm.maine.edu/~rhodes/SPVTut/index.html for a full tutorial > on the program. > > Hope this helps Also RAPPER generates 'bioloical like' random conformations (dosen't quite fit the idea of 'unfolded', but could be usefull). http://raven.bioc.cam.ac.uk/ > Cheers! > > > On Oct 14, 2004, at 8:50 AM, GABRIEL PONS IRAZAZABAL wrote: > >> To illustrate the principles of protein folding I am trying to get a >> pdb file >> with a relatively long stretch of a chain completely unfolded (50-100 >> residues). >> Anybody knows where can I get it or how to generate it by easy >> modelling? >> >> Thanks >> >> ------------------------------------------------- >> This mail sent through IMP: http://horde.org/imp/ >> >> ---------------------------------------------------------------- >> rasmol-+ >> >> To change your address, unsubscribe, view previous messages/history, >> receive messages as weekly digests, or for any other information >> about the RasMol EMail List, please go to >> http://www.umass.edu/microbio/rasmol/raslist.htm >> >> ---------------------------------------------------------------- >> rasmol-- >> >> > Gale Rhodes, Professor of Chemistry > University of Southern Maine > PO Box 9300 > Portland, Maine 04104-9300 > http://www.usm.maine.edu/~rhodes > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Sequence Search Mailing List X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: [ssml] Re: Slides to demonstrate conservation of protein structure? Date: Fri, 15 Oct 2004 19:46:21 +0100 (BST) To: Rasmol Mailing List , I am planning to put the sides (such as they are) at http://www.biomoleculesalive.org Anyone object to .ppt? With .ppt you can edit the slides more easily, hoever, I could take a snap of each slide and upload several .png files instead. The latter is easier for people to see freely, but the former is more flexible for people to use / adapt. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_t9UfOBzEDMyfbINB2vTbCw)" ++++------+------+------+------+------+------+------+------+------+------+ From: saravanan dayalan Subject: secondary struct info Date: Mon, 18 Oct 2004 08:07:36 +0000 To: rasmol@lists.umass.edu This is a multipart mime message --Boundary_(ID_t9UfOBzEDMyfbINB2vTbCw) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_t9UfOBzEDMyfbINB2vTbCw)-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: [ssml] Re: Slides to demonstrate conservation of protein structure? Date: Mon, 18 Oct 2004 19:19:41 +0100 (BST) To: Gerard DVD Kleywegt Cc: Rasmol Mailing List I will put them somewhere soon, as I can't get the molvis.org to work. This item on the radio seems pertinent... Microsoft, PowerPoint and the Decline of Civilization http://www.bbc.co.uk/radio4/factual/rams/mon1545.ram and http://www.norvig.com/Gettysburg/ I have seen a fair number of 'pitches' in the style of science. On Mon, 18 Oct 2004, Gerard DVD Kleywegt wrote: >> I am planning to put the sides (such as they are) at >> >> http://www.biomoleculesalive.org >> >> Anyone object to .ppt? With .ppt you can edit the slides more easily, >> hoever, I could take a snap of each slide and upload several .png files >> instead. The latter is easier for people to see freely, but the former is >> more flexible for people to use / adapt. > >hi dan, > >that site crashes my browser i'm afraid. could you send me a copy of your >slides by e-mail ? thanks ! > >--gerard > >****************************************************************** > Gerard J. Kleywegt > [Research Fellow of the Royal Swedish Academy of Sciences] >Dept. of Cell & Molecular Biology University of Uppsala > Biomedical Centre Box 596 > SE-751 24 Uppsala SWEDEN > > http://xray.bmc.uu.se/gerard/ mailto:gerard@xray.bmc.uu.se >****************************************************************** > The opinions in this message are fictional. Any similarity > to actual opinions, living or dead, is purely coincidental. >****************************************************************** > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: [ssml] Re: Slides to demonstrate conservation of protein structure? Date: Mon, 18 Oct 2004 14:58:08 -0400 To: rasmol@lists.umass.edu At 10/18/04, Dan Bolser wrote: >I will put them somewhere soon, as I can't get the molvis.org to work. Dan, I assume you meant molvisindex.org (since molvis.org is the journal molecular vision). Let me know if I can help, but be aware that molvisindex.org only accepts links to resources that are already on another server that you maintain. You can't upload content, except for descriptions of what's at the other end of a link. However, biomoleculesalive.org does accept uploads and seems ideal for your slides! -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop Biochem Structure Tutorials http://MolviZ.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: [ssml] Re: Slides to demonstrate conservation of protein structure? Date: Mon, 18 Oct 2004 21:02:35 +0100 (BST) To: rasmol@lists.umass.edu On Mon, 18 Oct 2004, Eric Martz wrote: >At 10/18/04, Dan Bolser wrote: >>I will put them somewhere soon, as I can't get the molvis.org to work. > > >Dan, I assume you meant molvisindex.org (since molvis.org is the journal >molecular vision). Let me know if I can help, but be aware that >molvisindex.org only accepts links to resources that are already on another >server that you maintain. You can't upload content, except for descriptions >of what's at the other end of a link. > >However, biomoleculesalive.org does accept uploads and seems ideal for your >slides! Sorry for the slopy email, I actually ment biomoleculesalive.org. The upload forms hang half way through the process. I have logged a 'bug', and am waiting for them to get back to me. Dan. > >-Eric > > >/* - - - - - - - - - - - - - - - - - - - - - - - - - - - >Protein Explorer - 3D Visualization: http://proteinexplorer.org >Workshops: http://www.umass.edu/molvis/workshop >Biochem Structure Tutorials http://MolviZ.org >World Index of Molecular Visualization Resources: http://molvisindex.org >ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il >Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm >PDB Lite Macromolecule Finder: http://pdblite.org >Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > >Eric Martz, Professor Emeritus, Dept Microbiology >U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz >- - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MSMail-Priority: High boundary="8.0._E44__." ++++------+------+------+------+------+------+------+------+------+------+ From: "Administrator" Subject: ADV: Staff Announcement Date: Tue, 19 Oct 04 21:20:49 GMT To: nnor@bio.umass.edu This is a multi-part message in MIME format. --8.0._E44__. 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Thursday, October 21, 2004 Visit our website at http://www.avtechdirect-education.com If you wish to unsubscribe from this list, please go to http://www.computeradvice.org/unsubscribelink.asp Avtech Direct 22647 Ventura Blvd. Suite 374 Woodland Hills, CA 91364 --8.0._E44__.-- LIST rasmol ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: new Jmol- and Rasmol-oriented resource Date: Thu, 21 Oct 2004 23:31:54 -0400 To: LIST Jmol users , hello, I have created a new resource for Jmol, Rasmol, and Chime developers called Color Gradients. you can use it to create script commands that apply a gradient color scheme to your molecule of choice. this is similar to the 'color group' command already present in Rasmol, but with some improvements: 1. choose from among four different gradient styles (rainbow, blue-white-red, black-white, or white-black). 2. create gradients that apply to a single chain, span multiple chains, or apply separately to each chain of a multi-chain structure. up to four chains are supported at this time. Color Gradients is comptible with Jmol, Rasmol, and Chime, and is available here: (you can also access it under the Resources menu at my home page, .) it will run in any Web browser; not even javascript is required. ;-) to use Color Gradients, you will need to enter the chain designators, and the starting and ending residue numbers for each chain. the output is a simple html file containing your script commands, from which you can select all, copy, and paste into your spt file (or an empty text file). plans for the future include allowing a pdb file to be uploaded directly, to read chains and residues from the file itself, and other output and command formatting options. if anyone has any suggestions for improving this resource, or if it doesn't work as expected, please feel free to send me email (offlist, if you prefer). regards, tim -- Timothy Driscoll molvisions - see, grasp, learn. usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: new Jmol- and Rasmol-oriented resource Date: Fri, 22 Oct 2004 08:51:48 +0100 (BST) To: LIST rasmol Cc: LIST Jmol users On Thu, 21 Oct 2004, timothy driscoll wrote: >hello, > >I have created a new resource for Jmol, Rasmol, and Chime developers >called Color Gradients. you can use it to create script commands that >apply a gradient color scheme to your molecule of choice. this is >similar to the 'color group' command already present in Rasmol, but with >some improvements: > >1. choose from among four different gradient styles (rainbow, >blue-white-red, black-white, or white-black). > >2. create gradients that apply to a single chain, span multiple chains, >or apply separately to each chain of a multi-chain structure. up to >four chains are supported at this time. > > >Color Gradients is comptible with Jmol, Rasmol, and Chime, and is >available here: > > > > >(you can also access it under the Resources menu at my home page, >.) it will run in any Web browser; not even >javascript is required. ;-) > >to use Color Gradients, you will need to enter the chain designators, >and the starting and ending residue numbers for each chain. the output >is a simple html file containing your script commands, from which you >can select all, copy, and paste into your spt file (or an empty text >file). > >plans for the future include allowing a pdb file to be uploaded >directly, to read chains and residues from the file itself, and other >output and command formatting options. > > >if anyone has any suggestions for improving this resource, or if it >doesn't work as expected, please feel free to send me email (offlist, if >you prefer). This looks really great. One thing I expected was that the gradient would be 'squashed' to fit the length of the selection, so I would always see one blue, one white and one red even if I only selected three residues. Selecting around 40 residues I only see (a very nice:) gradient from white to red. One other thing I spotted using the grayscale was the following color "color [255,-0,0]", which rasmol doesn't like. I was attempting to build something vaguely similar (in concept) with the 'pdbHighlight' project, basically a resource for visually annotating PDB files. Although I haven't found time to make my perl scripts into a CGI page yet. http://bioinformatics.org/pdbHighlight/ This has been a work in progress for a couple of years ;) One thing I would love to see is if you could 'serve' your scripts as a web service with an API, then rasmol / jmol / chime could be configured to lookup the results of that web service on a certain command (i.e. based on a config file which would expand the language syntax). The only practical difference with this approach is that it avoids the need to copy / paste from one platform to another, but it also opens up the possibility of sending all kinds of cool commands to peoples molecular viewers on request. Cheers, Dan. > > >regards, > >tim > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: [Jmol-users] Re: new Jmol- and Rasmol-oriented resource Date: Fri, 22 Oct 2004 14:00:09 -0400 To: jmol-users@lists.sourceforge.net, LIST rasmol On 2004-10-22 (06:38) timothy driscoll wrote: >On 2004-10-22 (08:51) Dan Bolser wrote: > >>On Thu, 21 Oct 2004, timothy driscoll wrote: >> >>> >>>1. choose from among four different gradient styles (rainbow, >>>blue-white-red, black-white, or white-black). >>> >>>2. create gradients that apply to a single chain, span multiple >>>chains, or apply separately to each chain of a multi-chain >>>structure. up to four chains are supported at this time. >>> >>> >>>Color Gradients is comptible with Jmol, Rasmol, and Chime, and is >>>available here: >>> >>> >>> >>> >> >>This looks really great. One thing I expected was that the gradient >>would be 'squashed' to fit the length of the selection, so I would >>always see one blue, one white and one red even if I only selected >>three residues. hello, FYI, I have just updated the Color Gradients resource to include error-checking, and improve the color algorithms. if anyone has any other gradients that may prove useful for visualizing 3D structures, please feel free to make suggestions. :-) regards, tim -- Timothy Driscoll molvisions - see, grasp, learn. usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: New home for this molvis-list Date: Sat, 23 Oct 2004 14:24:40 -0400 To: rasmol@lists.umass.edu Dear Subscribers to this Molecular Visualization EMail List: Changes at the University of Massachusetts require that this list be relocated. UMass has kindly hosted this list (using listproc software) since I founded it as the "RasMol List" in 1995. Subscribership has leveled off at about 600 and traffic has been steady at an average of about 2 messages/day for the past several years. I have done some investigating and am leaning towards using Bioinformatics.Org as the new home for molvis-list (to run under the Mailman list support software). Does anyone wish to suggest alternatives? If you want to check it out, click on Mailing Lists (left-hand menu) at bioinformatics.org (going to http://bioinformatics.org/mailman/listinfo/). Most of the lists are inactive or have minimal activity. A couple with substantial activity are BiO_Bulletin_Board and Bioclusters. I looked for a free email list hosting service that seemed appropriate. www.bio.net is possible but is primarily usenet based, and seemed to suffer a bit from lack of maintenance. (I have no personal experience with usenets). The NSF Digital Library hosts email lists, but these appear to be limited to those about digital library science. Project MERLOT and BiomoleculesAlive.Org don't host email lists. Sincerely, -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop Biochem Structure Tutorials http://MolviZ.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- research boundary="Boundary_(ID_IyztCe1X66zPD3NtAZmtMg)" User-Agent: Mozilla Thunderbird 0.8 (Windows/20040913) X-Accept-Language: en-us, en ++++------+------+------+------+------+------+------+------+------+------+ From: Alex Allardyce Subject: ChemAxon - Free cheminformatics software for teaching and academic Date: Mon, 25 Oct 2004 09:52:48 +0200 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_IyztCe1X66zPD3NtAZmtMg) Good day, I write to you to inform you that our company has recently created an Academic Package to provide free cheminformatics software for teaching and academic research. ChemAxon makes a range of Java based cheminformatics toolkits which are used throughout life science research and for chemical communications, for a list of our current clients please see here http://www.chemaxon.com/aboutus.html. A brief listing of these tools and functionalities is given below; * *Marvin *for editing and viewing chemical structures, reactions and queries, * *Calculator Plugins* for prediction of various properties based on structure (pKa, logP, logD, H-bond aceptor/donor, etc), * *JChem Base* for structure and reaction searching and database handling, * *JChem Cartridge* for Oracle® database integration, * *Standardiser* for structure canonisation, * *Reactor *for structure transformations and virtual synthesis, * *Screen *for pharmacophore and structure based screening, * *JKlustor* for clustering and diversity analysis, * we are also currently completing our toolkit for *drug design*. All of these tools are made available, including support and upgrades, at no cost to academic institutions. There are some conditions related to this offer but these are centred around "no commercial benefit" and crediting our company when you implement and publish data derived from our tools. The full conditions are linked below. As this offer is of limited immediate commercial value to us but we believe of a great value to the community, I would appreciate if you would consider the details of this program and forward this mail to any colleagues who may be interested or publicise this genuine offer within your online / print community. Thanks you for your attention and feel free to return to me if you have any questions or comments. Alex Allardyce Communications Director *Links for more information* Academmic Package instructions, conditions and the license application : http://www.chemaxon.hu/forum/ftopic193.html Press release: http://www.chemaxon.com/CHEMAXON_ANNOUNCES_FREE_SOFTWARE_FOR_THE_ACADEMIC_COMMUNITY_VIA_THE_JCHEM_AND_MARVIN_ACADEMIC_PACKAGE.pdf To find out more about our tools: http://www.chemaxon.com/products.html To see existing implementations of our tools - including several academic implementations (Java enabled browser or Java required): http://www.chemaxon.hu/forum/index.php?c=19 Chemaxon Ltd Máramaros köz 3/a Budapest, 1037 Hungary Tel.: +361 4532658 Fax.: +361 4532659 e-mail: aa@chemaxon.com --Boundary_(ID_IyztCe1X66zPD3NtAZmtMg) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_IyztCe1X66zPD3NtAZmtMg)-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Edward Werner Cook Subject: Fw: Best hardware configuration for molecular modeling Date: Tue, 26 Oct 2004 13:01:02 -0400 To: rasmol@lists.umass.edu ----- Original Message ----- Sent: Tuesday, October 26, 2004 08:37 From: "Edward Werner Cook" Subject: Re: Best hardware configuration for molecular modeling To: ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_JcoinHwVCopY24IaFZjb+A)" X-ctinetworks-corpmail-MailScanner-Information: Please contact the ISP for more information X-ctinetworks-corpmail-MailScanner: Found to be clean X-MailScanner-From: macampbell@davidson.edu References: ++++------+------+------+------+------+------+------+------+------+------+ From: "A.Malcolm Campbell" Subject: Viewers Date: Fri, 29 Oct 2004 15:27:25 -0400 To: rasmol@lists.umass.edu --Boundary_(ID_JcoinHwVCopY24IaFZjb+A) Tim, What do you think about the viewer http://pymol.sourceforge.net/ I am still trying to figure out an OSX way around Chime. I like web pages with buttons. I like Java because it works with all platforms. Do you think Pymol is a good option? What is your vote for a long-term solution. Thanks, Malcolm ________________________________________________________ A. Malcolm Campbell, Ph.D. Associate Professor of Biology Davidson College Director of GCAT (www.bio.davidson.edu/GCAT) Co-Editor-In-Chief Cell Biology Education (www.cellbioed.org) Box 7118 (US Mail) 209 Ridge Road (shipping) Davidson College Davidson, NC 28036 704-894-2692 (phone) 704-894-2512 (fax) www.bio.davidson.edu/campbell --Boundary_(ID_JcoinHwVCopY24IaFZjb+A) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_JcoinHwVCopY24IaFZjb+A)-- boundary="Boundary_(ID_kDYSmSzBLFKJFB5Zq7X1KQ)" X-ctinetworks-corpmail-MailScanner-Information: Please contact the ISP for more information X-ctinetworks-corpmail-MailScanner: Found to be clean X-MailScanner-From: macampbell@davidson.edu References: ++++------+------+------+------+------+------+------+------+------+------+ From: "A.Malcolm Campbell" Subject: Mistaken Reply Date: Fri, 29 Oct 2004 15:28:40 -0400 To: rasmol@lists.umass.edu --Boundary_(ID_kDYSmSzBLFKJFB5Zq7X1KQ) I apologize for the last email. It was a reply to Tim but went to the list. Malcolm ________________________________________________________ A. Malcolm Campbell, Ph.D. Associate Professor of Biology Davidson College Director of GCAT (www.bio.davidson.edu/GCAT) Co-Editor-In-Chief Cell Biology Education (www.cellbioed.org) Box 7118 (US Mail) 209 Ridge Road (shipping) Davidson College Davidson, NC 28036 704-894-2692 (phone) 704-894-2512 (fax) www.bio.davidson.edu/campbell --Boundary_(ID_kDYSmSzBLFKJFB5Zq7X1KQ) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_kDYSmSzBLFKJFB5Zq7X1KQ)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: This "RasMol" List Moving to molvis-list@bioinformatics.org Date: Sun, 31 Oct 2004 12:27:11 -0400 To: rasmol@lists.umass.edu Cc: jeff@bioinformatics.org Dear subscriber to the Molecular Visualization Freeware ("RasMol") EMail list: I am in the process of moving this email list from the University of Massachusetts listproc to mailman at bioinformatics.org. The name of the new list is molvis-list. The archives will henceforth be searchable, and organized by thread as well as date and author. Shortly you will receive a message from the new molvis-list asking you to confirm your subscription. If you do not reply as instructed, you will no longer be subscribed to this list. After you have confirmed your subscription, you will receive a welcome message with details. I would like to thank Jeff Bizzaro for his help in setting up the new list at bioinformatics.org. Sincerely, -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop Biochem Structure Tutorials http://MolviZ.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Correction: no confirmation required for molvis-list; archives Date: Sun, 31 Oct 2004 18:44:08 -0400 To: rasmol@lists.umass.edu A correction to my previous message about the changeover to the molvis-list at bioinformatics.org: You will NOT need to reply to confirm your subscription (because I am subscribing you as the administrator of the list). Once you receive your "Welcome to molvis-list" message, you are subscribed. This should happen before November 1. The old "rasmol" list at UMass is now closed to further traffic. Its archives will remain available until I move them to bioinformatics.org, after which they will be available there. Both the old and new archives are already accessible from the FAQ at the new molvis-list (URL will be in your Welcome message). -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop Biochem Structure Tutorials http://MolviZ.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ Ending Oct 31, 2004.