Beginning Jan 1, 2002: ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Inter-chain contact area? Date: Mon, 07 Jan 2002 20:09:36 -0500 To: rasmol@lists.umass.edu, pdb-l@rcsb.org Is there a server (preferred) or free software package (user-friendly for Windows or DOS, not linux/unix/Iris!) where one can request a calculation of the total contact surface area in square Angstroms between any two specified chains within a PDB file? For example, for 2VAB, I'd like to know the contact area between chains A and P, and between chains A and B. I've not found this capability in: PDB Other Sources e.g. CSU, castP WHAT IF (WWW version) WebLab DeepView An AltaVista search for 'protein surface area' (But maybe I didn't notice the right tool in the above resources ...) A Google search for 'calculate protein surface area' (got several unix utilities, not user friendly; found ENVIRON at http://bioweb.pasteur.fr/seqanal/interfaces/environ.html but didn't get any result with 2VAB; found SPOCK for Irix) The "Protein-Protein Interaction Server Thanks, -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), 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: Inter-chain contact area? Date: Mon, 07 Jan 2002 20:24:19 -0500 To: rasmol@lists.umass.edu, pdb-l@rcsb.org Sorry, my previous message got sent prematurely. I was just going to add: The "Protein-Protein Interaction Server" at http://www.biochem.ucl.ac.uk/bsm/PP/server/index.html appears to be just what I need but seems unable to accept PDB files uploaded from Windows (even when return ^M characters are stripped out), and appears not to have been updated since 1998 (so I assume is not under active development). -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-- Content-return: allowed boundary="Boundary_(ID_RDvoCgtE8IbQiccnMD99Yg)" ++++------+------+------+------+------+------+------+------+------+------+ From: David Margulies Subject: RE: Inter-chain contact area? Date: Mon, 07 Jan 2002 21:08:29 -0500 To: "'rasmol@lists.umass.edu'" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --Boundary_(ID_RDvoCgtE8IbQiccnMD99Yg) Eric: I just searched, found http://www.biochem.ucl.ac.uk/bsm/PP/server/ and using netscape loaded 1VAC (from my mac) and did an A to B. Then I downloaded 2VAB and easily got the web server to do an A/B calculation. You can access these results at http://www.biochem.ucl.ac.uk/bsm/PP/server/results/cs1010455516_14772/ and http://www.biochem.ucl.ac.uk/bsm/PP/server/results/cs1010455559_14812/. Hope this helps. D > ---------- > From: Eric Martz > Reply To: rasmol@lists.umass.edu > Sent: Monday, January 7, 2002 8:09 PM > To: rasmol@lists.umass.edu; pdb-l@rcsb.org > Subject: Inter-chain contact area? > > Is there a server (preferred) or free software package (user-friendly for > Windows or DOS, not linux/unix/Iris!) where one can request a calculation > of the total contact surface area in square Angstroms between any two > specified chains within a PDB file? > > For example, for 2VAB, I'd like to know the contact area between chains A > and P, and between chains A and B. > > I've not found this capability in: > PDB Other Sources e.g. CSU, castP > WHAT IF (WWW version) > WebLab > DeepView > An AltaVista search for 'protein surface area' > (But maybe I didn't notice the right tool in the above resources ...) > > A Google search for 'calculate protein surface area' (got several unix > utilities, not user friendly; found > ENVIRON at http://bioweb.pasteur.fr/seqanal/interfaces/environ.html but > didn't get any result with 2VAB; found SPOCK for Irix) > > The "Protein-Protein Interaction Server > > > Thanks, -Eric Martz > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > The Protein Explorer: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > PDB Lite molecule finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > > --Boundary_(ID_RDvoCgtE8IbQiccnMD99Yg) RE: Inter-chain contact area?

Eric:
I just searched, found http://www.biochem.ucl.ac.uk/bsm/PP/server/ and using netscape loaded 1VAC (from my mac) and did an A to B.  Then I downloaded 2VAB and easily got the web server to do an A/B calculation. You can access these results at http://www.biochem.ucl.ac.uk/bsm/PP/server/results/cs1010455516_14772/ and http://www.biochem.ucl.ac.uk/bsm/PP/server/results/cs1010455559_14812/.

Hope this helps.

D

    ----------
    From:   Eric Martz
    Reply To:       rasmol@lists.umass.edu
    Sent:   Monday, January 7, 2002 8:09 PM
    To:     rasmol@lists.umass.edu; pdb-l@rcsb.org
    Subject:        Inter-chain contact area?

    Is there a server (preferred) or free software package (user-friendly for
    Windows or DOS, not linux/unix/Iris!) where one can request a calculation
    of the total contact surface area in square Angstroms between any two
    specified chains within a PDB file?

    For example, for 2VAB, I'd like to know the contact area between chains A
    and P, and between chains A and B.

    I've not found this capability in:
      PDB Other Sources e.g. CSU, castP
      WHAT IF (WWW version)
      WebLab
      DeepView
      An AltaVista search for 'protein surface area'
    (But maybe I didn't notice the right tool in the above resources ...)

      A Google search for 'calculate protein surface area' (got several unix
    utilities, not user friendly; found
    ENVIRON at http://bioweb.pasteur.fr/seqanal/interfaces/environ.html but
    didn't get any result with 2VAB; found SPOCK for Irix)

    The "Protein-Protein Interaction Server


    Thanks, -Eric Martz


    /* - - - - - - - - - - - - - - - - - - - - - - - - - - -
    The Protein Explorer: http://proteinexplorer.org
    Workshops: http://www.umass.edu/molvis/workshop
    World Index of Molecular Visualization Resources: http://molvisindex.org
    PDB Lite molecule finder: http://pdblite.org
    Molecular Visualization EMail List:
          http://www.umass.edu/microbio/rasmol/raslist.htm

    Eric Martz, Professor (Immunology), Dept Microbiology
    U Mass, Amherst MA US  413-545-2325/FAX 413-545-2532
                  http://www.umass.edu/molvis/martz
    - - - - - - - - - - - - - - - - - - - - - - - - - - - */


--Boundary_(ID_RDvoCgtE8IbQiccnMD99Yg)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Markus Winter Subject: Program for docking protein structures? Date: Tue, 08 Jan 2002 15:42:50 +1300 To: rasmol@lists.umass.edu Hi all, is there a web server or a free program (MacOS 9 or X) that would allow me to check if two protein fragments I'm interested in can bind (e.g. can I dock them onto each other)? Best Regards Markus -- Dr. Markus Winter 1st Floor, Room 15 The Liggins Institute University of Auckland Private Bag 92019 2-6 Park Avenue Grafton Auckland New Zealand Tel: 0064 (0)9 373 7599 (wait for message then type extension) 3960 Fax: 0064 (0)9 373 7497 mobile: 021 150 9621 ----------------------------------------------------------------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: Douglas Kojetin Subject: Re: Program for docking protein structures? Date: Mon, 07 Jan 2002 22:09:56 -0500 (EST) To: rasmol@lists.umass.edu I've got another semi-related question. Is there a program that will ... a) measure the surface area of a protein .. and b) measure a specified area of a surface of a protein (description below) To give an example -- say we want to measure certain interaction patches on the surface of a protein in its active and inactive forms and get values for the areas to see how the patches change upon activation (maybe the interactions patches increrase or decrease -- I would like to get a value rather than estimate a percentage). Thanks! Doug Kojetin On Tue, 8 Jan 2002, Markus Winter wrote: > Hi all, > > is there a web server or a free program (MacOS 9 or X) that would allow me > to check if two protein fragments I'm interested in can bind (e.g. can I > dock them onto each other)? > > Best Regards > > Markus > > > -- > > Dr. Markus Winter > 1st Floor, Room 15 > The Liggins Institute > University of Auckland > Private Bag 92019 > 2-6 Park Avenue > Grafton > Auckland > New Zealand > Tel: 0064 (0)9 373 7599 (wait for message then type extension) 3960 > Fax: 0064 (0)9 373 7497 > mobile: 021 150 9621 > > > ----------------------------------------------------------------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-Accept-Language: it References: <200201080240.PAA06983@mailhost.auckland.ac.nz> ++++------+------+------+------+------+------+------+------+------+------+ From: Eugenia Polverini Subject: Re: Program for docking protein structures? Date: Tue, 08 Jan 2002 09:32:14 +0100 To: rasmol@lists.umass.edu Hi! There is Autodock3, that is free for academic (you had to sign only a software distribution agrement). I think that it is a very good program. You can find it at http://www.scripps.edu/pub/olson-web/doc/autodock/index.html All the best Eugenia Markus Winter ha scritto: > Hi all, > > is there a web server or a free program (MacOS 9 or X) that would allow me > to check if two protein fragments I'm interested in can bind (e.g. can I > dock them onto each other)? > > Best Regards > > Markus > > -- > > Dr. Markus Winter > 1st Floor, Room 15 > The Liggins Institute > University of Auckland > Private Bag 92019 > 2-6 Park Avenue > Grafton > Auckland > New Zealand > Tel: 0064 (0)9 373 7599 (wait for message then type extension) 3960 > Fax: 0064 (0)9 373 7497 > mobile: 021 150 9621 > -- Eugenia Polverini, Ph.D. Dept. of Physics University of Parma Parco Area delle Scienze, 7/A 43100 Parma ITALY Phone: +39 0521 905254 Fax: +39 0521 905223 E-Mail: eugenia.polverini@fis.unipr.it ----------------------------------------------------------------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: Inter-chain contact area? Date: Tue, 08 Jan 2002 10:46:41 -0500 To: rasmol@lists.umass.edu Cc: murad@godel.bioc.columbia.edu Dear Dr. Martz take a look at the SPIN-PP server at http://trantor.bioc.columbia.edu/cgi-bin/SPIN/ various properties (including contact surface areas) of of all protein-protein interfaces in the PDB are pre calculated and are available for searching and browsing. peptide chains shorter than 20 AA are not included in this database so you will find the information you want about the 2vab A and B chains interface but not A and P (short peptide). A an updated and expanded version of SPIN will be out in about 1-2 months. -- Murad Nayal M.D. Ph.D. Department of Biochemistry and Molecular Biophysics College of Physicians and Surgeons of Columbia University 630 West 168th Street. New York, NY 10032 Tel: 212-305-6884 Fax: 212-305-6926 ----------------------------------------------------------------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: Oliver Choroba Subject: Program for cavity volumes Date: Tue, 08 Jan 2002 16:03:07 +0000 To: rasmol@lists.umass.edu Sorry to continue the line of similar problems. I am in fact interested in a (preferably) Macintosh software package which can calculate active site (cavity) surface areas and volumes. The program should work with self-made pdf files, i.e. modelled structures. I have not been able to find anything suitable in the contributions so far. Many thanks. Oliver -- Dr. Oliver W. Choroba, MRSC Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, UK Tel.: +(44)-(0)1223-336710, Fax.: +(44)-(0)1223-336362 ----------------------------------------------------------------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_rrkL/4XxEYTEEkslL6W7mw)" ++++------+------+------+------+------+------+------+------+------+------+ From: David Margulies Subject: writing gif files Date: Wed, 09 Jan 2002 12:41:04 -0500 To: "rasmol@lists.umass.edu (E-mail)" 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_rrkL/4XxEYTEEkslL6W7mw) using Rasmac_PPC_32bit on a G4 cube, if I write "write gif " I get back "Output Error: Only 8-bit GIF files supported" How can i get rasmol to write gif files directly? D --Boundary_(ID_rrkL/4XxEYTEEkslL6W7mw) writing gif files

using Rasmac_PPC_32bit on a G4 cube, if I write
"write gif <filename.gif>"

I get back
"Output Error:  Only 8-bit GIF files supported"

How can i get rasmol to write gif files directly?

D

--Boundary_(ID_rrkL/4XxEYTEEkslL6W7mw)-- <913F8FBFBCDEAC439132B6C806C89FF0014E3AB7@niaid-mail2.niaid.nih.gov> Originator-info: login-token=Mulberry:01t46iMi770qLJ/Cq4/g/Sj0ruHV9CwhskA9CX7Q4=; token_authority=postmaster@andrew.cmu.edu Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: wm0p Subject: Re: writing gif files Date: Wed, 09 Jan 2002 14:57:13 -0500 To: rasmol@lists.umass.edu D, Try 'Export', then 'GIF...' -WM --On Wed, Jan 9, 2002 12:41 PM -0500 David Margulies wrote: > > using Rasmac_PPC_32bit on a G4 cube, if I write > "write gif " > > I get back > "Output Error: Only 8-bit GIF files supported" > > How can i get rasmol to write gif files directly? > > D ----------------------------------------------------------------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: Program for cavity volumes Date: Thu, 10 Jan 2002 10:50:53 -0500 To: rasmol@lists.umass.edu At 01/08/2002, you wrote: >Sorry to continue the line of similar problems. I am in fact >interested in a (preferably) Macintosh software package which can >calculate active site (cavity) surface areas and volumes. The program >should work with self-made pdf files, i.e. modelled structures. I >have not been able to find anything suitable in the contributions so >far. >Many thanks. > >Oliver > >-- >Dr. Oliver W. Choroba, MRSC > >Department of Chemistry, Cambridge University, >Lensfield Road, Cambridge CB2 1EW, UK >Tel.: +(44)-(0)1223-336710, Fax.: +(44)-(0)1223-336362 Have you tried castP ("Identification of protein pockets and cavities")? At the PDB, from the Structure Explorer page, click on Other Sources, and look under Analysis. -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-- References: <200201101542.g0AFgGF01061@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Oliver Choroba Subject: Re: Program for cavity volumes Date: Sat, 12 Jan 2002 16:25:05 +0000 To: rasmol@lists.umass.edu Dear Eric, Many thanks for your note. I just cannot get it to work properly on my Mac. Some software problems involving Netscape Communicator 4.73, by the looks of it. I also seem not to able to feed a home-made pdf file. Thanks anyway, I keep trying Best Oliver >At 01/08/2002, you wrote: >>Sorry to continue the line of similar problems. I am in fact >>interested in a (preferably) Macintosh software package which can >>calculate active site (cavity) surface areas and volumes. The program >>should work with self-made pdf files, i.e. modelled structures. I >>have not been able to find anything suitable in the contributions so >>far. >>Many thanks. >> >>Oliver >> >>-- >>Dr. Oliver W. Choroba, MRSC >> >>Department of Chemistry, Cambridge University, >>Lensfield Road, Cambridge CB2 1EW, UK >>Tel.: +(44)-(0)1223-336710, Fax.: +(44)-(0)1223-336362 > >Have you tried castP ("Identification of protein pockets and cavities")? >At the PDB, from the Structure Explorer page, click on Other Sources, and >look under Analysis. > >-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: Help! Chime under Mac OS 9.2.2? Date: Mon, 14 Jan 2002 07:01:05 -0500 To: RasMol List , webmaster@mdlchime.com hello, has anyone had trouble using the Chime plug-in under Mac Os 9.2.2? here are the symptoms: I tried everything: reinstall Chime, then Netscape, increase memory, delete Mime type associations, clear off all traces of NC, and then reinstall NC and Chime with extensions off, etc. And it's not site of JS specific, it's just the basic plug-in and I continue to get the following message: "Could not load the plug-in "Chemscape Chime 2.6" for Mime type 'chemical/x-pdb . . ." Also get the same message when I try the script test on Eric's site, except with a different Mime type. System setup: 1. OS 9.2.2 2. NC 4.79 3. Chime 2.6 SP3. Also tried 2.0a, but still no luck 4. MIME types are enabled 5. Can't see ATP model, and get the above mentioned dialog box 6 and 7.. Not using PE, and can't view any Chime site 8. Fails upon loading of the plug-in 9. Error message mentioned above 10. Can't even get to a comforting JS error. help? thanks, tim _________________________________________ timothy driscoll molvisions.com - 3D molecular visualization 80 fiske ave, waltham, ma 02453 usa e: driscoll@molvisions.com p: 508.864.6516 f: 781.899.4108 ------------------------------------------------------------- god bless america ----------------------------------------------------------------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: <20020114070106-r01010800-338fdc97-0910-010c@192.168.1.13> ++++------+------+------+------+------+------+------+------+------+------+ From: "Michael H. Patrick" Subject: Re: Help! Chime under Mac OS 9.2.2? Date: Mon, 14 Jan 2002 08:00:42 -0600 To: rasmol@lists.umass.edu me too!!!! I've just quit using my Mac since I haven't been able to find anyone who has recognized there is a problem much less recommend a solution. If I need to use Chime, I just use a PC laptop.....not a great solution as far as I'm concerned, but.... M. Patrick >hello, > >has anyone had trouble using the Chime plug-in under Mac Os 9.2.2? >here are the >symptoms: > >I tried everything: reinstall Chime, then Netscape, increase >memory, delete Mime type associations, clear off all traces of NC, and then >reinstall NC and Chime with extensions off, etc. And it's not site of JS >specific, it's just the basic plug-in and I continue to get the following >message: > >"Could not load the plug-in "Chemscape Chime 2.6" for Mime type >'chemical/x-pdb . . ." Also get the same message when I try the script test >on Eric's site, except with a different Mime type. > >System setup: > >1. OS 9.2.2 >2. NC 4.79 >3. Chime 2.6 SP3. Also tried 2.0a, but still no luck >4. MIME types are enabled >5. Can't see ATP model, and get the above mentioned dialog box >6 and 7.. Not using PE, and can't view any Chime site >8. Fails upon loading of the plug-in >9. Error message mentioned above >10. Can't even get to a comforting JS error. > > >help? > >thanks, > >tim >_________________________________________ >timothy driscoll >molvisions.com - 3D molecular visualization >80 fiske ave, waltham, ma 02453 usa >e: driscoll@molvisions.com >p: 508.864.6516 >f: 781.899.4108 >------------------------------------------------------------- >god bless america > ----------------------------------------------------------------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: <20020114070106-r01010800-338fdc97-0910-010c@192.168.1.13> ++++------+------+------+------+------+------+------+------+------+------+ From: Judy Voet Subject: Re: Help! Chime under Mac OS 9.2.2? Date: Mon, 14 Jan 2002 10:00:05 -0500 To: rasmol@lists.umass.edu >I have OS 9.2.2 and Netscape 4.77 and chime seems to work fine. I'm >not sure which version of chime I have, though. It's from 1998. Are you sure it's not the new version of netscape that is the problem? Judy >hello, > >has anyone had trouble using the Chime plug-in under Mac Os 9.2.2? >here are the >symptoms: > >I tried everything: reinstall Chime, then Netscape, increase >memory, delete Mime type associations, clear off all traces of NC, and then >reinstall NC and Chime with extensions off, etc. And it's not site of JS >specific, it's just the basic plug-in and I continue to get the following >message: > >"Could not load the plug-in "Chemscape Chime 2.6" for Mime type >'chemical/x-pdb . . ." Also get the same message when I try the script test >on Eric's site, except with a different Mime type. > >System setup: > >1. OS 9.2.2 >2. NC 4.79 >3. Chime 2.6 SP3. Also tried 2.0a, but still no luck >4. MIME types are enabled >5. Can't see ATP model, and get the above mentioned dialog box >6 and 7.. Not using PE, and can't view any Chime site >8. Fails upon loading of the plug-in >9. Error message mentioned above >10. Can't even get to a comforting JS error. > > >help? > >thanks, > >tim >_________________________________________ >timothy driscoll >molvisions.com - 3D molecular visualization >80 fiske ave, waltham, ma 02453 usa >e: driscoll@molvisions.com >p: 508.864.6516 >f: 781.899.4108 >------------------------------------------------------------- >god bless america > -- Judith G. Voet, J. H. Hammons Professor Swarthmore College jvoet1@swarthmore.edu Department of Chemistry 610-328-8520 500 College Avenue FAX 610-328-7355 Swarthmore, PA 19081-1390 ----------------------------------------------------------------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: Help! Chime under Mac OS 9.2.2? Date: Mon, 14 Jan 2002 10:49:48 -0500 To: rasmol@lists.umass.edu I don't think it is NC-specific; I have had NC 4.5-4.79 running with Chime 2.0-2.6 SP3 running under Mac OS 9.1 for a while, without major problems... -tim On 01.14.02 at 10:00 AM, jvoet1@swarthmore.edu (Judy Voet) wrote: > >I have OS 9.2.2 and Netscape 4.77 and chime seems to work fine. I'm > >not sure which version of chime I have, though. It's from 1998. > > Are you sure it's not the new version of netscape that is the problem? > Judy > > >hello, > > > >has anyone had trouble using the Chime plug-in under Mac Os 9.2.2? > >here are the > >symptoms: > > > >I tried everything: reinstall Chime, then Netscape, increase > >memory, delete Mime type associations, clear off all traces of NC, and then > >reinstall NC and Chime with extensions off, etc. And it's not site of JS > >specific, it's just the basic plug-in and I continue to get the following > >message: > > > >"Could not load the plug-in "Chemscape Chime 2.6" for Mime type > >'chemical/x-pdb . . ." Also get the same message when I try the script test > >on Eric's site, except with a different Mime type. > > > >System setup: > > > >1. OS 9.2.2 > >2. NC 4.79 > >3. Chime 2.6 SP3. Also tried 2.0a, but still no luck > >4. MIME types are enabled > >5. Can't see ATP model, and get the above mentioned dialog box > >6 and 7.. Not using PE, and can't view any Chime site > >8. Fails upon loading of the plug-in > >9. Error message mentioned above > >10. Can't even get to a comforting JS error. > > > > > >help? > > > >thanks, > > > >tim > >_________________________________________ > >timothy driscoll > >molvisions.com - 3D molecular visualization > >80 fiske ave, waltham, ma 02453 usa > >e: driscoll@molvisions.com > >p: 508.864.6516 > >f: 781.899.4108 > >------------------------------------------------------------- > >god bless america > > > > > -- > Judith G. Voet, J. H. Hammons Professor Swarthmore College > jvoet1@swarthmore.edu Department of Chemistry > 610-328-8520 500 College Avenue > FAX 610-328-7355 Swarthmore, > PA 19081-1390 > > > _________________________________________ timothy driscoll molvisions.com - 3D molecular visualization 80 fiske ave, waltham, ma 02453 usa e: driscoll@molvisions.com p: 508.864.6516 f: 781.899.4108 ------------------------------------------------------------- god bless america ----------------------------------------------------------------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/10.0.0.1309 X-OriginalArrivalTime: 14 Jan 2002 19:33:46.0431 (UTC) FILETIME=[622FCCF0:01C19D32] ++++------+------+------+------+------+------+------+------+------+------+ From: Warren Gallagher Subject: Re: Help! Chime under Mac OS 9.2.2? Date: Mon, 14 Jan 2002 13:34:21 -0600 To: rasmol@lists.umass.edu 14. January, 2001 Re: 1/14/02 6:01 AM > has anyone had trouble using the Chime plug-in under Mac Os 9.2.2? here are > the > symptoms: > > I tried everything: reinstall Chime, then Netscape, increase > memory, delete Mime type associations, clear off all traces of NC, and then > reinstall NC and Chime with extensions off, etc. And it's not site of JS > specific, it's just the basic plug-in and I continue to get the following > message: > !~~~~~~~~~~~~~~~~~~~~~~~~~ I am running NC 4.78 with Chime 2.6/sp3 with MacOS 9.2.2 in Classic mode under MacOS X. It seems to work fine. !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Warren Gallagher Associate Professor Chemistry Department University of Wisconsin-Eau Claire Eau Claire, WI 54702 TEL: (715) 836-5388 FAX: (715) 836-4979 ----------------------------------------------------------------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: Help! Chime under Mac OS 9.2.2? Date: Mon, 14 Jan 2002 14:40:42 -0500 To: rasmol@lists.umass.edu On 01.14.02 at 1:34 PM, wgallagh@uwec.edu (Warren Gallagher) wrote: > 14. January, 2001 > > Re: 1/14/02 6:01 AM > > has anyone had trouble using the Chime plug-in under Mac Os 9.2.2? here are > > the > > symptoms: > > > > I tried everything: reinstall Chime, then Netscape, increase > > memory, delete Mime type associations, clear off all traces of NC, and then > > reinstall NC and Chime with extensions off, etc. And it's not site of JS > > specific, it's just the basic plug-in and I continue to get the following > > message: > > > !~~~~~~~~~~~~~~~~~~~~~~~~~ > > I am running NC 4.78 with Chime 2.6/sp3 with MacOS 9.2.2 in Classic mode > under MacOS X. It seems to work fine. > > > !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Warren Gallagher > Associate Professor > Chemistry Department > University of Wisconsin-Eau Claire > Eau Claire, WI 54702 > TEL: (715) 836-5388 > FAX: (715) 836-4979 > if I may ask, did you have NC/chime installed and then update your OS, or did you install NC/chime after 9.2.2 was present? thanks, tim _________________________________________ timothy driscoll molvisions.com - 3D molecular visualization 80 fiske ave, waltham, ma 02453 usa e: driscoll@molvisions.com p: 508.864.6516 f: 781.899.4108 ------------------------------------------------------------- god bless america ----------------------------------------------------------------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 V6.0.5762.3 Thread-Topic: Help! Chime under Mac OS 9.2.2? Thread-Index: AcGdM5yBLmZiOGusRcW9BZ5dAkxZmwArVotB Content-Class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: X-OriginalArrivalTime: 15 Jan 2002 16:30:20.0514 (UTC) FILETIME=[EC8FE420:01C19DE1] ++++------+------+------+------+------+------+------+------+------+------+ From: "Gallagher, Warren H." Subject: RE: Help! Chime under Mac OS 9.2.2? Date: Tue, 15 Jan 2002 10:30:19 -0600 To: rasmol@lists.umass.edu 14. January, 2002 Re: ...if I may ask, did you have NC/chime installed and then update your OS, or did > you install NC/chime after 9.2.2 was present? !~~~~~~~~~~~~~~~~~~~~~~~ NC/Chime were installed before I did the update to 9.2.1. I believe I was running 9.1 when I installed NC/Chime; it was whatever version of MacOS 9 that came installed on my iBook when I purchased it last June. Warren !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Warren Gallagher Associate Professor Chemistry Department University of Wisconsin-Eau Claire Eau Claire, WI 54702 TEL: (715) 836-5388 FAX: (715) 836-4979 ----------------------------------------------------------------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-- charset=iso-8859-1 X-Accept-Language: en References: <20020114070106-r01010800-338fdc97-0910-010c@192.168.1.13> ++++------+------+------+------+------+------+------+------+------+------+ From: Jean-Marc Neuhaus Subject: Re: Help! Chime under Mac OS 9.2.2? Date: Wed, 16 Jan 2002 11:59:56 +0100 To: rasmol@lists.umass.edu Timothy Driscoll wrote: > hello, > > has anyone had trouble using the Chime plug-in under Mac Os 9.2.2? here are the > symptoms: > > I tried everything: reinstall Chime, then Netscape, increase > memory, delete Mime type associations, clear off all traces of NC, and then > reinstall NC and Chime with extensions off, etc. And it's not site of JS > specific, it's just the basic plug-in and I continue to get the following > message: > > "Could not load the plug-in "Chemscape Chime 2.6" for Mime type > 'chemical/x-pdb . . ." Also get the same message when I try the script test > on Eric's site, except with a different Mime type. > > System setup: > > 1. OS 9.2.2 > 2. NC 4.79 > 3. Chime 2.6 SP3. Also tried 2.0a, but still no luck > 4. MIME types are enabled > 5. Can't see ATP model, and get the above mentioned dialog box > 6 and 7.. Not using PE, and can't view any Chime site > 8. Fails upon loading of the plug-in > 9. Error message mentioned above > 10. Can't even get to a comforting JS error. > > help? > > thanks, > > tim > _________________________________________ > timothy driscoll > molvisions.com - 3D molecular visualization > 80 fiske ave, waltham, ma 02453 usa > e: driscoll@molvisions.com > p: 508.864.6516 > f: 781.899.4108 > ------------------------------------------------------------- > We've had a similar problem with the Chime plug-in on a Mac. The solution was to install Netscape 4.75, rather than 4.77 in our case. We then installed Chime and it worked. -- Prof. Jean-Marc Neuhaus Laboratoire de Biochimie, Institut de Botanique, Université de Neuchâtel Rue Emile-Argand 9, Case Postale 2, CH-2007 Neuchâtel, Switzerland Tel: +41 32 718 2207 , Fax: +41 32 718 2201 E-mail: jean-marc.neuhaus@unine.ch , Web pages: http://www.unine.ch/bota/bioch/ OPEN POSITIONS: Professor for Plant Physiology, see http://www.unine.ch/bota/Advert.html Post-doc in Plant Cell Biology, see http://www.unine.ch/bota/bioch/bioche.html See also the National Center of Competence in Research: http://www.unine.ch/nccr/ general informations on Biology in Neuchâtel: http://www.unine.ch/biol/ ----------------------------------------------------------------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 ++++------+------+------+------+------+------+------+------+------+------+ From: Todd Carlson Subject: write commands from chime - help Date: Wed, 16 Jan 2002 11:28:10 -0500 To: "<" My pocket guide to RasMol scripts lists a number of export commands including: write gif filename write script filename I wanted to use these in a Chime page homework assignment. Students would manipuate a chime image and then push the write button to save their work on files on a disk in the a: drive to be turned in to me. However, I have not been able to get these to work. Here is a simple page with a button to execute these scripts. The color change commands are there for debugging purposes so I know the script is executing completely. http://faculty.gvsu.edu/carlsont/chime/write/write.html Does someone know why this doesn't work for me? Thanks for you help. Todd Carlson Dept of Chemistry GVSU ----------------------------------------------------------------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: write commands from chime - help Date: Wed, 16 Jan 2002 11:58:40 -0500 To: rasmol@lists.umass.edu On 01.16.02 at 11:28 AM, carlsont@gvsu.edu (Todd Carlson) wrote: > My pocket guide to RasMol scripts lists a number of export commands including: > > write gif filename > write script filename > > I wanted to use these in a Chime page homework assignment. Students would > manipuate a chime image and then push the write button to save their work on > files on a disk in the a: drive to be turned in to me. > > However, I have not been able to get these to work. Here is a simple page with > a button to execute these scripts. The color change commands are there for > debugging purposes so I know the script is executing completely. > > http://faculty.gvsu.edu/carlsont/chime/write/write.html > > Does someone know why this doesn't work for me? Thanks for you help. > > Todd Carlson > Dept of Chemistry > GVSU > > afaik, these rasmol commands don't function in chime (telling a plug-in to write a file to your local disk is a security no-no). you can use the chime menu to copy a chime script to the clipboard, though, and use cmd-shift-3 on the mac to take a screenshot...not quite as elegant, I know! -tim _________________________________________ timothy driscoll molvisions.com - 3D molecular visualization 80 fiske ave, waltham, ma 02453 usa e: driscoll@molvisions.com p: 508.864.6516 f: 781.899.4108 ------------------------------------------------------------- god bless america ----------------------------------------------------------------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-- Originator-info: login-token=Mulberry:01yAzNtj95/SbaelU8D439E1tsSONTQEY1gfsb/ow=; token_authority=postmaster@andrew.cmu.edu Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: wm0p Subject: Re: write commands from chime - help Date: Wed, 16 Jan 2002 12:22:58 -0500 To: rasmol@lists.umass.edu --On Wed, Jan 16, 2002 11:28 AM -0500 Todd Carlson wrote: > I wanted to use these in a Chime page homework > assignment. Students would manipuate a chime image and > then push the write button to save their work on files on > a disk in the a: drive to be turned in to me. > > However, I have not been able to get these to work. > Does someone know why this doesn't work for me? Thanks > for you help. > > Todd, We have a similar assignment with this recipe: Get the Chime image you want; select 'Edit'; then 'Copy' from menu. The image is on the clipboard and can be pasted into a Word document (or manipulated with an image processing pgm). -Will ----------------------------------------------------------------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: ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re: write commands from chime - help Date: Wed, 16 Jan 2002 18:55:27 +0100 To: rasmol@lists.umass.edu To make a screenshot from a script, you can use the script command clipboard instead of commands from the chime menu Paul Pillot ----- Original Message ----- Sent: Wednesday, January 16, 2002 5:28 PM From: "Todd Carlson" Subject: write commands from chime - help To: ">" < > My pocket guide to RasMol scripts lists a number of export commands including: > > write gif filename > write script filename > > I wanted to use these in a Chime page homework assignment. Students would manipuate a chime image and then push the write button to save their work on files on a disk in the a: drive to be turned in to me. > > However, I have not been able to get these to work. Here is a simple page with a button to execute these scripts. The color change commands are there for debugging purposes so I know the script is executing completely. > > http://faculty.gvsu.edu/carlsont/chime/write/write.html > > Does someone know why this doesn't work for me? Thanks for you help. > > Todd Carlson > Dept of Chemistry > GVSU > > > > > ----------------------------------------------------------------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 X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id g0GJnRF13443 ++++------+------+------+------+------+------+------+------+------+------+ From: Todd Carlson Subject: Re: write commands from chime - help Date: Wed, 16 Jan 2002 14:47:07 -0500 To: rasmol@lists.umass.edu Thanks for all the quick replies. I have done this assignment before using the clipboard command but that just gets a static image which doesn't always give me the information I need. I have had the students use the copy chime script command to create a script which I load to regenerate their image. However, that was a bit difficult for beginners and we had some compatibility problems. They would paste their chime script into a text editor and save the file as file.spt but some text editors would put an extra txt extension on the end of the file name so chime wouldn't recognize it. I had to go through and edit the file names one each disk the students turned in (and this is for a very large class, ug). Also, we found that the copy chime script command did not work on some of our campus computers. Our IT people never figured out why. All were running the same version of netscape/chime from the same server, but on some the copy command loaded nothing in the clipboard. It was very odd. Anyone else run into this? Todd >>> paul.pillot@wanadoo.fr 01/16/02 12:55PM >>> To make a screenshot from a script, you can use the script command clipboard instead of commands from the chime menu Paul Pillot ----- Original Message ----- Sent: Wednesday, January 16, 2002 5:28 PM From: "Todd Carlson" Subject: write commands from chime - help To: ">" < > My pocket guide to RasMol scripts lists a number of export commands including: > > write gif filename > write script filename > > I wanted to use these in a Chime page homework assignment. Students would manipuate a chime image and then push the write button to save their work on files on a disk in the a: drive to be turned in to me. > > However, I have not been able to get these to work. Here is a simple page with a button to execute these scripts. The color change commands are there for debugging purposes so I know the script is executing completely. > > http://faculty.gvsu.edu/carlsont/chime/write/write.html > > Does someone know why this doesn't work for me? Thanks for you help. > > Todd Carlson > Dept of Chemistry > GVSU > > > > > ----------------------------------------------------------------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 V5.50.4522.1200 X-MSMail-priority: Normal X-Virus-Scanned: Passed References: ++++------+------+------+------+------+------+------+------+------+------+ From: Duane Sears Subject: Re: write commands from chime - help Date: Wed, 16 Jan 2002 12:52:57 -0800 To: rasmol@lists.umass.edu Todd, This response doesn't answer your question directly, but I've noticed an oddity with the Chime Edit/Copy command on the popup menu that might relate to your problem. I use the Chime Edit/Copy command to copy Chime-rendered images to the clipboard so that these can be pasted into various documents such as those generated by Word, PowerPoint, Image Composer, Adobe, etc. For some reason unknown to me, the Chime Edit/Copy function won't supplant text if it already exists in the clipboard; if the clipboard already contains text, "pasting" after invoking the Chime Edit/Copy command will only end up pasting the text rather than the hoped-for image. However, an easy fix for this problem is to open the clipboard and delete its contents before invoking the Chime Edit/Copy command; afterwards, the Chime Edit/Copy command works just fine and any new image copied with the Chime Edit/Copy command will supplant an existing image in the clipboard. The Clipbrd.exe program is in the system32 folder of my Windows 2000 PC but I keep a shortcut to the program on my desktop because I use it so often. Thus, my suggestion is that it might be necessary to empty the clipboard first before using the Chime Edit/Copy Chime Script command. I haven't tested this particular problem, but I do know that the problem I described above occurs with Windows 95, 98, and 2000. Hope this helps. Duane ============================================== Prof. Duane W. Sears Dept. Mol. Cell. Dev. Biology University of California Santa Barbara, CA 93106 Office: (805) 893-3499 Lab: (805) 893-4272 Fax: (805) 893-4724 Biochemistry instructional web site: http://tutor.lscf.ucsb.edu/instdev/sears/biochemistry Immunology instructional web site: http://tutor.lscf.ucsb.edu/instdev/sears/immunology ============================================== ----- Original Message ----- Sent: Wednesday, January 16, 2002 11:47 AM From: "Todd Carlson" Subject: Re: write commands from chime - help To: > Thanks for all the quick replies. I have done this assignment before using the clipboard command but that just gets a static image which doesn't always give me the information I need. I have had the students use the copy chime script command to create a script which I load to regenerate their image. However, that was a bit difficult for beginners and we had some compatibility problems. They would paste their chime script into a text editor and save the file as file.spt but some text editors would put an extra txt extension on the end of the file name so chime wouldn't recognize it. I had to go through and edit the file names one each disk the students turned in (and this is for a very large class, ug). Also, we found that the copy chime script command did not work on some of our campus computers. Our IT people never figured out why. All were running the same version of netscape/chime from the same server, but on some the copy command loaded nothing in the clipboard. It was very odd. Anyone else run into this? > > Todd > > > >>> paul.pillot@wanadoo.fr 01/16/02 12:55PM >>> > To make a screenshot from a script, you can use the script command > clipboard > instead of commands from the chime menu > > Paul Pillot > > ----- Original Message ----- > From: "Todd Carlson" > To: ">" < > Sent: Wednesday, January 16, 2002 5:28 PM > Subject: write commands from chime - help > > > > My pocket guide to RasMol scripts lists a number of export commands > including: > > > > write gif filename > > write script filename > > > > I wanted to use these in a Chime page homework assignment. Students would > manipuate a chime image and then push the write button to save their work on > files on a disk in the a: drive to be turned in to me. > > > > However, I have not been able to get these to work. Here is a simple page > with a button to execute these scripts. The color change commands are there > for debugging purposes so I know the script is executing completely. > > > > http://faculty.gvsu.edu/carlsont/chime/write/write.html > > > > Does someone know why this doesn't work for me? Thanks for you help. > > > > Todd Carlson > > Dept of Chemistry > > GVSU > > > > > > > > > > > > > > ----------------------------------------------------------------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: write commands from chime - help Date: Wed, 16 Jan 2002 16:31:40 -0500 To: RasMol List On 01.16.02 at 12:52 PM, sears@lifesci.ucsb.edu (Duane Sears) wrote: > Todd, > > This response doesn't answer your question directly, but I've noticed an > oddity with the Chime Edit/Copy command on the popup menu that might relate > to your problem. I use the Chime Edit/Copy command to copy Chime-rendered > images to the clipboard so that these can be pasted into various documents > such as those generated by Word, PowerPoint, Image Composer, Adobe, etc. > For some reason unknown to me, the Chime Edit/Copy function won't supplant > text if it already exists in the clipboard; if the clipboard already > contains text, "pasting" after invoking the Chime Edit/Copy command will > only end up pasting the text rather than the hoped-for image. However, an > easy fix for this problem is to open the clipboard and delete its contents > before invoking the Chime Edit/Copy command; afterwards, the Chime Edit/Copy > command works just fine and any new image copied with the Chime Edit/Copy > command will supplant an existing image in the clipboard. The Clipbrd.exe > program is in the system32 folder of my Windows 2000 PC but I keep a > shortcut to the program on my desktop because I use it so often. > > Thus, my suggestion is that it might be necessary to empty the clipboard > first before using the Chime Edit/Copy Chime Script command. I haven't > tested this particular problem, but I do know that the problem I described > above occurs with Windows 95, 98, and 2000. > > Hope this helps. > > Duane you shouldn't need to clear your clipboard to uuse the Copy Chime Script function. I've never had any trouble copying a Chime script to the clipboard using the Chime menu, on Mac OS 8.6-9.1, or Win2k, using NC 4.5-4.79 and any Chime 2 version. I have noticed this function doesn't work at all on Mac IE, fwiw. I never use Edit/Copy so I can't comment on that. I do have two possible work-arounds, though: 1. Macs have a wonderful OS-level feature that might help with the images (then again, it might not!): use Cmd-Shift 4 to change the mouse pointer to a crosshair; then click and drag the mouse to take a quick snapshot of whatever you surround. this feature is related to the auto screen shot available via Cmd-Shift 3, but lets you define the area in the resulting picture. both save out a pict file on your HD main dir. I don't know if windows has an equivalent feature. 2. this is more back-end work, but maybe you could write a chime interface that uses the "view show user" command? click a button that sends this command to chime, and capture the output in a form text field. the student can send the form directly to you. -tim _________________________________________ timothy driscoll molvisions.com - 3D molecular visualization 80 fiske ave, waltham, ma 02453 usa e: driscoll@molvisions.com p: 508.864.6516 f: 781.899.4108 ------------------------------------------------------------- god bless america ----------------------------------------------------------------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: Cutting Edge Approaches to Drug Design - 2nd meeting: 13/3/2002 Date: Wed, 16 Jan 2002 17:09:12 -0500 To: rasmol@lists.umass.edu > Dear Colleague, > > RE: Cutting Edge Approaches to Drug Design II: 13/3/2002 > > On behalf of the committees of the Royal Society of Chemistry Biological > and Medicinal Chemistry Sector and Molecular Modelling Group, I should > like to tell you about a one day meeting we intend to hold early in 2002. > It is called Cutting Edge Approaches to Drug Design II and will be held on > 13th March 2002. > > This meeting is a follow up to a very successful one-day meeting we held > in 2001 which attracted over 110 delegates. Talks will cover vital areas > of the modern drug discovery process, including biological target finding, > virtual chemistry, lead optimisation, Absorption Distribution Metabolism > and Excretion, and a number of worked examples. The meeting will be headed > by a plenary lecture from Prof Janet Thornton, FRS, the newly appointed > head of the European Bioinformatics Institute and founder of Inpharmatica, > who will present her vision of the future of bioinformatics and its impact > on drug discovery. > > I include below a circular for this meeting which includes registration > details: > > <> > There is also a website available for the Cutting Edge Approaches series > of lectures, which should contain any on-going changes to the meeting: > > http://www.jenner.ac.uk/CEAtoDD/CEAtDD.htm > > A hope that you can make it to the meeting. Please feel free to pass this > on to anyone who might be interested. > > Best Wishes > > Dr Darren R Flower > > Chair, RSC Molecular Modelling Group > > Edward Jenner Institute for Vaccine Research > High Street > Compton > Berkshire, UK > RG0 7NN > > Tel: 44 (0) 1635 577954 > fax: 44 (0) 1635 577901 / 577908 > > e-mail: darren.flower@jenner.ac.uk > > http://www.jenner.ac.uk/res-bio.htm > > http://www.rsc.org/lap/rsccom/dab/ind006.htm > > PS > > Apologies if you have recently received more than one communication about > this meeting. Unfortunately, different agencies are involved in > publicising it, and their contacts may overlap. You were identified as > someone who might be interested in this meeting through your involvement > or interest in some form of computational informatics, be that > Bioinformatics, Molecular Modelling, Chemoinformatics, Computer Science, > etc. ----------------------------------------------------------------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-Accept-Language: en References: <20020116163142-r01010800-9b476c59-0910-010c@192.168.1.13> ++++------+------+------+------+------+------+------+------+------+------+ From: T & S Carlson Subject: Re: write commands from chime - help Date: Wed, 16 Jan 2002 22:26:08 -0500 To: rasmol@lists.umass.edu I have a "view show user" button in my Move To Utility page http://faculty.gvsu.edu/carlsont/grant/moveutil/moveutil.htm but this would only get the orientation. It won't preserve atom colors for example. In the assignment I have done, I have had the students select and color certain parts of the structure (color the phe side chain yellow, the alpha carbons green, the peptide group blue, etc). Another possiblility would be to pass information to javascript and have javascripts save or e-mail the relevent data. I have used javascript to control feedback from chime in my amino acid quiz: http://faculty.gvsu.edu/carlsont/232/aaquiz/quiz.htm but I don't know how to get this kind of information about the image on the screen to pass from chime to js. Todd > 1. Macs have a wonderful OS-level feature that might help with the images (then > again, it might not!): use Cmd-Shift 4 to change the mouse pointer to a > crosshair; then click and drag the mouse to take a quick snapshot of whatever > you surround. this feature is related to the auto screen shot available via > Cmd-Shift 3, but lets you define the area in the resulting picture. both save > out a pict file on your HD main dir. I don't know if windows has an equivalent > feature. > > 2. this is more back-end work, but maybe you could write a chime interface that > uses the "view show user" command? click a button that sends this command to > chime, and capture the output in a form text field. the student can send the > form directly to you. > > -tim > _________________________________________ > timothy driscoll > molvisions.com - 3D molecular visualization > 80 fiske ave, waltham, ma 02453 usa > e: driscoll@molvisions.com > p: 508.864.6516 > f: 781.899.4108 > ------------------------------------------------------------- > god bless america > ----------------------------------------------------------------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: <200201162200.g0GM00F18901@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: John Tweedie Subject: RasMol fontstroke command Date: Thu, 17 Jan 2002 17:56:43 +1300 To: rasmol@lists.umass.edu Hello Has anyone managed to get the rasmol command "set fontstroke" to work in chime? I am using a G3 Mac with Netscape 4.7 and chime 2. Regards John Tweedie -- John W. Tweedie Associate Professor in Biochemistry Institute of Molecular BioSciences College of Sciences, Massey University PO Box 11-222 Palmerston North New Zealand Phone (Office): (64) (6) 350 5515 Ext2581 Phone (Home): (64) (6) 358 0150 Fax: (64) (6) 350 5688 E-mail: j.tweedie@massey.ac.nz ----------------------------------------------------------------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: "Herbert J. Bernstein" Subject: Re: RasMol fontstroke command Date: Thu, 17 Jan 2002 07:03:07 -0500 (EST) To: rasmol@lists.umass.edu The RasMol "set fontstroke" command is one of the many changes to RasMol introduced with the open source 2.7 series. Unfortunately, Chime is a closed source derivative of an earlier version of RasMol. If Chime were to become an open source program, we could add the recent RasMol changes to Chime. -- H. J. Bernstein ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Thu, 17 Jan 2002, John Tweedie wrote: > Hello > > Has anyone managed to get the rasmol command "set fontstroke" to work > in chime? I am using a G3 Mac with Netscape 4.7 and chime 2. > > Regards > > John Tweedie > -- > John W. Tweedie > Associate Professor in Biochemistry > Institute of Molecular BioSciences > College of Sciences, Massey University > PO Box 11-222 Palmerston North > New Zealand > > Phone (Office): (64) (6) 350 5515 Ext2581 > Phone (Home): (64) (6) 358 0150 > Fax: (64) (6) 350 5688 > E-mail: j.tweedie@massey.ac.nz > > ----------------------------------------------------------------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 boundary="Boundary_(ID_GiaO/0vZdpzsIFb22Fc+rA)" X-MSMail-priority: Normal References: <3C46F573.28634B80@mrc-lmb.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Jens Birktoft Subject: calculated hydrodynamic properties Date: Thu, 17 Jan 2002 23:51:28 -0500 To: pdb-l@rcsb.org, rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_GiaO/0vZdpzsIFb22Fc+rA) I would be grateful if somebody could let me know about any programs/methods that calculate the hydrodynamic properties of a protein from its PDB coordinates. Thanks Jens J. Birktoft Research Professor Dept Chemistry, New York University --Boundary_(ID_GiaO/0vZdpzsIFb22Fc+rA)
 
I would be grateful if somebody could let me know about any programs/methods that calculate the hydrodynamic properties of a protein from its PDB coordinates.
 
Thanks
 
Jens J. Birktoft
Research Professor
Dept Chemistry, New York University
--Boundary_(ID_GiaO/0vZdpzsIFb22Fc+rA)-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 boundary="Boundary_(ID_/s8Z02MflFYaUfrRwx/pWg)" X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: RasTop 2.0 Release Date: Sun, 20 Jan 2002 23:24:51 -0800 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_/s8Z02MflFYaUfrRwx/pWg) RasTop version 2.0 release is available on the web at http://www.geneinfinity.org/rastop. RasTop is a user-friendly graphical interface build on top of RasMol (version 2.7.2.1) available for Windows platforms. RasTop allows the rapid analysis of macromolecules in a multiple window environment and offers numerous enhancements to select and manipulate groups of atoms. This is a major update over the 1.3.1 version. The interface now accepts multiple molecules. It has high color resolution and improvement of the rendering (depth queuing, multidirectional headlight, new cylinder code, better ribbons). The Richards - Connolly surfaces are now complete. A script can be ran automatically on molecule opening. The interface has also some improvements - download and check :>) Many thanks to the many of you who already send me comments and bug reports. It is very important that I get feedback from you on this version. There will be bugs and we need a very stable multiple molecule environment. Compatibility with recent versions of Windows is another sensitive point. Thanks to all. Philippe Valadon --------------------------- *** RasTop *** --------------------------- Philippe Valadon P.O. Box 13014, La Jolla, CA 92039, USA. valadon@ix.netcom.com --Boundary_(ID_/s8Z02MflFYaUfrRwx/pWg)
RasTop version 2.0 release is available on the web at http://www.geneinfinity.org/rastop.
 
RasTop is a user-friendly graphical interface build on top of RasMol (version 2.7.2.1) available for Windows platforms.  RasTop allows the rapid analysis of macromolecules in a multiple window environment and offers numerous enhancements to select and manipulate groups of atoms.
 
This is a major update over the 1.3.1 version. The interface now accepts multiple molecules. It has high color resolution and improvement of the rendering (depth queuing, multidirectional headlight, new cylinder code, better ribbons).  The Richards - Connolly surfaces are now complete. A script can be ran automatically on molecule opening. The interface has also some improvements - download and check :>)
 
Many thanks to the many of you who already send me comments and bug reports. It is very important that I get feedback from you on this version. There will be bugs and we need a very stable multiple molecule environment. Compatibility with recent versions of Windows is another sensitive point.
 
Thanks to all.
 
Philippe Valadon
 
---------------------------
   *** RasTop ***  
---------------------------
Philippe Valadon
P.O. Box 13014, La Jolla, CA 92039, USA.
valadon@ix.netcom.com
 
 
 
 
 
 
 
--Boundary_(ID_/s8Z02MflFYaUfrRwx/pWg)-- X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id g0L8M2220703 ++++------+------+------+------+------+------+------+------+------+------+ From: Naoum Salame Subject: Re: RasTop 2.0 Release Date: Mon, 21 Jan 2002 09:22:08 +0100 To: rasmol@lists.umass.edu Cher Philippe, Content d'avoir enfin de tes nouvelles et de savoir que la version 2 de RasTop est disponible. Mes deux précédents messages étant restés sans réponse, je m'apprêtais à quérir de tes nouvelles auprès de Bernstein. Je souhaite vivement consacrer un mini site à RasTop sur notre site, préparant ainsi sa diffusion dans le système éducatif français, en attendant la sortie d'une version en français. M'autorises-tu à le faire, et pouvons-nous envisager immédiatement la traduction de la version 2 (à moins que cela ne soit dans tes projets) ? M'autorises-tu également à en proposer le téléchargement à partir de notre site (Je rappelle que nous sommes institut national, sous tutelle du ministère de la Recherche et du ministère de l'Education, sans but lucratif) ? Nous avons de nouveaux programmes de biologie qui entrent en vigueur. La génétique moléculaire et les visualisations tridimensionnelles des molécules y occupent une place très importante. Nous avons déjà préparé de multiples applications dans lesquelles les comparaisons de séquences et de molécules sont indispensables. Je vais mettre une équipe d'enseignants sur l'utilisation de RasTop dans ces applications pour que tout cela soit prêt avant fin juin et opérationnel dès début septembre. J'ai hâte d'avoir de tes nouvelles en retour. Cordialement Naoum Salamé Institut National de Recherche Pédagogique 91, rue Gabriel Péri, 92120 MONTROUGE, FRANCE Tel.: (033) 1 46128712 ; Fax : (033) 1 46128701 ; email : salame@inrp.fr Site Biogeo : http://www.inrp.fr/Acces/Biogeo/accueil.htm Site Biotic : http://www.inrp.fr/Acces/biotic/accueil.htm ----------------------------------------------------------------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-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id g0L8RB220749 ++++------+------+------+------+------+------+------+------+------+------+ From: Naoum Salame Subject: Sorry. Date: Mon, 21 Jan 2002 09:25:57 +0100 To: rasmol@lists.umass.edu Sorry for the previous message about RasTop, witch was intended to Philippe Valandon. Naoum Salamé Institut National de Recherche Pédagogique 91, rue Gabriel Péri, 92120 MONTROUGE, FRANCE Tel.: (033) 1 46128712 ; Fax : (033) 1 46128701 ; email : salame@inrp.fr Site Biogeo : http://www.inrp.fr/Acces/Biogeo/accueil.htm Site Biotic : http://www.inrp.fr/Acces/biotic/accueil.htm ----------------------------------------------------------------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 V5.00.2919.6600 X-MSMail-priority: Normal References: <002d01c1a24c$d1d9a340$cfa5b2d1@smeksbcr> <3C4C26EE.5D2DC909@albrecht.net> ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Valadon Subject: Re: RasTop 2.0 Release Date: Mon, 21 Jan 2002 00:36:38 -0800 To: rasmol@lists.umass.edu, Mario Albrecht ----- Original Message ----- Sent: Monday, January 21, 2002 6:34 AM From: "Mario Albrecht" Subject: Re: RasTop 2.0 Release To: "Philippe" > Dear Philippe, > > This is really a great step forward to an ideal Protein Viewer :-))) > Congratulations!!! > > Just one question: How can I visualize surface potential on the > Connolly surface? How can I load it? > I would like to visualize GRASP potential. > > Thank you much, > > Mario > Dear Mario, Many thanks for the compliment. I shall answer on the list as it may interest other people. There is at the present time no algorithm available in rasmol core to calculate surface electrostatic potential, but the way to color the surface is present, written by Roger Sayle who probably had some plans in that area. As far as I can understand, we need a dielectric constant, a pH value (7?), a set of standard values for usual atom types, and a formula (Coulomb law?) to calculate the potential at every point of the surface. If someone on the list is aware of these information, we could try to do something together. The question of importing surfaces or drawing continuous surfaces is a bit more complex and beyond my scope. There are people "out there" who do that perfectly, and the matter is more to convince them to write into or give their code to rasmol. Philippe ----------------------------------------------------------------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 V5.00.2919.6600 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Valadon Subject: potential Date: Mon, 21 Jan 2002 04:16:10 -0800 To: rasmol@lists.umass.edu, Mario Albrecht ----- Original Message ----- Sent: Tuesday, January 22, 2002 1:56 AM From: "Mario Albrecht" Subject: Re: RasTop 2.0 Release To: "Philippe Valadon" > Dear Philippe, > > there is a menu item called "potential". > So this is still out of work? > > Thanks, > > Mario Hi Mario, Looking at the code, it seems that some molecular files contain the potential data and in that case, rasmol can color the dot surface according to these values. It is unclear to me which files or formats are usable or necessary. Maybe Roger Sayle could shed some light here. Regards, Philippe ----------------------------------------------------------------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-- Mario Albrecht ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: potential Date: Wed, 23 Jan 2002 09:39:14 -0700 (MST) To: rasmol@lists.umass.edu Cc: Philippe Valadon , > Looking at the code, it seems that some molecular files contain the > potential data and in that case, rasmol can color the dot surface > according to these values. It is unclear to me which files or formats > are usable or necessary. Maybe Roger Sayle could shed some light here. If the b-factor field of PDB files or the partial charge field of mol2, alchem, mopacy or xyz files contains suitable partial charges, RasMol can use these in the "color dots potential" command. This just performs a simple Coulomb's law summation over each dot on the surface: sum(q/r^2). As an example, the aspirin.alc distributed with RasMol contains partial charges that can be used with "color dots potential". I've always used in-house software to generate PDB files with assigned partial charges (for example, AMBER, Charmm or MMFF charges), but perhaps there's some public domain software out there that could do the same. I think babel2 contains an implementation of Marsilli and Gasteiger's partial charge method that should be suitable for small molecules. Roger -- Roger Sayle, E-mail: roger@eyesopen.com OpenEye Scientific Software, WWW: http://www.eyesopen.com/ Suite 1107, 3600 Cerrillos Road, Tel: (+1) 505-473-7385 Santa Fe, New Mexico, 87507. Fax: (+1) 505-473-0833 ----------------------------------------------------------------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 V5.50.4522.1200 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Tamas Gunda Subject: Re: potential Date: Wed, 23 Jan 2002 21:53:02 +0100 To: rasmol@lists.umass.edu Mol2mol (although its is not freeware) can associate partial charges (or other computed data) from different files with the atoms and output to a pdb file a la Chime/Rasmol or PDBQ style Tamas Gunda ------------ Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Academy of Sciences University of Debrecen, POBox 36 H-4010 Debrecen Hungary tamasgunda@tigris.klte.hu ----- Original Message ----- > > > Looking at the code, it seems that some molecular files contain the > > potential data and in that case, rasmol can color the dot surface > > according to these values. It is unclear to me which files or formats > > are usable or necessary. Maybe Roger Sayle could shed some light here. > > If the b-factor field of PDB files or the partial charge field of mol2, > alchem, mopacy or xyz files contains suitable partial charges, RasMol > can use these in the "color dots potential" command. This just performs > a simple Coulomb's law summation over each dot on the surface: sum(q/r^2). > > As an example, the aspirin.alc distributed with RasMol contains partial > charges that can be used with "color dots potential". > > I've always used in-house software to generate PDB files with assigned > partial charges (for example, AMBER, Charmm or MMFF charges), but perhaps > there's some public domain software out there that could do the same. > I think babel2 contains an implementation of Marsilli and Gasteiger's > partial charge method that should be suitable for small molecules. > > Roger > -- > Roger Sayle, E-mail: roger@eyesopen.com > OpenEye Scientific Software, WWW: http://www.eyesopen.com/ > Suite 1107, 3600 Cerrillos Road, Tel: (+1) 505-473-7385 > Santa Fe, New Mexico, 87507. Fax: (+1) 505-473-0833 > > > ----------------------------------------------------------------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 fails on MacG4's with >1 Gig memory Date: Fri, 25 Jan 2002 18:37:45 -0500 To: rasmol@lists.umass.edu [Michael Morales of Garland Publishers gave me permission to share this very useful information with the list. He sent this message to Dr. Sasse at MDL. -Eric Martz] Dear Dr. Sasse: I realize the Chime plug-in is an "unsupported" product, since it's a give-away, but I thought you should be aware of a new incompatibility issue that we recently came across that will eventually effect many Mac users. I wouldn't contact you directly if I didn't think this was significant. On new G4 Towers and Titanium PowerBooks with a large amount of installed memory (typically 1 Gig or more) the Chime plug-in does not work. The user receives the standard "Could not load the plug-in "Chemscape Chime 2.6" for Mime type 'chemical/x-pdb . . ." And there is no way around this, and it is not caused by software or MIME conflicts. The problem was reproduced on a number of new Macs at different locations, and we had no idea what was causing this. Finally, Peter Walter, a scientist at UCSF, realized that all these machines had one thing in common-- that virtual memory was automatically disabled by the very large amounts of installed RAM. Dr. Walter pulled the RAM chips out of his computer, and the plug-in then worked just as it should. So our working theory is that the automatic disabling of Virtual Memory on the Mac creates a system conflict with the Chime plug-in. As far as we know, there is no way to prevent the OS from doing this. None of us are programmers, let alone computer scientists, and so this is about as far as we can take it. We hope that you can help us come up with a way to use the Chime plug-in on these new Macs without having to physically remove the RAM. Please let us know if you have any ideas about this problem, and whether you think there may be a reasonable work around. Machine specs were various but typically: 700MHz G4 1.5 Gig RAM Mac 0S 9.2.2 Thank you. Sincerely, Mike Morales ----------------------------------------- Michael Morales Garland Science Publishing 537 14th Street, #5 San Francisco, CA 94103 (415) 861-4878 (415) 552-1693 fax mike@morales.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-- References: <200201252327.g0PNRi224583@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "James W. Caras" Subject: Re: Chime fails on MacG4's with >1 Gig memory Date: Sat, 26 Jan 2002 16:48:04 -0600 To: rasmol@lists.umass.edu Hi everyone- I use a Mac G4 tower with 1.5 gigs of RAM, and did experience this problem. I thought that I began to get this problem when I installed OS X, and that the new OS was the problem, but I also installed more memory about this time as well. However, I have found a (somewhat strange) solution that does not require me to remove my beloved RAM. I have found that I while I experience this problem with Netscape/Chime when I boot under OS 9.1, it does not occur when I run Netscape within the classic (9.1) environment of OS X. Hard to understand, but works... Regards, Jamie >[Michael Morales of Garland Publishers gave me permission to share this >very useful information with the list. He sent this message to Dr. Sasse at >MDL. -Eric Martz] > >Dear Dr. Sasse: > >I realize the Chime plug-in is an "unsupported" product, since it's a >give-away, but I thought you should be aware of a new incompatibility issue >that we recently came across that will eventually effect many Mac users. I >wouldn't contact you directly if I didn't think this was significant. > >On new G4 Towers and Titanium PowerBooks with a large amount of installed >memory (typically 1 Gig or more) the Chime plug-in does not work. The user >receives the standard "Could not load the plug-in "Chemscape Chime 2.6" for >Mime type 'chemical/x-pdb . . ." And there is no way around this, and it is >not caused by software or MIME conflicts. > >The problem was reproduced on a number of new Macs at different locations, >and we had no idea what was causing this. Finally, Peter Walter, a >scientist at UCSF, realized that all these machines had one thing in >common-- that virtual memory was automatically disabled by the very large >amounts of installed RAM. Dr. Walter pulled the RAM chips out of his >computer, and the plug-in then worked just as it should. > >So our working theory is that the automatic disabling of Virtual Memory on >the Mac creates a system conflict with the Chime plug-in. As far as we >know, there is no way to prevent the OS from doing this. None of us are >programmers, let alone computer scientists, and so this is about as far as >we can take it. > >We hope that you can help us come up with a way to use the Chime plug-in on >these new Macs without having to physically remove the RAM. Please let us >know if you have any ideas about this problem, and whether you think there >may be a reasonable work around. > >Machine specs were various but typically: > >700MHz G4 >1.5 Gig RAM >Mac 0S 9.2.2 folder. So it's not an OSX/classic emulator problem.> > >Thank you. > >Sincerely, Mike Morales >----------------------------------------- >Michael Morales >Garland Science Publishing >537 14th Street, #5 >San Francisco, CA 94103 >(415) 861-4878 >(415) 552-1693 fax >mike@morales.com > -- _______________________________ Dr. James Caras The Institute for Cellular and Molecular Biology The University of Texas at Austin MBB 3.122 2500 Speedway Austin, TX 78712 caras@mail.utexas.edu (512) 471-0416 ----------------------------------------------------------------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-- chime-team@mdli.com, johno@mdli.com ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime Troubleshooting Guide Updated Date: Sun, 27 Jan 2002 14:03:19 -0500 To: rasmol@lists.umass.edu Cc: caras@mail.utexas.edu, mike@morales.com, pwalter@biochem.ucsf.edu, I have updated my Chime Troubleshooting Guide at http://www.umass.edu/microbio/chime/beta/pe_alpha/protexpl/troubles.htm I have included the new MacG4 >1 gigabyte memory issue. http://www.umass.edu/microbio/chime/beta/pe_alpha/protexpl/troubles.htm#mac memory I am particularly interested in knowing any suggestions to fix the "IE Mystery Issue" which has plagued me for nearly a year. My primary workstation has this problem, so all my development of PE for IE has to be on another computer! http://www.umass.edu/microbio/chime/beta/pe_alpha/protexpl/troubles.htm#iem ystery Suggestions for improving this guide, especially for the Mac (which I rarely use) are invited. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), 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: Nithin Rai Subject: Re: calculated hydrodynamic properties Date: Mon, 28 Jan 2002 19:03:10 +0000 (GMT) To: rasmol@lists.umass.edu Cc: pdb-l@rcsb.org Hi Jens,, Sorry if this reply is a little late, but there are 3 programs that i know of for calculating hydrodynamic properties from pdb: HYDRO, SOLPRO and BeaMS You can find the former 2 at: http://leonardo.fcu.um.es/macromol/ or for the latter you could e-mail the author: rocco@vega.cba.unige.it Hope this helps Nithin (now at nithin@inpharmatica.co.uk)A On Thu, 17 Jan 2002, Jens Birktoft wrote: > > I would be grateful if somebody could let me know about any programs/methods that calculate the hydrodynamic properties of a protein from its PDB coordinates. > > Thanks > > Jens J. Birktoft > Research Professor > Dept Chemistry, New York University > ----------------------------------------------------------------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-Accept-Language: es ++++------+------+------+------+------+------+------+------+------+------+ From: Gabriel Pons Subject: how usefull are chime tutorials Date: Wed, 30 Jan 2002 16:02:14 +0100 To: rasmol@lists.umass.edu My name is Gabriel Pons and I am professor of Biochemistry at the School of medicine in Barcelona. I am developing some tutorial in chime and even with protein explorer on protein structure. Anybody with experience in teaching could give me some ideas in order to know how usefull is a tutorial for the students? 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-- X-Accept-Language: en References: <3C580AF6.F7E82199@bellvitge.bvg.ub.es> ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: Re: how usefull are chime tutorials Date: Wed, 30 Jan 2002 11:44:05 -0500 To: rasmol@lists.umass.edu Gabriel, In my undergraduate course on Molecular Biology, we use chime tutorials every day to illustrate structure. My class is conducted in a PC lab where each student can manipulate the molecules during class. The most useful ones for basic nucleic acid and protein structure are those at the Carnegie Mellon site. For more advanced work, my students construct their own tutorials as term projects. Our new ones, plus the archive, are posted here: http://www2.kenyon.edu/depts/biology/BMB/chime.htm Good luck, Joan Gabriel Pons wrote: > My name is Gabriel Pons and I am professor of Biochemistry at the School > of medicine in Barcelona. I am developing some tutorial in chime and > even with protein explorer on protein structure. Anybody with experience > in teaching could give me some ideas in order to know how usefull is a > tutorial for the students? > 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-- User-Agent: Microsoft-Entourage/10.0.0.1309 X-OriginalArrivalTime: 30 Jan 2002 16:58:54.0127 (UTC) FILETIME=[6626BBF0:01C1A9AF] ++++------+------+------+------+------+------+------+------+------+------+ From: Warren Gallagher Subject: Re: how usefull are chime tutorials Date: Wed, 30 Jan 2002 10:58:20 -0600 To: rasmol@lists.umass.edu 30. January,2002 Gabriel, Re: 1/30/02 9:02 AM > My name is Gabriel Pons and I am professor of Biochemistry at the School > of medicine in Barcelona. I am developing some tutorial in chime and > even with protein explorer on protein structure. Anybody with experience > in teaching could give me some ideas in order to know how usefull is a > tutorial for the students? > Thanks !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ I have put together a web-based, interactive tutorial for embedding Chime images and buttons into web pages using a simple text editor. The tutorial is used by students enrolled in my undergraduate biophysical chemistry course. You might be interested in taking a look at it as you develop your own tutorial. The URL for this tutorial is http://www.chem.uwec.edu/EmbeddingChimes/ !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Warren Gallagher Associate Professor Chemistry Department University of Wisconsin-Eau Claire Eau Claire, WI 54702 TEL: (715) 836-5388 FAX: (715) 836-4979 ----------------------------------------------------------------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-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id g0UHSO200013 ++++------+------+------+------+------+------+------+------+------+------+ From: Jean Richelle Subject: HBondChainsFlag: how to set it Date: Wed, 30 Jan 2002 18:26:12 +0100 To: RasMol List Dear all, Does anybody knows how to set true the HBondChainsFlag (in order to compute HBonds between chains) from the command line ? Jean _____________________________________________________________________________ Jean Richelle Service de Conformation des Macromolécules Biologiques Tel: +32 02 650 3587 et de Bioinformatique - Université libre de Bruxelles FAX: +32 02 648 8954 av. F.D. Roosevelt 50 - CP160/16, B-1050 Bruxelles, Belgium _____________________________________________________________________________ ----------------------------------------------------------------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: how usefull are chime tutorials Date: Wed, 30 Jan 2002 12:53:07 -0500 To: rasmol@lists.umass.edu On 01.30.02 at 4:02 PM, gpons@bellvitge.bvg.ub.es (Gabriel Pons) wrote: > My name is Gabriel Pons and I am professor of Biochemistry at the School > of medicine in Barcelona. I am developing some tutorial in chime and > even with protein explorer on protein structure. Anybody with experience > in teaching could give me some ideas in order to know how usefull is a > tutorial for the students? > Thanks > hi gabriel, there are several excellent (and free) molvis software packages, including rasmol and rastop, swiss-pdb viewer. molmol, VMD, etc. each has its strengths and weaknesses; IMO chime is the very best for creating student-oriented tutorials. there are many good chime-based tutorials available, and they run the gamut from simple to extremely comprehensive, highly interactive to very pedagogical. for one decent list of such resources, you may want to check out the World Index at . the basic advantage to the student, of course, is in seeing a structure in interactive 3D instead of static 2D. chime and rasmol do this better than any other programs. in addition, chime can be enhanced many-fold by embedding it in a full-featured html interface. this type of interface can be fully customized, including buttons, color keys, text, audio, supplemental info via hyperlinks, and more. in addition, chime can be used in direct conjunction with other web media formats like flash and quicktime to create a true multimedia product. this does not necessarily require a mammoth budget, either - it can be done in very simple yet effective ways. even as simple as embedding chime and a qt movie on the same html page can be very powerful. I imagine almost every instructor on this list has produced 3D molvis tutorial(s) for their own classes, many using Chime in some way. in addition, many textbooks have Web-based, CD-based, and combo CD-Web multimedia that incorporates chime, including Alberts (Cell Biology and Essential Cell Biology); Lodish; Voet, Voet & Pratt; Kuby Immunology, etc. two good web examples are Lehninger Biochemistry Biochemistry (Stryer) by the way, both of these sites have (lehninger), or will soon have (stryer), excellent protein and nucleic acid structure modules. chime has severe platform and browser limitations, and lacks useful technical support most of the time. however, I think the widespread adoption of chime-based media by publishers and instructors alike points to its utility in teaching. hopefully this will create enough positive pressure to institute a consistent base of upgrading, bug fixing, and support. it certainly merits it! regards, tim _________________________________________ timothy driscoll molvisions.com - 3D molecular visualization 80 fiske ave, waltham, ma 02453 usa e: driscoll@molvisions.com p: 508.864.6516 f: 781.899.4108 ------------------------------------------------------------- god bless america ----------------------------------------------------------------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-Accept-Language: en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: Re: chime tutorial page Date: Wed, 30 Jan 2002 13:14:55 -0500 To: rasmol@lists.umass.edu Thanks, Warren; this site looks very helpful. Joan Warren Gallagher wrote: > 30. January,2002 > > Gabriel, > > Re: 1/30/02 9:02 AM > > My name is Gabriel Pons and I am professor of Biochemistry at the School > > of medicine in Barcelona. I am developing some tutorial in chime and > > even with protein explorer on protein structure. Anybody with experience > > in teaching could give me some ideas in order to know how usefull is a > > tutorial for the students? > > Thanks > !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > I have put together a web-based, interactive tutorial for embedding > Chime images and buttons into web pages using a simple text editor. The > tutorial is used by students enrolled in my undergraduate biophysical > chemistry course. You might be interested in taking a look at it as you > develop your own tutorial. The URL for this tutorial is > > http://www.chem.uwec.edu/EmbeddingChimes/ > > !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Warren Gallagher > Associate Professor > Chemistry Department > University of Wisconsin-Eau Claire > Eau Claire, WI 54702 > TEL: (715) 836-5388 > FAX: (715) 836-4979 > ----------------------------------------------------------------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: <3C580AF6.F7E82199@bellvitge.bvg.ub.es> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: how usefull are chime tutorials Date: Wed, 30 Jan 2002 13:51:29 -0500 To: rasmol@lists.umass.edu Joan Slonczewski, Warren Gallagher and others: Please consider listing your on-line Chime resources at http://molvisindex.org, the World Index of Molecular Visualization Resources. Just select the appropriate category (some of Warren's may belong in "How to create new tutorials with Chime"), then click on "Submit a new resource". You fill out a simple form, no password or account is needed. As soon as I OK new submissions (usually same day), they are automatically indexed on the web pages by author, subject (e.g. name of molecule), and title in the appropriate category. Also, you can edit already-indexed resources at any time. It is important that you describe your Chime resources with a paragraph to say what is special about them. I'd like to see enough detail that if someone finds a dozen Chime sites indexed under "DNA", the descriptions right there on the index pages will allow them to pick just one or a handful to actually visit. If you have to visit every one, it takes too long, so good descriptions are important. If tutorials are student-authored and not carefully faculty-edited, it would be good to mention "student-authored" in the description. Also, you may want to link the World Index of Molecular Visualization Resources to your class websites. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), 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-Originating-IP: [12.91.235.210] X-OriginalArrivalTime: 30 Jan 2002 23:05:31.0055 (UTC) FILETIME=[9D5793F0:01C1A9E2] ++++------+------+------+------+------+------+------+------+------+------+ From: "Pat O'Hern" Subject: Re: how usefull are... to whom? Date: Wed, 30 Jan 2002 23:05:30 +0000 To: rasmol@lists.umass.edu Gabriel- I think I interpreted your question about the usefulness of Chime tutorials a little differently than most on this board. I thought you were asking: how useful are the tutorials to the students? Do they help them learn? Are the tutorials worth the effort in terms of increased understanding and appreciation of molecular structure? (If this was not your question, you can stop reading now.) I think Chime tutorials can be at least as useful as any other audio-visual teaching aid, and probably more so. But the trick is: 1) the students have to use active learning rather than just passively sitting there watching; and 2) the Chime tutorials must count heavily toward their grade in the class. So, for example, Joan Slonczewsk's approach of having every student follow along on their own computer during every lecture is superb! But how many schools can offer those facilities? And how many instructors are willing to revise their syllabus and teaching style to implement such an approach? The best success I have had is with junior and senior undergraduate students in a biochemistry course. Working in small groups, they had to research a single protein and create a Chime tutorial describing and illustrating the structure/function relationships for the other students. The project counted 30% of their grade. The best ones were published on our internet site so they could refer to it in their resumes. By forcing them to pick the molecule apart, understand the interactions with prosthetic groups, include the alterations introduced by mutations, and showing these aspects in Chime, they (often for the first time) developed an appreciation for the beauty of the system and for the visualization tools. However, it sure took a lot of coaching on my part. So, as I said, I think the educational return from Chime tutorials, like CD-ROMs, study guides, and even text books, are as useful as the effort that the instructor and the students are willing to invest. I would be interested to know others' experience with this. Pat O'Hern Patricia A. O'Hern, Ph.D. Computer-based Training and Web Design 318 N. Decatur Lane Decatur, GA 30033 Ph: (404) 508-0375 FX: (404) 508-0128 pat_ohern@hotmail.com _________________________________________________________________ MSN Photos is the easiest way to share and print your photos: http://photos.msn.com/support/worldwide.aspx ----------------------------------------------------------------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 V5.50.4133.2400 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Robert Bateman Subject: Re: how usefull are... to whom? Date: Wed, 30 Jan 2002 20:22:29 -0600 To: rasmol@lists.umass.edu I agree completely with Pat O'Hern. Active learning is critical if molecular visualizations are to be more than cartoons. As some of you know, my approach has been to have students research, design, and construct a series of kinemages on a topic of their choosing. Details of our project can be found at http://orca.st.usm.edu/~rbateman/kinemage and a tutorial on how to author kinemages at http://orca.st.usm.edu/~rbateman/kinemage/tutorial.htm . A short description of our project will be coming out shortly in J. Chem. Ed. and a full paper will be submitted to another journal shortly. For those who don't know, kinemages are the original mol vis freeware and still quite useful despite being widely ignored. Version 6 of Mage and Prekin (the view/editing and authoring programs, respectively) have just been released by the Richardson lab at http://kinemage.biochem.duke.edu . There are versions for most computer platforms and a java version of Mage as well. Bob Bateman ________ Robert C. Bateman, Jr. Professor and Chair Department of Chemistry and Biochemistry University of Southern Mississippi Hattiesburg, MS 39406-5043 Robert.Bateman@usm.edu www.chem.usm.edu 601-266-4701 (department office) 601-266-6075 (fax) ----------------------------------------------------------------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-Accept-Language: es References: ++++------+------+------+------+------+------+------+------+------+------+ From: Gabriel Pons Subject: Re: how usefull are... to whom? Date: Thu, 31 Jan 2002 08:50:44 +0100 To: rasmol@lists.umass.edu Thanks to everybody for your help but Pat O´Hern was the only one that guessed my question. I was not asking about how usefull are tutorials on chime or other resources. I know they are very usefull and I have experience on them. The question is, supose you develop your first tutorial and you use it for the first time in a biochemistry course. What kind of objective strategies you would use to evaluate that the tutorial is working? Pat O'Hern ha escrito: > Gabriel- > > I think I interpreted your question about the usefulness of Chime tutorials > a little differently than most on this board. I thought you were asking: how > useful are the tutorials to the students? Do they help them learn? Are the > tutorials worth the effort in terms of increased understanding and > appreciation of molecular structure? > > (If this was not your question, you can stop reading now.) > > I think Chime tutorials can be at least as useful as any other audio-visual > teaching aid, and probably more so. But the trick is: 1) the students have > to use active learning rather than just passively sitting there watching; > and 2) the Chime tutorials must count heavily toward their grade in the > class. > > So, for example, Joan Slonczewsk's approach of having every student follow > along on their own computer during every lecture is superb! But how many > schools can offer those facilities? And how many instructors are willing to > revise their syllabus and teaching style to implement such an approach? > > The best success I have had is with junior and senior undergraduate students > in a biochemistry course. Working in small groups, they had to research a > single protein and create a Chime tutorial describing and illustrating the > structure/function relationships for the other students. The project counted > 30% of their grade. The best ones were published on our internet site so > they could refer to it in their resumes. By forcing them to pick the > molecule apart, understand the interactions with prosthetic groups, include > the alterations introduced by mutations, and showing these aspects in Chime, > they (often for the first time) developed an appreciation for the beauty of > the system and for the visualization tools. However, it sure took a lot of > coaching on my part. > > So, as I said, I think the educational return from Chime tutorials, like > CD-ROMs, study guides, and even text books, are as useful as the effort that > the instructor and the students are willing to invest. > > I would be interested to know others' experience with this. > > Pat O'Hern > > Patricia A. O'Hern, Ph.D. > Computer-based Training > and Web Design > 318 N. Decatur Lane > Decatur, GA 30033 > > Ph: (404) 508-0375 > FX: (404) 508-0128 > pat_ohern@hotmail.com > > _________________________________________________________________ > MSN Photos is the easiest way to share and print your photos: > http://photos.msn.com/support/worldwide.aspx > ----------------------------------------------------------------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: Jean Richelle Subject: Re: HBondChainsFlag: how to set it Date: Thu, 31 Jan 2002 09:14:51 +0100 To: rasmol@lists.umass.edu Hi, For those who are interested, I found the solution, here it is: set hbond chain true Jean >Dear all, > >Does anybody knows how to set true the HBondChainsFlag (in order to >compute HBonds between chains) from the command line ? > >Jean ----------------------------------------------------------------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 boundary="Boundary_(ID_l9tt3ZEXWEluLK+Uzrwtfw)" X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Chime ans Netscape 6.2 Date: Thu, 31 Jan 2002 09:51:54 +0100 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_l9tt3ZEXWEluLK+Uzrwtfw) To all Chimeleons : I installed 2 days ago, the chime plugins files from my Communicator plugins folder, to the Netscape 6.2 folder. Since that day, every Chime presentations I tried work ! The only exceptions are, the Chime projects using the Live Connect feature, that is to say, those using javascripts like the executeScript() method (like protein explorer, some tutorials like those from Timothy Driscolls). I made my tests with my personnal computer, using Netscape 6.2.1, french version, with Win Me. I didn't test it on other platforms. I'd like to know if others can make Chime work with Netscape 6.2 on other computers, before modifying my projects to include this new browser. Chime Files in the Plug-in folder : npchime.dll npchime.zip chime.html (readme file for Chime) chime26.isu - Paul Pillot --Boundary_(ID_l9tt3ZEXWEluLK+Uzrwtfw)
To all Chimeleons :
 
I installed 2 days ago, the chime plugins files from my Communicator plugins folder, to the Netscape 6.2 folder.
Since that day, every Chime presentations I tried work !
The only exceptions are, the Chime projects using the Live Connect feature, that is to say, those using javascripts like the executeScript() method (like protein explorer, some tutorials like those from Timothy Driscolls).
I made my tests with my personnal computer, using Netscape 6.2.1, french version, with Win Me.
I didn't test it on other platforms.
I'd like to know if others can make Chime work with Netscape 6.2 on other computers, before modifying my projects to include this new browser.
 
Chime Files in the Plug-in folder :
npchime.dll
npchime.zip
chime.html   (readme file for Chime)
chime26.isu
 
- Paul Pillot
--Boundary_(ID_l9tt3ZEXWEluLK+Uzrwtfw)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: how usefull are... to whom? Date: Thu, 31 Jan 2002 06:37:23 -0500 To: rasmol@lists.umass.edu hi gabriel, my apologies for misreading your question; pat's response is certainly in line with my experience. in the spirit of full disclosure, I do not hold a teaching position - though I was a student for many years (too many). I would like to add one comment: having students create their own tutorials is a great idea - that is how I was introduced to Chime and RasMol. however, be mindful of how much time your students spend dealing with the code (the "non-science") that implements their presentations. I fell into that trap with my first presentation, writing a flashy interface that took up way too much of my time. of course, I learned a lot of html and javascript, but...I'm guessing you want your students to learn more of the science ;-) I think you need a very user-friendly presentation maker, one that frees you and your students to focus on "pick[ing] the molecule apart" since that is what will benefit the majority of students. there is likely a decent bunch of pre-written stuff if you don't want to write your own. best, tim On 01.31.02 at 8:50 AM, gpons@bellvitge.bvg.ub.es (Gabriel Pons) wrote: > Thanks to everybody for your help but Pat O´Hern was the only one that guessed > my question. > I was not asking about how usefull are tutorials on chime or other resources. I > know they are very usefull and I have experience on them. > The question is, supose you develop your first tutorial and you use it for the > first time in a biochemistry course. What kind of objective strategies you would > use to evaluate that the tutorial is working? > > Pat O'Hern ha escrito: > > > Gabriel- > > > > I think I interpreted your question about the usefulness of Chime tutorials > > a little differently than most on this board. I thought you were asking: how > > useful are the tutorials to the students? Do they help them learn? Are the > > tutorials worth the effort in terms of increased understanding and > > appreciation of molecular structure? > > > > (If this was not your question, you can stop reading now.) > > > > I think Chime tutorials can be at least as useful as any other audio-visual > > teaching aid, and probably more so. But the trick is: 1) the students have > > to use active learning rather than just passively sitting there watching; > > and 2) the Chime tutorials must count heavily toward their grade in the > > class. > > > > So, for example, Joan Slonczewsk's approach of having every student follow > > along on their own computer during every lecture is superb! But how many > > schools can offer those facilities? And how many instructors are willing to > > revise their syllabus and teaching style to implement such an approach? > > > > The best success I have had is with junior and senior undergraduate students > > in a biochemistry course. Working in small groups, they had to research a > > single protein and create a Chime tutorial describing and illustrating the > > structure/function relationships for the other students. The project counted > > 30% of their grade. The best ones were published on our internet site so > > they could refer to it in their resumes. By forcing them to pick the > > molecule apart, understand the interactions with prosthetic groups, include > > the alterations introduced by mutations, and showing these aspects in Chime, > > they (often for the first time) developed an appreciation for the beauty of > > the system and for the visualization tools. However, it sure took a lot of > > coaching on my part. > > > > So, as I said, I think the educational return from Chime tutorials, like > > CD-ROMs, study guides, and even text books, are as useful as the effort that > > the instructor and the students are willing to invest. > > > > I would be interested to know others' experience with this. > > > > Pat O'Hern > > > > Patricia A. O'Hern, Ph.D. > > Computer-based Training > > and Web Design > > 318 N. Decatur Lane > > Decatur, GA 30033 > > > > Ph: (404) 508-0375 > > FX: (404) 508-0128 > > pat_ohern@hotmail.com > > > > _________________________________________________________________ > > MSN Photos is the easiest way to share and print your photos: > > http://photos.msn.com/support/worldwide.aspx > > > > > _________________________________________ timothy driscoll molvisions.com - 3D molecular visualization 80 fiske ave, waltham, ma 02453 usa e: driscoll@molvisions.com p: 508.864.6516 f: 781.899.4108 ------------------------------------------------------------- god bless america ----------------------------------------------------------------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-Originating-IP: [12.91.236.30] X-OriginalArrivalTime: 31 Jan 2002 13:43:15.0884 (UTC) FILETIME=[3C06BEC0:01C1AA5D] ++++------+------+------+------+------+------+------+------+------+------+ From: "Pat O'Hern" Subject: Assessing educational effectiveness Date: Thu, 31 Jan 2002 13:43:15 +0000 To: rasmol@lists.umass.edu Gabriel- Don't sweat the small stuff! :) No, seriously, it seems to me that there is an entire industry devoted to trying to establish whether or not *any* teaching method, program or aid is "worth it". It's a noble quest, but I seldom see any consensuses reached. The problem, in part, is that the results vary so much depending on who's counting and on how much effort individual teachers and indiviual students put into any learning process. So most of us just determine for ourselves what we will define as a "successful" outcome and just go for it. For myself, I seem some lovely and potentially highly effective CD-ROMs and companion web sites. I have fought the IT department to have them installed in the computer lab, spent a class period showing my students how to use the materials, and assigned a new module every week. The result - nothing, nada! They wouldn't do it on their own no matter how helpful I told them it would be (with, of course, a few notable exceptions). On the other hand, anything that counts a lot of points towards their grade *does* work. That can be anything from discussion sessions led by upperclassmen to the Chime tutorials. Go figure. I will say that when I did have the students do a Chime project, I know how much they learned. I saw the enthusiasm build as they began to understand how their protein worked and how to show it in Chime. And I saw a few students (like Tim Driscoll) who were enchanted enough to want to learn more in graduate school. So I was satisfied. My advice would be for you to decide what you want Chime tutorials to accomplish and how much effort you yourself are willing or able to devote to it. Then try it and see if it works. Then tell us. Pat PS- Tim is right about students getting bogged down in the HTML coding. For my classes, I created a frames template and embed buttons and showed them an example of what I was looking for. Surprisingly, someone in each team seemed to be able to take it from there. >The question is, supose you develop your first tutorial and you use >it for >the first time in a biochemistry course. What kind of >objective >strategies you would use to evaluate that the tutorial is >working? Patricia A. O'Hern, Ph.D. Computer-based Training and Web Design 318 N. Decatur Lane Decatur, GA 30033 Ph: (404) 508-0375 FX: (404) 508-0128 pat_ohern@hotmail.com Patricia A. O'Hern, Ph.D. Computer-based Training and Web Design 318 N. Decatur Lane Decatur, GA 30033 Ph: (404) 508-0375 FX: (404) 508-0128 pat_ohern@hotmail.com _________________________________________________________________ Join the world’s largest e-mail service with MSN Hotmail. http://www.hotmail.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-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: Chime ans Netscape 6.2 Date: Thu, 31 Jan 2002 08:25:06 -0600 (CST) To: rasmol@lists.umass.edu Hi, This is a very interesting result as I experienced a similar issue when I played around with using Chime with Linux and the crossover plugin. But I also identified that executeScript() did not work when trying to get Protein Explorer to run. Anyhow, I will add that Mozilla (version 0.9.7) on a Win98 laptop works by doing what you suggested. This is not at all surprising as I think that Netscape 6.2.1 is based on version 0.9.4 of Mozilla. Regards Bruce Southey On Thu, 31 Jan 2002, Paul Pillot wrote: > To all Chimeleons : > > I installed 2 days ago, the chime plugins files from my Communicator plugins folder, to the Netscape 6.2 folder. > Since that day, every Chime presentations I tried work ! > The only exceptions are, the Chime projects using the Live Connect feature, that is to say, those using javascripts like the executeScript() method (like protein explorer, some tutorials like those from Timothy Driscolls). > I made my tests with my personnal computer, using Netscape 6.2.1, french version, with Win Me. > I didn't test it on other platforms. > I'd like to know if others can make Chime work with Netscape 6.2 on other computers, before modifying my projects to include this new browser. > > Chime Files in the Plug-in folder : > npchime.dll > npchime.zip > chime.html (readme file for Chime) > chime26.isu > > - Paul Pillot > ----------------------------------------------------------------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: Karen Ocorr Subject: Re: Chime ans Netscape 6.2 Date: Thu, 31 Jan 2002 10:27:13 -0500 To: rasmol@lists.umass.edu FYI, I have been using Chime with Netscape 6.2 for some time now with no problems. I am using Windows 2000. Karen Ocorr At 09:51 AM 1/31/2002 +0100, you wrote: > To all Chimeleons : I installed 2 days ago, the chime plugins files >from my Communicator plugins folder, to the Netscape 6.2 folder. Since that >day, every Chime presentations I tried work ! The only exceptions are, the >Chime projects using the Live Connect feature, that is to say, those using >javascripts like the executeScript() method (like protein explorer, some >tutorials like those from Timothy Driscolls). I made my tests with my >personnal computer, using Netscape 6.2.1, french version, with Win Me. I >didn't test it on other platforms. 6.2 on other computers, before >modifying my projects to include this new browser. folder : >npchime.dll npchime.zip (readme file for Chime) >chime26.isu - Paul Pillot _________________________________________________________________________ Karen Ocorr, Ph.D. Biology Department University of Michigan Ann Arbor, MI. 48109-1048 Phone: 734/ 647-2470 Fax: 734/ 647-0884 E-mail: kocorr@umich.edu Home Page: http://biology.lsa.umich/~www/bio310/kohome.html Web Sites: http://biology.lsa.umich.edu/~www/bio310 http://biology.lsa.umich.edu/~www/bio225Winter/ http://biology.lsa.umich.edu/~www/bio100 _________________________________________________________________________ ----------------------------------------------------------------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-Accept-Language: en References: ++++------+------+------+------+------+------+------+------+------+------+ From: debanzie Subject: Re: how usefull are... to whom? Date: Thu, 31 Jan 2002 10:08:49 -0600 To: rasmol@lists.umass.edu Hi, I strongly agree with Dr. O'Hern's comments regarding active learning. However, I've been looking for a solution that takes less of the students' time since macromolecular structure is not the focus of the courses involved (Genetics, Cell Biology). The approach I'm looking at is to have the students answer questions based on their examination of Chime structures. By doing so, they are required to think about what they are looking at rather than just let it "wash over" them. An example can be seen at: http://arapaho.nsuok.edu/~biology/Assignments/AGN04.html I realize that the content is very basic compared to that many of you are working with, but the general approach is applicable to more complex content also. John de Banzie -- John de Banzie Biology Department Northeastern State University 611 N. Grand Ave. Tahlequah, OK 74464 (918) 456-5511 ext. 3828 Pat O'Hern wrote: > Gabriel- > > I think I interpreted your question about the usefulness of Chime tutorials > a little differently than most on this board. I thought you were asking: how > useful are the tutorials to the students? Do they help them learn? Are the > tutorials worth the effort in terms of increased understanding and > appreciation of molecular structure? > > (If this was not your question, you can stop reading now.) > > I think Chime tutorials can be at least as useful as any other audio-visual > teaching aid, and probably more so. But the trick is: 1) the students have > to use active learning rather than just passively sitting there watching; > and 2) the Chime tutorials must count heavily toward their grade in the > class. > > So, for example, Joan Slonczewsk's approach of having every student follow > along on their own computer during every lecture is superb! But how many > schools can offer those facilities? And how many instructors are willing to > revise their syllabus and teaching style to implement such an approach? > > The best success I have had is with junior and senior undergraduate students > in a biochemistry course. Working in small groups, they had to research a > single protein and create a Chime tutorial describing and illustrating the > structure/function relationships for the other students. The project counted > 30% of their grade. The best ones were published on our internet site so > they could refer to it in their resumes. By forcing them to pick the > molecule apart, understand the interactions with prosthetic groups, include > the alterations introduced by mutations, and showing these aspects in Chime, > they (often for the first time) developed an appreciation for the beauty of > the system and for the visualization tools. However, it sure took a lot of > coaching on my part. > > So, as I said, I think the educational return from Chime tutorials, like > CD-ROMs, study guides, and even text books, are as useful as the effort that > the instructor and the students are willing to invest. > > I would be interested to know others' experience with this. > > Pat O'Hern > > Patricia A. O'Hern, Ph.D. > Computer-based Training > and Web Design > 318 N. Decatur Lane > Decatur, GA 30033 > > Ph: (404) 508-0375 > FX: (404) 508-0128 > pat_ohern@hotmail.com > > _________________________________________________________________ > MSN Photos is the easiest way to share and print your photos: > http://photos.msn.com/support/worldwide.aspx > ----------------------------------------------------------------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-Accept-Language: en References: <3.0.5.32.20020131102713.00b51c58@k.imap.itd.umich.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: T & S Carlson Subject: What are they learning from Chime? Date: Thu, 31 Jan 2002 11:33:39 -0500 To: rasmol@lists.umass.edu A professor in our department shared with me recently that she tried using an entirely Chime-based approach to teaching protein structure recently. While the students were all able to answer questions in a Chime format, she observed that they did not do very well at generalizing or conceptualizing the information. In other words, when they had to create their own explanations of concepts or answer questions on a conventional written exam, they didn't do very well. This was not a rigourous examination of learning outcomes but just anectdotal observations. Nevertheless, it is important to keep in mind that what we think they learn and what they actually learn may be different. Todd Carlson GVSU ----------------------------------------------------------------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-Accept-Language: en References: <3.0.5.32.20020131102713.00b51c58@k.imap.itd.umich.edu> <3C5971E3.726781CE@gvsu.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Steven Rafferty Subject: Re: What are they learning from Chime? Date: Thu, 31 Jan 2002 12:50:39 -0500 To: carlsont@gvsu.edu Cc: rasmol@lists.umass.edu For what its worth, I don't assume that the Rasmol lab that I run in our introductory biochemistry class teaches students much about biomolecular structure; we cover that aspect in formal lectures. The big advantage of Rasmol and in learning how to access the protein data bank is simply in showing students that the the wealth of biomolecular structural information is theirs for the taking. The payoff comes not in second year, when we introduce these topics, but in third and especially in fourth year, when motivated students incorporate molecular graphics into their course work and undergraduate thesis projects. -- Steven Rafferty Chemistry Department, Trent University 1600 West Bank Drive Peterborough, ON Canada K9J 7B8 srafferty@trentu.ca http://www.trentu.ca/chemistry/srafferty/ 705-748-1011 x1309 ----------------------------------------------------------------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-- charset=us-ascii X-Accept-Language: en,pdf References: <3.0.5.32.20020131102713.00b51c58@k.imap.itd.umich.edu> <3C5971E3.726781CE@gvsu.edu> <3C5983EF.37E362D3@trentu.ca> ++++------+------+------+------+------+------+------+------+------+------+ From: Jeff Cohlberg Subject: Re: What are they learning from Chime? Date: Thu, 31 Jan 2002 11:40:16 -0800 To: rasmol@lists.umass.edu In our first-semester biochemistry classes, all students learn to use Rasmol, then complete (on their own) several exercises designed to help them learn protein structure. In some sections they are required to do a term paper on a protein of their choice which they illustrate with figures from Rasmol. In two recent sections of the course, 49 out of 77 students either agreed or strongly agreed with the statement, "Working with molecular modeling helped me to understand protein structure," 15 were neutral, and 13 disagreed or strongly disagreed. Jeff Cohlberg Steven Rafferty wrote: > For what its worth, I don't assume that the Rasmol lab that I run in our > introductory biochemistry class teaches students much about biomolecular > structure; we cover that aspect in formal lectures. The big advantage of > Rasmol and in learning how to access the protein data bank is simply in > showing students that the the wealth of biomolecular structural information > is theirs for the taking. The payoff comes not in second year, when we > introduce these topics, but in third and especially in fourth year, when > motivated students incorporate molecular graphics into their course work and > undergraduate thesis projects. > > -- > Steven Rafferty > Chemistry Department, Trent University > 1600 West Bank Drive > Peterborough, ON Canada K9J 7B8 > > srafferty@trentu.ca > http://www.trentu.ca/chemistry/srafferty/ > 705-748-1011 x1309 > -- Jeffrey A. Cohlberg, Professor Department of Chemistry and Biochemistry California State University, Long Beach 1250 Bellflower Blvd. Long Beach, CA 90840 phone (562) 985-4944 fax (209) 821-4471 ----------------------------------------------------------------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-- "http://www.unav.es/organica/umm", UN. X-Accept-Language: es, en, de References: <002201c1aa34$884db5a0$e2d70b50@zig> ++++------+------+------+------+------+------+------+------+------+------+ From: Luis Gracia Subject: Re: Chime ans Netscape 6.2 Date: Fri, 01 Feb 2002 14:27:39 +0000 To: rasmol@lists.umass.edu > Paul Pillot wrote: > > To all Chimeleons : > > I installed 2 days ago, the chime plugins files from my Communicator > plugins folder, to the Netscape 6.2 folder. > Since that day, every Chime presentations I tried work ! > The only exceptions are, the Chime projects using the Live Connect > feature, that is to say, those using javascripts like the > executeScript() method (like protein explorer, some tutorials like > those from Timothy Driscolls). > I made my tests with my personnal computer, using Netscape 6.2.1, > french version, with Win Me. > I didn't test it on other platforms. > I'd like to know if others can make Chime work with Netscape 6.2 on > other computers, before modifying my projects to include this new > browser. > > Chime Files in the Plug-in folder : > npchime.dll > npchime.zip > chime.html (readme file for Chime) > chime26.isu > > - Paul Pillot i have tried it under Windows XP, copying the chime files from the internet explorer plugins directory to the netscape 6.2.1, and normally it works. But I have to say it crashed once. Luis Gracia ----------------------------------------------------------------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_f8+3VFLH8CrZo9cwdk7oEg)" X-Accept-Language: en,pdf ++++------+------+------+------+------+------+------+------+------+------+ From: david marcey Subject: How useful are Chime tutorials? Date: Sat, 02 Feb 2002 01:24:22 +0000 To: rasmol@lists.umass.edu --Boundary_(ID_f8+3VFLH8CrZo9cwdk7oEg) In response to Gabriel Pons' question... A paper by White, et al. describing the assessment of molecular visuslization techniques in lecture and laboratory settings is coming out in Biochemistry and Molecular Biology Education (BaMBEd). BaMBEd is changing publishers, moving from Elsevier to Highwire Press in the near future. You will be able to access this journal from http://www.highwire.org/. IMHO, any useful assessment tools for evaluating Chime-coupled learning that are developed by Chimeleans should be shared on this listserve. And it should be pointed out that, in addition to the valuable learning experiences that student construction of Chime tutorials provides, it also is an effective gauge of student learning. In order for students to build a Chime button that evokes a pedagogically useful response of a molecule, students engage in variuous degrees of learning about macromolecular structure-function relationships. The sophistication of the biochemistry that students illustrate through Chime scripting can be useful in evaluating the depth of their learning. I strongly agree that student work needs to be thoroughly reviwed, edited, and sometimes rewritten before web publication. This comes from a long (6 year) experience of using Chime tutorials as student learning projects. Cheers, David <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>> David Marcey Fletcher Jones Professor of Developmental Biology CLU Department of Biology, MC3700 60 W. Olsen Rd. Thousand Oaks, CA 91360 (805)-493-3263, 3590 marcey@clunet.edu Visit The Online Macromolecular Museum at: http://www.clunet.edu/BioDev/omm/gallery.htm <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>> --Boundary_(ID_f8+3VFLH8CrZo9cwdk7oEg) In response to Gabriel Pons' question...

A paper by White, et al. describing the assessment of molecular visuslization techniques in lecture and laboratory settings is coming out in Biochemistry and Molecular Biology Education (BaMBEd). BaMBEd is changing publishers, moving from Elsevier to Highwire Press in the near future.  You will be able to access this journal from http://www.highwire.org/.

IMHO, any useful assessment tools for evaluating Chime-coupled learning that are developed by Chimeleans should be shared on this listserve. And it should be pointed out that, in addition to the valuable learning experiences that student construction of Chime tutorials provides, it also is an effective gauge of student learning. In order for students to build a Chime button that evokes a pedagogically useful response of a molecule, students engage in variuous degrees of learning about macromolecular structure-function relationships. The sophistication of the biochemistry that students illustrate through Chime scripting can be useful in evaluating the depth of their learning. I strongly agree that student work needs to be thoroughly reviwed, edited, and sometimes rewritten before web publication. This comes from a long (6 year) experience of using Chime tutorials as student learning projects.

Cheers, David

<<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>>
David Marcey
Fletcher Jones Professor of Developmental Biology
CLU Department of Biology, MC3700
60 W. Olsen Rd.
Thousand Oaks, CA 91360
(805)-493-3263, 3590
marcey@clunet.edu
Visit The Online Macromolecular Museum at:
      http://www.clunet.edu/BioDev/omm/gallery.htm
<<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>>
  --Boundary_(ID_f8+3VFLH8CrZo9cwdk7oEg)-- X-pair-Authenticated: 209.139.108.58 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: workstations wanted (ARCiB project) Date: Sat, 02 Feb 2002 20:42:03 -0500 To: rasmol@lists.umass.edu Workstations and Remote Access Wanted Accessible Retired Computers in Biology (ARCiB) Project Work Funded in part by the National Science Foundation The Accessible Retired Computers in Biology (ARCiB) project at Dowling College has been funded by the NSF. The project provides ongoing transitional support for software packages, especially those associated with structural biology, as existing hardware platforms are replaced. This will reduce disruption to research and education programs that use these software packages. ARCiB will be used to help support existing packages and make them available by remote access. If packages are open source and the developer would like to transfer all or part of the support, ARCiB will offer both an archive location for source and binaries as well as making the packages available. Undergraduates are actively involved in this research program for maintaining multi-platform interoperability. The project is soliciting donations of older, but working, graphics workstations and/or remote access to such workstations. Business and schools that are willing to donate such computers or to provide remote access to them for use in porting releases of software important to biology should contact the ARCiB project at Dowling College. It is very important that donated systems be complete with operating system, compilers, licenses, keyboard, monitor and mouse, and the necessary documentation to allow the project to rename and renumber the workstation to work on a new local area network. Systems made available for remote access should support SSH. Business and schools making such donations would be doing a service to the community. This service would be gratefully and publicly acknowledged. Right now, we are particularly interested in Sun, DEC/Compaq, SGI and IBM workstations. Please send email describing what you have available to yaya@dowling.edu. Please do not ship systems without prior arrangement. We want to give each donated machine proper attention. ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 yaya@dowling.edu ===================================================== P.S. For those with a particular interest in RasMol, I should point out that RasMol is, of course, one of the packages that ARCiB will support. As Eric Martz has noted, we want donations of older computers as testbeds so we can verify that newer versions of important software packages such as RasMol still run on them. -- HJB ----------------------------------------------------------------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-Accept-Language: en,es-ES ++++------+------+------+------+------+------+------+------+------+------+ From: shalpine@earthlink.net Subject: How useful are chime tutorials Date: Mon, 04 Feb 2002 11:54:01 -0800 To: RASter display of MOLecular structure Dear Gabriel: As a multimedia educational developer, I see your question pointing to very fundamental issues ("How useful are chime tutorials"). I've worked on several CD-Roms and companion Websites for college level-textbooks (Lodish Molecular Cell Biology CD-Rom, Kuby Immunology Website to name two previously mentioned here). For me, the effectiveness of multimedia material is critically important. Pat O'Hern hit on two key elements: student engagement and grade outcome. However, I believe that only when we have software that K-16 students can use to prepare their own multimedia assignments - without having to learn languages like HTML and wrestle with poorly designed interfaces - only when the student can work within the same format as the instructional content will electronic educational media reach its full potential. Thank you for initiating an interesting discussion. Susana Susana Maria Halpine Artist-Biochemist Candle Light Productions 239 Sunridge Street Playa del Rey, CA 90293 (310) 306-8399 shalpine@earthlink.net http://home.earthlink.net/~shalpine Women Chemists Committee Chair American Chemical Society, Los Angeles Section ----------------------------------------------------------------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: What are they learning from Chime? Date: Mon, 04 Feb 2002 16:57:04 -0500 To: rasmol@lists.umass.edu [I'm forwarding this message from Don Harden to circumvent technical difficuties. "Similar" apparently refers to the results sent in an earlier message by Jeff Cohlberg. -Eric Martz] A study of undergraduate biochemistry students in Georgia found similar results. "RasMol and Mage in the Undergraduate Biochemistry Curriculum", J. Chem. Educ. (2000), 77(3), 401-406. -- Dr. Don Harden harden@Gsu.EDU Department of Chemistry 547 NSC Georgia State University ph: (404) 651-3580 Atlanta, Ga. 30302 fax: (404) 651-1416 ----------------------------------------------------------------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: write commands from chime - help Date: Mon, 04 Feb 2002 17:01:12 -0500 To: rasmol@lists.umass.edu [I am forwarding this message from Henry Brzeski to the list to circumvent technical difficulties. -Eric Martz] Todd > I wanted to use these in a Chime page homework assignment. > Students would manipuate a chime image and then push the write > button to save their work on files on a disk in the a: drive to > be turned in to me. This is not a direct reply to your question but is something that might help if you want. Some time back in a previous job I also wanted to log student responses to Chime tutorials. I spoke with a guy who understood the internet far better than I did and he suggested mounting the page in a particular fashion so that all accesses could be logged by a ?Unix script? which tracked all interactions with the page and the IDs of all atoms clicked on in Chime. This was done in a Lotus Notes environment and each user had to log on so that the server could pick up both the student's identity as well as which atoms were clicked. All the messages from Chime were logged in a file along with the student's ID. This meant that you could see if the student took 20 clicks to get to the desired position or managed to do it in 2. The purpose of this tutorial was to see if the instructions were clear or confusing and so try and maximise the uses for Chime I was then offered a new job and did not manage to pursue this project to the end but the idea was to import the logged clicks into a database and look for common mistakes and also to try and write a program or replay the clicks to see how the student was accessing the structure. Neither of these ideas was realised. (The best laid plans of mice and men aft gang aglay - Robbie Burns) If you are interested in this oblique solution to your problem then let me know. h Dr Henry Brzeski Executive Director The Windber Research Institute 600 Somerset Avenue Windber Pennsylvania 15963 USA Phone +1 814-467-9844 Direct line +1 814-467-9464 Fax +1 814-467-6334 ----------------------------------------------------------------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 V5.00.2919.6600 boundary="Boundary_(ID_9ZfT4JsL4uE/Zup9rQxrDw)" X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: RasTop on Macintosh Date: Fri, 01 Feb 2002 17:20:49 -0800 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_9ZfT4JsL4uE/Zup9rQxrDw) Dear Mac users, Thanks to the testing of Patrick Dansette form the CNRS, France, and Joel Sussman from the Weissman Institute, Israel, RasTop works fine on Mac using Virtual PC. If you have Virtual PC installed on your machine, do not hesitate to download RasTop (www.geneinfinity.org/rastop) and see RasMol in action with a powerful graphic interface. Many of you asked my to port RasTop for X-windows, a windowing system found on Unix, Linux, and now Mac OSX. Unfortunately, RasTop uses a programming method that is specific for Windows platform and is not easy to port. With open-source projects, it is more usual to write the interface for X-windows and to port it to Windows after all. It would be tremendous if someone considers this project. The impact would be just enormous for the community and I am sure it would generate a lot of support. Thanks, Philippe --------------------------- *** RasTop *** --------------------------- Philippe Valadon P.O. Box 13014, La Jolla, CA 92039, USA. valadon@ix.netcom.com --Boundary_(ID_9ZfT4JsL4uE/Zup9rQxrDw)

Dear Mac users,
 
Thanks to the testing of Patrick Dansette form the CNRS, France, and Joel Sussman from the Weissman Institute, Israel, RasTop works fine on Mac using Virtual PC. If you have Virtual PC installed on your machine, do not hesitate to download RasTop (www.geneinfinity.org/rastop) and see RasMol in action with a powerful graphic interface.
 
Many of you asked my to port RasTop for X-windows, a windowing system found on Unix, Linux, and now Mac OSX. Unfortunately, RasTop uses a  programming method that is specific for Windows platform and is not easy to port. With open-source projects, it is more usual to write the interface for X-windows and to port it to Windows after all. It would be tremendous if someone considers this project. The impact would be just enormous for the community and I am sure it would generate a lot of support.
 
Thanks,
Philippe
 
---------------------------
   *** RasTop ***  
---------------------------
Philippe Valadon
P.O. Box 13014, La Jolla, CA 92039, USA.
valadon@ix.netcom.com
 
--Boundary_(ID_9ZfT4JsL4uE/Zup9rQxrDw)-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 boundary="Boundary_(ID_1fZo/fp57w1t/QB2WzAYmg)" X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: RasTop on Macintosh Date: Fri, 01 Feb 2002 17:08:25 -0800 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_1fZo/fp57w1t/QB2WzAYmg) Dear Mac users, Thanks to the testing of Patrick Dansette form the CNRS, France, and Joel Sussman from the Weissman Institute, Israel, RasTop works fine on Mac using Virtual PC. If you have Virtual PC installed on your machine, do not hesitate to download RasTop (www.geneinfinity.org/rastop) and see RasMol in action with a powerful graphic interface. Many of you asked my to port RasTop for X-windows, a windowing system found on Unix, Linux, and now Mac OSX. Unfortunately, RasTop uses a programming method that is specific for Windows platform and is not easy to port. With open-source projects, it is more usual to write the interface for X-windows and to port it to Windows after all. It would be tremendous if someone considers this project. The impact would be just enormous for the community and I am sure it would generate a lot of support. Thanks, Philippe --------------------------- *** RasTop *** --------------------------- Philippe Valadon P.O. Box 13014, La Jolla, CA 92039, USA. valadon@ix.netcom.com --Boundary_(ID_1fZo/fp57w1t/QB2WzAYmg)
Dear Mac users,
 
Thanks to the testing of Patrick Dansette form the CNRS, France, and Joel Sussman from the Weissman Institute, Israel, RasTop works fine on Mac using Virtual PC. If you have Virtual PC installed on your machine, do not hesitate to download RasTop (www.geneinfinity.org/rastop) and see RasMol in action with a powerful graphic interface.
 
Many of you asked my to port RasTop for X-windows, a windowing system found on Unix, Linux, and now Mac OSX. Unfortunately, RasTop uses a  programming method that is specific for Windows platform and is not easy to port. With open-source projects, it is more usual to write the interface for X-windows and to port it to Windows after all. It would be tremendous if someone considers this project. The impact would be just enormous for the community and I am sure it would generate a lot of support.
 
Thanks,
Philippe
 
---------------------------
   *** RasTop ***  
---------------------------
Philippe Valadon
P.O. Box 13014, La Jolla, CA 92039, USA.
valadon@ix.netcom.com
 
--Boundary_(ID_1fZo/fp57w1t/QB2WzAYmg)-- X-Originating-IP: [12.91.236.21] X-OriginalArrivalTime: 05 Feb 2002 13:48:01.0334 (UTC) FILETIME=[BA3BB560:01C1AE4B] ++++------+------+------+------+------+------+------+------+------+------+ From: "Pat O'Hern" Subject: Dr. Brzeski's email? Date: Tue, 05 Feb 2002 13:48:01 +0000 To: rasmol@lists.umass.edu

I am interested in Dr. Brzeski's Unix tracking of student responses. He suggested we contact him for further information. However, he did not include an email address in his posting. What is the best way to contact him?

Thanks,

Pat O'Hern





Patricia A. O'Hern, Ph.D.
Computer-based Training
and Web Design
318 N. Decatur Lane
Decatur, GA 30033
Ph: (404) 508-0375
FX: (404) 508-0128
pat_ohern@hotmail.com

Join the world’s largest e-mail service with MSN Hotmail. Click Here
----------------------------------------------------------------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: Brzeski's email Date: Tue, 05 Feb 2002 09:53:50 -0500 To: rasmol@lists.umass.edu Cc: pat_ohern@hotmail.com Henry Brzeski's NEW email is h.brzeski@wriwindber.org -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-- charset=us-ascii X-Accept-Language: en X-OriginalArrivalTime: 05 Feb 2002 15:51:11.0794 (UTC) FILETIME=[EF4A6920:01C1AE5C] ++++------+------+------+------+------+------+------+------+------+------+ From: Brian White Subject: Evaluations of mol vis Date: Tue, 05 Feb 2002 11:02:33 -0500 To: rasmol@lists.umass.edu Another interesting article about using visualizations is: Wu, H.-K., J.S. Krajcik, and E. Soloway, Journal of Research in Science Teaching 38(7) (2001) 821-842. Brian -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@umb.edu http://omega.cc.umb.edu/~bwhite/ ----------------------------------------------------------------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: "J. Ricky Cox" Subject: Re: Evaluations of mol vis Date: Tue, 05 Feb 2002 10:38:54 -0600 To: rasmol@lists.umass.edu Dear List:

Since there are many references floating around on this topic, I cannot resist adding to the list (see below).  My experience with molecular visualization is summarized in the papers below.  Although some assessment is included in these papers, I am well aware that a more structured and aggressive approach to "grading" the usefulness of molecular visualization tools (chime, PE, RasMol, etc.) is needed.  I am currently working on a project to integrate (and assess) visualization projects in a large biochemistry class (over 60 students).  Overall, I agree with others who have commented on the need to put the visualization tools in the hands of students and not just use it to enhance instructor-based lectures.

Thanks,

Ricky


------------------
Cox, J. R. =93Teaching Noncovalent Interactions in the Biochemistry Curriculum Through Molecular Visualization: The Search for pi Interactions=94 J. Chem. Educ. 2000, 77, 1424-1428.
http://jchemed.chem.wisc.edu/Journal/Issues/2000/= Nov/abs1424.html


Canning, D. R. and Cox, J. R. =93Teaching the Structural Nature of Biological Molecules: Molecular Visualization in the Classroom and in the Hands of Students=94 Chem. Educ. Res. Prac. Eur. 2001, 2, 109-122.
http://www.uoi.gr/conf_sem/cerapie/2001_May/contents.html=


Peterson, R. R. and Cox, J. R. =93Integrating Computational Chemistry int= o a Project-Oriented Biochemistry Laboratory Experience: A New Twist on the Lysozyme Experiment=94 J. Chem. Educ. 2001, 78, 1551-1555.
http://jchemed.chem.wisc.edu/Journal/Issues/2001/= Nov/abs1551.html

----------------------


----------------------------------------------------------------
Dr. J. Ricky Cox
Assistant Professor of Chemistry
Murray State University
456 Blackburn Science Bldg.
Murray, KY  42071-3346  
Phone:  270-762-6543    
Fax:  270-762-6474      
http://www.mursuky.edu/qacd/cos/che/faculty/jrc.htm
-----------------------------------------------------------------        ----------------------------------------------------------------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: Mitch Barker Subject: Non web based Simple Molecule visualizer Date: Mon, 11 Feb 2002 09:58:01 -0500 To: rasmol@lists.umass.edu Hello, We're writing a commercial application in which we'd like to display molecular structures. Our customers are chemists and most likely can provide structures in the usual common formats such as .mol, .chx, sk2, etc. The main focus of our app is running automated equipment, and the visualization is for depicting the chemicals used by the equipment. In other words, we're not writing a visualization application, but we'd like to depict the chemicals as structures as opposed to just text. We had a web based version, and chime worked perfectly. Now we are making a non-web version (microsoft) so I'm looking for an equivalent. No fancy bells and whistles such as rotation, just a simple visual depiction. I've found a few activeX controls, but they are quite expensive (>$500) Thanks for any suggestions. Mitch www.avantium.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: Second Annual UMass Bioinformatics Conference Date: Mon, 11 Feb 2002 10:48:47 -0500 To: rasmol@lists.umass.edu Second Annual UMass Bioinformatics Conference
The University of Massachusetts Lowell
Lowell, Massachusetts, USA
Thursday - Friday, May 2-3, 2002

Call For Presentations and Posters

The goal of this second conference will be to foster University-Industry relations in Bioinformatics.=A0 We encourage and solicit participation by faculty and students in biology, chemistry, mathematics, and computer science whose goals are to advance state-of-the-art systems in Bioinformatics, Cheminformatics, Genomics, and Proteomics.
Suggested topics include but of course are not limited to:

University-Industry Partnerships in Bioinformatics and Genomics * Proteomics * Advances in Microarray Technology and Data Analysis * Gene Mapping (Statistical Genomics) * Protein-protein interactions * in Silico Gene Detection * Pharmacogenomics * Using Bioinformatics Technologies in the Classroom/Curriculum Development * Evolutionary Genomics=A0 * Bioinformatics Tools: Their Use and Development * Data Visualization * Environmental Informatics * Data Mining * Neuroinformatics * Computational Structural Biology * Physiological Genomics * Phylogenetics and Molecular Evolution * Ethical, Legal and Social Implications of Genome Research

Submission deadline is March 15, 2002.

Send abstracts as attachments to James_LyonsWeiler@uml.edu, or by post to
James Lyons-Weiler
University of Massachusetts Lowell
One University Avenue
Lowell, MA 01854
Re: Paper for 2002 Bioinformatics Conference

Abstracts submitted via email must be submitted as word (*.doc) or text (*.txt) documents. Files containing papers must be named after the first author (e.g., LyonsWeiler.doc or LyonsWeiler.txt). Submissions must include the e-mail address of the corresponding presenter.

Additional information can be found at http://www.cs.uml.edu/bioinformatics/2002conference

Keynote Speakers will include:
Dr. James Cassatt, Ph.D., Director, Division of Cell Biology and Biophysics, National Institute of General Medical Sciences at NIH, and member of Bioinformatics Development Committee
=A0
Dr. Phil Reilly, M.D., J.D., CEO, Interleukin Genetics Incorporated

Please forward this email to all interested faculty in your department.

The UMASS Lowell Bioinformatics Conference Committee
=A0=A0=A0 James Lyons-Weiler, Biological Sciences, Co-Chair
=A0=A0=A0 James_LyonsWeiler@uml.edu
=A0=A0=A0 Georges Grinstein, Computer Science, Co-Chair
=A0=A0=A0 grinstein@cs.uml.edu
=A0=A0=A0 Kenneth Marx, Chemistry
=A0=A0=A0 kenneth_marx@uml.edu
=A0=A0=A0 Susan Braunhut, Biological Sciences
=A0=A0=A0 Susan_Braunhut@uml.edu
=A0=A0=A0 Haim Levkowitz, Computer Science
=A0=A0=A0 haim@cs.uml.edu
=A0=A0=A0 Anne Marie Hurley, Mathematics
=A0=A0=A0 AnnMarie_Hurley@uml.edu
=A0=A0=A0 Lee Jones, Mathematics
=A0=A0=A0 Lee_Jones@uml.edu
=A0=A0=A0 Eugene Mellican, Philosophy
=A0=A0=A0 Eugene_Mellican@uml.edu
=A0=A0=A0 David Lapointe, UMASS Worcester
=A0=A0=A0 David.Lapointe@umassmed.edu
=A0=A0=A0 Dane Netherton, Advancement Office
=A0=A0=A0 dane_netherton@uml.edu
=A0=A0=A0 Urska Cvek
=A0=A0=A0 Graduate Student Representative

last updated 2/7/02
--
James Lyons-Weiler, PhD
Department of Biological Sciences;
Laboratory of Molecular Systematics and Evolutionary Genomics;
Center for Bioinformatics and Computational Biology
One University Avenue
University of Massachusetts, Lowell
Lowell, MA 01854

Lab: 978-934-2865=A0 [http://bio.uml.edu/LW/Lab.html]
Office:978-934-2874
Fax: 978-934-3044
Email: James_LyonsWeiler@uml.edu
Home Page: http://bio.uml.edu/LW/JLW.html
Center: http://bio.uml.edu/LW/Center.html


----------------------------------------------------------------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_PLYEjT+Mx85LPUBrPL+TDg)" ++++------+------+------+------+------+------+------+------+------+------+ From: "Roberts, Rebecca" Subject: RE: Second Annual UMass Bioinformatics Conference Date: Mon, 11 Feb 2002 14:38:15 -0500 To: "'rasmol@lists.umass.edu'" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --Boundary_(ID_PLYEjT+Mx85LPUBrPL+TDg) Eric, Thanks for sending this information along. I'm wondering if you think this would be an appropriate meeting for me to attend. I would not be able to present, however, I'm at the start of designing a new structural biology course and hope to use bioinformatics extensively. Do you think that I may make some good connections at such a meeting? I was especially interested in the section on Using Bioinformatics Technologies in the Classroom/Curriculum Development. thanks, BecX-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Bioinformatics in the classroom Date: Wed, 13 Feb 2002 13:59:20 -0600 (CST) To: "'rasmol@lists.umass.edu'" Cc: rroberts@ursinus.edu Hi, I changed the subject from RE:Second Annual UMass Bioinformatics Conference so I hope you don't mind. The Biology Student Workbench (http://peptide.ncsa.uiuc.edu), headed by Dr Eric Jakobsson (jake@ncsa.uiuc.edu), is orientated to introducing bioinformatics into the classroom. Our present group involves a wide range of people (high school teachers and University teachers) across the United States and we would welcome everybody around the world who are interested in this. At our web site, you will find a large number of tutorials (in addition to other information) developed by a range of people using the Biology Workbench (http://workbench.sdsc.edu). The Biology Workbench is actually a suite of bioinformatics tools that can be used on DNA and protein sequences and any subsequent alignments. I have forgotten how many tools but over 80 and has over 100 databases. Also, we have developed an alternative interface to the Biology Workbench - Student Interface to the Biology Workbench (SIB). You can find more information about it (and other information) at http://deltas.animal.uiuc.edu/sibdoc/ The actual interface is http://deltas.animal.uiuc.edu/sib/servlet/SIB (eventually I will make a more formal announcement of SIB). Please let me know if I can help further, Regards, Bruce Southey On Mon, 11 Feb 2002, Roberts, Rebecca wrote: > Eric, > > Thanks for sending this information along. I'm wondering if you think > this would be an appropriate meeting for me to attend. I would not be able > to present, however, I'm at the start of designing a new structural biology > course and hope to use bioinformatics extensively. Do you think that I may > make some good connections at such a meeting? I was especially interested > in the section on Using Bioinformatics Technologies in the > Classroom/Curriculum Development. > > thanks, > > Becky > > ---------------------------------------- > Dr. Rebecca A. Roberts > Assistant Professor > Department of Biology > Ursinus College > Collegeville PA 19426 > (610) 489-4111 ext 2665 > > -----Original Message----- > From: Eric Martz [mailto:emartz@microbio.umass.edu] > Sent: Monday, February 11, 2002 10:49 AM > To: rasmol@lists.umass.edu > Subject: Second Annual UMass Bioinformatics Conference > > > Second Annual UMass Bioinformatics Conference > The University of Massachusetts Lowell > Lowell, Massachusetts, USA > Thursday - Friday, May 2-3, 2002 > > Call For Presentations and Posters > > The goal of this second conference will be to foster University-Industry > relations in Bioinformatics. We encourage and solicit participation by > faculty and students in biology, chemistry, mathematics, and computer > science whose goals are to advance state-of-the-art systems in > Bioinformatics, Cheminformatics, Genomics, and Proteomics. > Suggested topics include but of course are not limited to: > > University-Industry Partnerships in Bioinformatics and Genomics * Proteomics > * Advances in Microarray Technology and Data Analysis * Gene Mapping > (Statistical Genomics) * Protein-protein interactions * in Silico Gene > Detection * Pharmacogenomics * Using Bioinformatics Technologies in the > Classroom/Curriculum Development * Evolutionary Genomics * Bioinformatics > Tools: Their Use and Development * Data Visualization * Environmental > Informatics * Data Mining * Neuroinformatics * Computational Structural > Biology * Physiological Genomics * Phylogenetics and Molecular Evolution * > Ethical, Legal and Social Implications of Genome Research > > Submission deadline is March 15, 2002. > > Send abstracts as attachments to James_LyonsWeiler@uml.edu, or by post to > James Lyons-Weiler > University of Massachusetts Lowell > One University Avenue > Lowell, MA 01854 > Re: Paper for 2002 Bioinformatics Conference > > Abstracts submitted via email must be submitted as word (*.doc) or text > (*.txt) documents. Files containing papers must be named after the first > author (e.g., LyonsWeiler.doc or LyonsWeiler.txt). Submissions must include > the e-mail address of the corresponding presenter. > > Additional information can be found at > http://www.cs.uml.edu/bioinformatics/2002conference > > > Keynote Speakers will include: > Dr. James Cassatt, Ph.D., Director, Division of Cell Biology and Biophysics, > National Institute of General Medical Sciences at NIH, and member of > Bioinformatics Development Committee > > Dr. Phil Reilly, M.D., J.D., CEO, Interleukin Genetics Incorporated > > Please forward this email to all interested faculty in your department. > > The UMASS Lowell Bioinformatics Conference Committee > James Lyons-Weiler, Biological Sciences, Co-Chair > James_LyonsWeiler@uml.edu > Georges Grinstein, Computer Science, Co-Chair > grinstein@cs.uml.edu > Kenneth Marx, Chemistry > kenneth_marx@uml.edu > Susan Braunhut, Biological Sciences > Susan_Braunhut@uml.edu > Haim Levkowitz, Computer Science > haim@cs.uml.edu > Anne Marie Hurley, Mathematics > AnnMarie_Hurley@uml.edu > Lee Jones, Mathematics > Lee_Jones@uml.edu > Eugene Mellican, Philosophy > Eugene_Mellican@uml.edu > David Lapointe, UMASS Worcester > David.Lapointe@umassmed.edu > Dane Netherton, Advancement Office > dane_netherton@uml.edu > Urska Cvek > Graduate Student Representative > > last updated 2/7/02 > -- > James Lyons-Weiler, PhD > Department of Biological Sciences; > Laboratory of Molecular Systematics and Evolutionary Genomics; > Center for Bioinformatics and Computational Biology > One University Avenue > University of Massachusetts, Lowell > Lowell, MA 01854 > > Lab: 978-934-2865 [http://bio.uml.edu/LW/Lab.html] > Office:978-934-2874 > Fax: 978-934-3044 > Email: James_LyonsWeiler@uml.edu > Home Page: http://bio.uml.edu/LW/JLW.html > Center: http://bio.uml.edu/LW/Center.html > > > > ----------------------------------------------------------------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_/QDvYV5Sy2HM/EKehH/iSA)" ++++------+------+------+------+------+------+------+------+------+------+ From: Jennifer Muzyka Subject: chime symposium at BCCE Date: Mon, 18 Feb 2002 12:02:44 -0500 To: rasmol@lists.umass.edu --Boundary_(ID_/QDvYV5Sy2HM/EKehH/iSA) At the upcoming Biennial Conference on Chemical Education in Bellingham, WA, there will be a symposium on "Chemscape Chime as a Visualization Tool." If you are interested in giving a presentation in this symposium, please submit your abstract at the conference web site: http://www.mgmaccess.net/bcce/app_callpapers.asp Please direct any questions related to this symposium to me. -Jennifer Jennifer Muzyka Associate Professor of Chemistry Centre College 600 W. Walnut St. Danville, KY 40422 muzyka@centre.edu http://web.centre.edu/~muzyka 859-238-5413 fax 859-236-7925 --Boundary_(ID_/QDvYV5Sy2HM/EKehH/iSA) At the upcoming Biennial Conference on Chemical Education in Bellingham, WA, there will be a symposium on "Chemscape Chime as a Visualization Tool."  If you are interested in giving a presentation in this symposium, please submit your abstract at the conference web site:  http://www.mgmaccess.net/bcce/app_callpapers.asp

Please direct any questions related to this symposium to me.
-Jennifer

Jennifer Muzyka
Associate Professor of Chemistry
Centre College
600 W. Walnut St.
Danville, KY  40422

muzyka@centre.edu
http://web.centre.edu/~muzyka
859-238-5413
fax 859-236-7925 --Boundary_(ID_/QDvYV5Sy2HM/EKehH/iSA)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Beware Klez.E worm Date: Tue, 19 Feb 2002 15:58:41 -0500 To: rasmol@lists.umass.edu A particularly vicious email worm is about for Windows, called W32.Klez.E@mm. Infected computers send email from forged senders/return addresses, with an attachment containing the worm. The worm infects your computer only if you run the attachment, so DON'T double-click on any attachments unless you're certain they are legitimate. Bucknell College, for one place, is heavily infected. My personal email has received a couple of hundred worm-laden emails from Bucknell computers in the past few days! I hope none get through to this list, but if a list-broadcast message should arrive with an attachment, DON'T EXECUTE IT. Remember, we're not supposed to attach files in messages to the list anyway! Update your virus scanner, and run it regularly! -Eric, your list manager ----------------------------------------------------------------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-Accept-Language: en References: <200202192046.g1JKkV221658@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: T & S Carlson Subject: Re: Beware Klez.E worm Date: Tue, 19 Feb 2002 22:23:04 -0500 To: rasmol@lists.umass.edu Thanks Does the e-mail or attachment have a telltale title/subject? Todd Eric Martz wrote: > > A particularly vicious email worm is about for Windows, called > W32.Klez.E@mm. Infected computers send email from forged senders/return > addresses, with an attachment containing the worm. The worm infects your > computer only if you run the attachment, so DON'T double-click on any > attachments unless you're certain they are legitimate. Bucknell College, > for one place, is heavily infected. My personal email has received a couple > of hundred worm-laden emails from Bucknell computers in the past few days! > I hope none get through to this list, but if a list-broadcast message > should arrive with an attachment, DON'T EXECUTE IT. Remember, we're not > supposed to attach files in messages to the list anyway! > > Update your virus scanner, and run it regularly! > > -Eric, your list manager > ----------------------------------------------------------------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 1.922 alpha; Atlas of Macromolecules Date: Mon, 25 Feb 2002 10:38:25 -0500 To: rasmol@lists.umass.edu I have put Protein Explorer 1.922 alpha on-line, and it is downloadable. In order to get to this version, go to http://proteinexplorer.org (1.901 beta) and then click on the big red link "Internet Explorer-compatible upgrade now available". New features: -A new Atlas of Macromolecules, including browsable links to over 70 PDB files divided into over a dozen sections, such as integral membrane proteins, whole virus capsids, anthrax toxins, immuno-molecules, unusual tertiary/quaternary structures, and "magnificent molecular machines". Some small screenshots decorate the Atlas. Nominations of molecules to include in the Atlas are welcome. To get to the Atlas, look for the large link at the bottom of the leftmost gray box on PE's FrontDoor. Or go directly to http://www.umass.edu/microbio/chime/beta/pe_alpha/protexpl/atlas.htm -Improvements in Seq3D: clicking on residues (or ranges) in the sequence listing can now highlight the 3D counterparts in all identical chains. Both the display and color lists now include "no change". Thus, you can spacefill without changing the color, or change the color but not the rendering. -New QuickViews color scheme "Chains (PE)" distinguishes chains by color more clearly than Chime's built-in scheme, now designated "Chains (Chime)". -Total number of chains is now reported in the Molecule Information Window, on the Sequences display, and display of the incorrect report from Chime in the message window is suppressed. -Troubleshooting is revised, and includes troubleshooting for IE as well as Netscape, and the 1 gigabyte Macintosh problem. -Now works just fine on the Macintosh, so although Mac user's can't use the new Windows-IE compatibility, they can use the new features listed above. 1.91 and 1.92 alpha have been tested extensively now, and seem to work well as intended in Windows Internet Explorer as well as Netscape (Windows or Macintosh). No major problems have been reported. This version will become 'beta' after I get around to fixing a few remaining loose ends concerning Internet Explorer compatibility, notably the tutorial movies. The plan is that later this year, it will mature to version 2.0 and replace the ancient version 1.0 at the Protein Data Bank. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), 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-- Content-return: allowed boundary="Boundary_(ID_OEYqnQFKJSEMoV54LCfbIg)" ++++------+------+------+------+------+------+------+------+------+------+ From: David Margulies Subject: RE: Protein Explorer 1.922 alpha; Atlas of Macromolecules Date: Mon, 25 Feb 2002 11:05:57 -0500 To: "'rasmol@lists.umass.edu'" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --Boundary_(ID_OEYqnQFKJSEMoV54LCfbIg) Eric: Looks good. I would nominate these for consideration to include: 1. 1qo3 (complex of MHC-I, H-2Dd, and NK inihibitory receptor, Ly49A) (the physiological site now appears to be defined by asymmetry-related element rather than the site seen in the AU) 2. 1efx and 1im9, two examples of KIR2/HLA-C complexes, the first is KIR2DL2/HLA-Cw3 and the second is KIR2DL1/HLA-Cw4 3. finally, 1hyr, 1jfm, and/or 1kcg. All examaples of NKG2D complexed: a) with MICA; b) with RAE-1b; and c) with ULBP David ---------- > From: Eric Martz > Reply To: rasmol@lists.umass.edu > Sent: Monday, February 25, 2002 10:38 AM > To: rasmol@lists.umass.edu > Subject: Protein Explorer 1.922 alpha; Atlas of Macromolecules > > I have put Protein Explorer 1.922 alpha on-line, and it is downloadable. > In > order to get to this version, go to http://proteinexplorer.org (1.901 > beta) > and then click on the big red link "Internet Explorer-compatible upgrade > now > available". > > New features: > > -A new Atlas of Macromolecules, including browsable links to over 70 PDB > files divided into over a dozen sections, such as integral membrane > proteins, whole virus capsids, anthrax toxins, immuno-molecules, unusual > tertiary/quaternary structures, and "magnificent molecular machines". Some > > small screenshots decorate the Atlas. > > > Nominations of molecules to include in > the Atlas are welcome. To get to the Atlas, look for the large link at the > > bottom of the leftmost gray box on PE's FrontDoor. Or go directly to > http://www.umass.edu/microbio/chime/beta/pe_alpha/protexpl/atlas.htm > > -Improvements in Seq3D: clicking on residues (or ranges) in the sequence > listing can now highlight the 3D counterparts in all identical chains. > Both > the display and color lists now include "no change". Thus, you can > spacefill > without changing the color, or change the color but not the rendering. > > -New QuickViews color scheme "Chains (PE)" distinguishes chains by color > more clearly than Chime's built-in scheme, now designated "Chains > (Chime)". > > -Total number of chains is now reported in the Molecule Information > Window, > on the Sequences display, and display of the incorrect report from Chime > in > the message window is suppressed. > > -Troubleshooting is revised, and includes troubleshooting for IE as well > as > Netscape, and the 1 gigabyte Macintosh problem. > > -Now works just fine on the Macintosh, so although Mac user's can't use > the > new Windows-IE compatibility, they can use the new features listed above. > > 1.91 and 1.92 alpha have been tested extensively now, and seem to work > well > as intended in Windows Internet Explorer as well as Netscape (Windows or > Macintosh). No major problems have been reported. This version will become > > 'beta' after I get around to fixing a few remaining loose ends concerning > Internet Explorer compatibility, notably the tutorial movies. The plan is > that later this year, it will mature to version 2.0 and replace the > ancient > version 1.0 at the Protein Data Bank. > > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > The Protein Explorer: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > PDB Lite molecule finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > > --Boundary_(ID_OEYqnQFKJSEMoV54LCfbIg) RE: Protein Explorer 1.922 alpha; Atlas of Macromolecules

Eric:
Looks good.  I would nominate these for consideration to include:

            1.  1qo3 (complex of MHC-I, H-2Dd, and NK inihibitory receptor, Ly49A)  (the physiological site now appears to be  defined by asymmetry-related element rather than the site seen in the AU)

            2. 1efx and 1im9,  two examples of KIR2/HLA-C complexes, the first is KIR2DL2/HLA-Cw3 and the second is KIR2DL1/HLA-Cw4

            3. finally, 1hyr, 1jfm, and/or 1kcg.  All examaples of NKG2D complexed: a) with MICA; b) with RAE-1b; and c) with ULBP

    David


            ----------
    From:   Eric Martz
    Reply To:       rasmol@lists.umass.edu
    Sent:   Monday, February 25, 2002 10:38 AM
    To:     rasmol@lists.umass.edu
    Subject:        Protein Explorer 1.922 alpha; Atlas of Macromolecules

    I have put Protein Explorer 1.922 alpha on-line, and it is downloadable. In
    order to get to this version, go to http://proteinexplorer.org (1.901 beta)
    and then click on the big red link "Internet Explorer-compatible upgrade now
    available".

    New features:

    -A new Atlas of Macromolecules, including browsable links to over 70 PDB
    files divided into over a dozen sections, such as integral membrane
    proteins, whole virus capsids, anthrax toxins, immuno-molecules, unusual
    tertiary/quaternary structures, and "magnificent molecular machines". Some
    small screenshots decorate the Atlas.


    Nominations of molecules to include in
    the Atlas are welcome. To get to the Atlas, look for the large link at the
    bottom of the leftmost gray box on PE's FrontDoor. Or go directly to
    http://www.umass.edu/microbio/chime/beta/pe_alpha/protexpl/atlas.htm

    -Improvements in Seq3D: clicking on residues (or ranges) in the sequence
    listing can now highlight the 3D counterparts in all identical chains. Both
    the display and color lists now include "no change". Thus, you can spacefill
    without changing the color, or change the color but not the rendering.

    -New QuickViews color scheme "Chains (PE)" distinguishes chains by color
    more clearly than Chime's built-in scheme, now designated "Chains (Chime)".

    -Total number of chains is now reported in the Molecule Information Window,
    on the Sequences display, and display of the incorrect report from Chime in
    the message window is suppressed.

    -Troubleshooting is revised, and includes troubleshooting for IE as well as
    Netscape, and the 1 gigabyte Macintosh problem.

    -Now works just fine on the Macintosh, so although Mac user's can't use the
    new Windows-IE compatibility, they can use the new features listed above.

    1.91 and 1.92 alpha have been tested extensively now, and seem to work well
    as intended in Windows Internet Explorer as well as Netscape (Windows or
    Macintosh). No major problems have been reported. This version will become
    'beta' after I get around to fixing a few remaining loose ends concerning
    Internet Explorer compatibility, notably the tutorial movies. The plan is
    that later this year, it will mature to version 2.0 and replace the ancient
    version 1.0 at the Protein Data Bank.



    /* - - - - - - - - - - - - - - - - - - - - - - - - - - -
    The Protein Explorer: http://proteinexplorer.org
    Workshops: http://www.umass.edu/molvis/workshop
    World Index of Molecular Visualization Resources: http://molvisindex.org
    PDB Lite molecule finder: http://pdblite.org
    Molecular Visualization EMail List:
          http://www.umass.edu/microbio/rasmol/raslist.htm

    Eric Martz, Professor (Immunology), Dept Microbiology
    U Mass, Amherst MA US  413-545-2325/FAX 413-545-2532
                  http://www.umass.edu/molvis/martz
    - - - - - - - - - - - - - - - - - - - - - - - - - - - */


--Boundary_(ID_OEYqnQFKJSEMoV54LCfbIg)-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: Protein Explorer 1.922 alpha; Atlas of Macromolecules Date: Mon, 25 Feb 2002 10:39:01 -0600 (CST) To: rasmol@lists.umass.edu Hi, This atlas plus PDB Files link to Don Harden and Dabney Dixon work is a great addition to finding starting places of useful molecules. I would suggest the Atlas should at least provide a link to PDB's Molecule of the month: http://www.rcsb.org/pdb/molecules/molecule_list.html David Goodsell has created a really great easy reading resource on currently 26 molecules (started Jan 2000). To a lesser extend ExPASy protein spotlight http://www.expasy.org/spotlight/ Regards, Bruce Southey ----------------------------------------------------------------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-Accept-Language: en References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Joseph J. Grabowski" Subject: Re: Protein Explorer 1.922 alpha; Atlas of Macromolecules Date: Mon, 25 Feb 2002 12:08:00 -0500 To: rasmol@lists.umass.edu Matt: What about TA for the summer? Cheers, Joe G. -- Joseph J. Grabowski Associate Professor, Department of Chemistry University of Pittsburgh Pittsburgh, PA 15260 Home Page: http://www.pitt.edu/~joeg Phone: 412-624-8632 Fax: 412-624-8611 ---------------------------------------------------------- Try not to become a man of success but rather to become a man of value. -- Albert Einstein ----------------------------------------------------------------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 mistry at ACS Boston meeting Mark Marten , wentmp@rpi.edu, "Chemed-L (E-mail)" , southey@ux1.cso.uiuc.edu, rasmol@lists.umass.edu, "Caldwell, Ben" , "\"Grisham, Charles\" <\"Charles M. Grisham\"" , Chemed-L , PatD@mail.uca.edu, whitehea@dickinson.edu, bering@mail.clarion.edu, pacsch@rit.edu, jpowers@kennesaw.edu, taylora@wabash.edu, reingold@juniata.edu, ssmith@hood.edu, robkires@udmercy.edu, sears@lifesci.ucsb.edu, Roger_Kaspar@BYU.edu, wscovel@bgnet.bgsu.edu, "Kim, Tom (E-mail)" boundary="Boundary_(ID_y89BFvR6yMhdfuwrtqH+jA)" ++++------+------+------+------+------+------+------+------+------+------+ From: "Fisher, Matt" Subject: call for papers - symposium on bioinformatics in undergrad bioche Date: Tue, 26 Feb 2002 18:19:13 -0500 To: "Erik J. Fernandez" , Sarah Harcum , Cc: "Fisher, Matt (E-mail)" 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_y89BFvR6yMhdfuwrtqH+jA) Please share this announcement with interested colleagues. A symposium on "Bioinformatics in the Undergraduate Biochemistry Curriculum" will be held as part of the American Chemical Society national meeting to be held in Boston from Sunday, August 18 - Thursday, August 22, 2002 Bioinformatics in the Undergraduate Biochemistry Curriculum What place does bioinformatics have in undergraduate biochemistry? What is an appropriate introduction to this topic? How have people incorporated bioinformatics into undergraduate biochemistry courses (lecture or lab)? This symposium will bring together individuals involved in bioinformatics and teachers of undergraduate biochemistry to share ideas, concerns, and strategies for how this relatively new aspect of modern biochemistry may be incorporated into the undergraduate curriculum. Matt Fisher, Department of Chemistry, Saint Vincent College, 300 Fraser Purchase Road, Latrobe, PA 15650, tel: (724) 539-9761 x2356, fax: (724) 537-4554, mfisher@stvincent.edu No paper abstracts will be accepted. All abstracts go through OASys, the on-line abstract submission system. To enter OASys, go to http://oasys.acs.org/oasys.htm , then select the CHED division. The next screen will display a list of symposia being held as part of the meeting; click on the bioinformatics symposium and follow the directions for submitting an abstract. Questions regarding the symposium can be directed to me. Thanks! Matt Fisher Matthew A. Fisher Department of Chemistry Saint Vincent College 300 Fraser Purchase Road Latrobe, PA 15650 voice: (724) 539-9761 ext. 2356 FAX: (724) 537-4554 mfisher@stvincent.edu http://facweb.stvincent.edu/chemistry/Fisher.html --Boundary_(ID_y89BFvR6yMhdfuwrtqH+jA)
Please share this announcement with interested colleagues. 
 
A symposium on "Bioinformatics in the Undergraduate Biochemistry Curriculum" will be held as part of the American Chemical Society national meeting to be held in Boston from Sunday, August 18 - Thursday, August 22, 2002

Bioinformatics in the Undergraduate Biochemistry Curriculum
What place does bioinformatics have in undergraduate biochemistry?  What is an appropriate introduction to this topic?  How have people incorporated bioinformatics into undergraduate biochemistry courses (lecture or lab)?  This symposium will bring together individuals involved in bioinformatics and teachers of undergraduate biochemistry to share ideas, concerns, and strategies for how this relatively new aspect of modern biochemistry may be incorporated into the undergraduate curriculum.  Matt Fisher, Department of Chemistry, Saint Vincent College, 300 Fraser Purchase Road, Latrobe, PA 15650, tel: (724) 539-9761 x2356, fax: (724) 537-4554, mfisher@stvincent.edu
 
No paper abstracts will be accepted.  All abstracts go through OASys, the on-line abstract submission system.  To enter OASys, go to http://oasys.acs.org/oasys.htm , then select the CHED division.  The next screen will display a list of symposia being held as part of the meeting; click on the bioinformatics symposium and follow the directions for submitting an abstract.
 
Questions regarding the symposium can be directed to me.
 
Thanks!
 
Matt Fisher

Matthew A. Fisher
Department of Chemistry
Saint Vincent College
300 Fraser Purchase Road
Latrobe, PA 15650
voice: (724) 539-9761 ext. 2356
FAX:   (724) 537-4554
mfisher@stvincent.edu
http://facweb.stvincent.edu/chemistry/Fisher.html 

--Boundary_(ID_y89BFvR6yMhdfuwrtqH+jA)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Ioannis Michalopoulos Subject: monitor & restrict Date: Mon, 04 Mar 2002 18:11:00 +0000 To: RasMol Email List Dear PDB developers and users, I have a rasmol script that monitors various atomic interactions: monitor ### #### monitor ### ### monitor #### ### etc. In the end, there is a restriction in order to display only the atoms around my ligand: restrict within (8.0,lig_ID) Unfortunately, while Rasmol can efficiently restrict atoms, it still shows all distances it monitors, even if the atoms participating in these interactions are out of the restricted space. I would be indebted if you could tell me if there is any way to restrict the monitor lines that are outwith the restricted space other than manually deleting/ commenting/ rewriting these extra "monitor ### ####" lines. If there is no direct way, is it a lot if I ask you to fix that in the next version? Thank you inadvance. Yours Faithfully, Dr Ioannis Michalopoulos -- .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' Dr Ioannis Michalopoulos Research Fellow in Bioinformatics School of Biochemistry and Molecular Biology Tel: +44 113 23 33072 University of Leeds Fax: +44 113 23 33167 Leeds LS2 9JT ioannis@bioinformatics.leeds.ac.uk UK http://www.bioinformatics.leeds.ac.uk/~ioannis/ .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' ----------------------------------------------------------------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: Ioannis Michalopoulos Subject: select special atom Date: Mon, 04 Mar 2002 18:18:19 +0000 To: RasMol Email List Dear Rasmol users, In the PDB files: 1g3l 1g1l 1ker 1keu some heteroatom names in DAU and TRH ligands are as follows: "O3,", "O4,", "O5,". With that commas these atoms are distinguished from "O3", "O4", "O5" which are also present in these ligands. In the case of 1ker, I tried to select "O5" and "O5,". This is what I got: RasMol> select DAU2573.O5 1 atom selected! RasMol> select DAU2573.O5, ^ Syntax error in expression! I tried various things, like select DAU2573.'O5,' select DAU2573."O5," select DAU2573.[O5,] which all failed. I wonder if there is any way I can directly select such an atom, instead of indirectly selecting it by typing: select DAU2573.O5? and not DAU2573.O5 Thank you in advance. Best Regards, Yannis -- .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' Dr Ioannis Michalopoulos Research Fellow in Bioinformatics School of Biochemistry and Molecular Biology Tel: +44 113 23 33072 University of Leeds Fax: +44 113 23 33167 Leeds LS2 9JT ioannis@bioinformatics.leeds.ac.uk UK http://www.bioinformatics.leeds.ac.uk/~ioannis/ .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' ----------------------------------------------------------------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: <02030418370701.24558@bmbpcu15> ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re: select special atom Date: Mon, 04 Mar 2002 20:15:21 +0100 To: rasmol@lists.umass.edu It's not a direct answer to your question, but to select a particular atom, you can make a selection by using the atom number ID. For example : RasMol> select atomno= (your atom's number) My two cents... Paul Pillot ----- Original Message ----- Sent: Monday, March 04, 2002 7:18 PM From: "Ioannis Michalopoulos" Subject: select special atom To: "RasMol Email List" > Dear Rasmol users, > > In the PDB files: 1g3l 1g1l 1ker 1keu some heteroatom names in DAU and TRH > ligands are as follows: "O3,", "O4,", "O5,". With that commas these atoms are > distinguished from "O3", "O4", "O5" which are also present in these ligands. > > In the case of 1ker, I tried to select "O5" and "O5,". This is what I got: > > RasMol> select DAU2573.O5 > 1 atom selected! > RasMol> select DAU2573.O5, > ^ > Syntax error in expression! > > I tried various things, like > > select DAU2573.'O5,' > > select DAU2573."O5," > > select DAU2573.[O5,] > > which all failed. I wonder if there is any way I can directly select such an > atom, instead of indirectly selecting it by typing: > > select DAU2573.O5? and not DAU2573.O5 > > Thank you in advance. > > Best Regards, > > Yannis > -- > .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. > /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ > X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X > `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' > Dr Ioannis Michalopoulos Research Fellow in Bioinformatics > School of Biochemistry and Molecular Biology Tel: +44 113 23 33072 > University of Leeds Fax: +44 113 23 33167 > Leeds LS2 9JT ioannis@bioinformatics.leeds.ac.uk > UK http://www.bioinformatics.leeds.ac.uk/~ioannis/ > .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. .-. > /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ > X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X > `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' > > ----------------------------------------------------------------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: =?iso-8859-1?q?Frederic=20Zilbermann?= Subject: Vectorial output Date: Mon, 18 Mar 2002 09:28:39 +0100 (CET) To: Liste Rasmol Hello everybody, First let me introduce myself : I'm a French research technician, working in the University of Montpellier, south of France. I'm actually working in a project which aims to provide multimedia biochemstry courses, by the way of internet and on the CD support. For this I have to make animations with Macromedia Flash 5. I often have to import in Flash pictures of molecules I got with Rasmol. The only problem is Flash is vectorial and my goal is to obtain vectorial pictures of these molecules, so their integrations in Flash will be much easier and the animations would look ok. As far as I tried, I only got bitmap (raster) pictures of molecules with rasmol. Is there a way to get vectorial pictures with Rasmol ? Or maybe with another molecule viewer ? Thanks for your answers Fred Zilbermann, Université Montpellier II, Montpellier ___________________________________________________________ Do You Yahoo!? -- Une adresse @yahoo.fr gratuite et en français ! Yahoo! Mail : http://fr.mail.yahoo.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-- Errors-to: Postmaster@kumc.edu Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: George Helmkamp Subject: Re: Vectorial output (on extended leave) Date: Mon, 18 Mar 2002 02:30:37 -0600 To: rasmol@lists.umass.edu I am currently away from my office and laboratory. If you need to communicate with a laboratory person, please contact Ms. Hong Li at hli@kumc.edu or Ms. Elizabeth Miller at emiller5@kumc.edu. The telephone number is 913.588.6958. Thank you. ----------------------------------------------------------------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/10.0.0.1309 X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id g2IGUL217410 ++++------+------+------+------+------+------+------+------+------+------+ From: "James W. Caras" Subject: Re: Vectorial output Date: Mon, 18 Mar 2002 10:30:29 -0600 To: rasmol@lists.umass.edu Hi Fred, RasMol supports the export of vector images as postscript files. Although I have not tried to open the resulting files in Flash, programs like Illustrator and Freehand do so nicely and I would anticipate Flash will as well (if it doesn't, you could always save as a flash-compatible file from within the other vector programs). There is one thing you should be aware of... In my experience, the postscript export in RasMol only works for some display types, such as Ball & Stick (I would think therefore wireframe and spacefill would work as well). I do not believe that ribbon, cartoon, etc. work for this, but try it, I could be wrong. Jamie On 3/18/02 2:28 AM, "Frederic Zilbermann" wrote: > Hello everybody, > > First let me introduce myself : I'm a French research > technician, working in the University of Montpellier, > south of France. > > I'm actually working in a project which aims to > provide multimedia biochemstry courses, by the way of > internet and on the CD support. For this I have to > make animations with Macromedia Flash 5. I often have > to import in Flash pictures of molecules I got with > Rasmol. The only problem is Flash is vectorial and my > goal is to obtain vectorial pictures of these > molecules, so their integrations in Flash will be much > easier and the animations would look ok. As far as I > tried, I only got bitmap (raster) pictures of > molecules with rasmol. > > Is there a way to get vectorial pictures with Rasmol ? > Or maybe with another molecule viewer ? > > Thanks for your answers > > Fred Zilbermann, Université Montpellier II, Montpellier > > ___________________________________________________________ > Do You Yahoo!? -- Une adresse @yahoo.fr gratuite et en français ! > Yahoo! Mail : http://fr.mail.yahoo.com > > ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' Dr. James Caras The Institute for Cellular and Molecular Biology The University of Texas at Austin MBB 3.122 2500 Speedway Austin, TX 78712 caras@mail.utexas.edu (512) 471-0416 ----------------------------------------------------------------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: Fergus Doherty Subject: Problem selecting numbered chains Date: Fri, 22 Mar 2002 15:01:13 +0000 To: rasmol@lists.umass.edu Hello all, A PDB file for the proteasome gives letters to chains, except for two which are numbered (there are 28 subunits). It doesn't seem possible to select the numbered chains as "select *1" selects residue 1 in all chains, as does "select 1". Any ideas. Apart from editing the file that is. If it has to be edited what characters could be used to replace the 1 and 2? Would any ASCII character do? -- _____________________________________________________________________ Fergus Doherty PhD, School of Biomedical Sciences, E66, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH mailto:Fergus.Doherty@nottingham.ac.uk Tel: 0115 970 9366 FAX: 0115 970 9969 Teaching URL: http://www.nottingham.ac.uk/biochemcourses ----------------------------------------------------------------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-Accept-Language: en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Marv Paule Subject: Re: Problem selecting numbered chains Date: Fri, 22 Mar 2002 09:06:42 -0700 To: rasmol@lists.umass.edu Don't you need a colon in front of the number? select :1 Marv Paule Fergus Doherty wrote: > Hello all, > A PDB file for the proteasome gives letters to chains, except for two > which are numbered (there are 28 subunits). It doesn't seem possible > to select the numbered chains as "select *1" selects residue 1 in all > chains, as does "select 1". Any ideas. > > Apart from editing the file that is. If it has to be edited what > characters could be used to replace the 1 and 2? Would any ASCII > character do? > -- > > _____________________________________________________________________ > Fergus Doherty PhD, > School of Biomedical Sciences, > E66, > University Medical School, > Queen's Medical Centre, > Nottingham NG7 2UH > > mailto:Fergus.Doherty@nottingham.ac.uk > Tel: 0115 970 9366 > FAX: 0115 970 9969 > Teaching URL: http://www.nottingham.ac.uk/biochemcourses > -- Marvin R. Paule Professor Department of Biochemistry and Molecular Biology Colorado State University Fort Collins, CO 80523-1870 phone: 970-491-6748 FAX: 970-491-0494 email: mpaule@lamar.colostate.edu internet: http://www.bmb.colostate.edu/people/faculty/paule.htm ----------------------------------------------------------------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-MailScanner: Found to be clean ++++------+------+------+------+------+------+------+------+------+------+ From: phil cunningham Subject: Inter atom distances Date: Mon, 25 Mar 2002 08:38:40 +0000 To: rasmol@lists.umass.edu Dear RasMol list Can any of you point me to a script (sed auk perl)to compute interatomic distances from PDB files? (and a wee discussion on the formula if possible) Cant believe there are not dozens out there!! Phil ---------------------- Phil Cunningham Senior Bioinformatics Officer King's College London Franklin Wilkins Building 150 Stamford Street London SE1 9NN tel 020 7848 4239 fax 020 7848 4290 email phil.cunningham@kcl.ac.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-- X-Accept-Language: de, en ++++------+------+------+------+------+------+------+------+------+------+ From: Mario Albrecht Subject: Inter atom distances, part 2 Date: Mon, 25 Mar 2002 11:54:49 +0100 To: rasmol@lists.umass.edu On Mon, 25 Mar 2002, phil cunningham wrote: > Dear RasMol list > Can any of you point me to a script (sed auk perl)to > compute interatomic distances from PDB files? (and a > wee discussion on the formula if possible) > Cant believe there are not dozens out there!! Additionally, does anyone know a web server or script that can compute the protein "diameter", that is, the maximum Calpha and/or Cbeta distance, of a PDB chain? Thanks, Mario -- ************************************************************************ * Mario Albrecht (Office telephone: ++49 (0)2241-14-2806)* * Address: Am Jesuitenhof 3, App. 1363 / 53117 Bonn / GERMANY * * (Home: Lortzingstr. 5 / 92665 Altenstadt / GERMANY) * * Telephone: ++49 (0)228-9675049 (Home: ++49 (0)9602-4231) * * E-mail: mario@albrecht.net, mario.albrecht@gmx.de * ************************************************************************ ----------------------------------------------------------------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: christian.simon@ppce.jussieu.fr (Christian Simon) Subject: Re: Inter atom distances Date: Mon, 25 Mar 2002 14:41:07 +0100 (FRA Hiver) To: rasmol@lists.umass.edu Dear Phil, > Can any of you point me to a script (sed auk perl)to > compute interatomic distances from PDB files? (and a What do you want to do exactly ? To compute the distances for all pairs ? Or just for a one or two ? Do you want to apply PBC ? How big is your PDB file (how many atoms, and thus how many pairs) ? Do you want instantaneous result (or can you wait several minutes ?) > wee discussion on the formula if possible) > Cant believe there are not dozens out there!! > Phil Depending on your answers, it can be very easy (and it does not deserve to be on the web)... or very difficult (maybe no one solved it with sed/awk/perl/Tcl or any scripting language...) -- Christian SIMON The Center for Molecular Modeling (CMM, Rm. 141A) University of Pennsylvania, Tel: (215)-898-1583 Department of Chemistry, Box 127 Fax: (215)-573-6233 231 S. 34th St. Philadelphia, PA 19104-6323 USA ----------------------------------------------------------------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-Accept-Language: en References: <3C9F01F9.D013E2F2@mario-albrecht.net> ++++------+------+------+------+------+------+------+------+------+------+ From: Marv Paule Subject: Re: Inter atom distances, part 2 Date: Mon, 25 Mar 2002 11:23:36 -0700 To: rasmol@lists.umass.edu Mario, The command is monitor atomno atomno You first select the two atoms whose distance apart you need to measure, then issue the command with the two numbers only. e.g. monitor 2882 300 You can then get rid of the measurements and the dotted lines between the atoms with the command monitors off Hope this helps. Marv Paule Mario Albrecht wrote: > On Mon, 25 Mar 2002, phil cunningham wrote: > > > Dear RasMol list > > Can any of you point me to a script (sed auk perl)to > > compute interatomic distances from PDB files? (and a > > wee discussion on the formula if possible) > > Cant believe there are not dozens out there!! > > Additionally, does anyone know a web server or > script that can compute the protein "diameter", that is, > the maximum Calpha and/or Cbeta distance, of a PDB chain? > > Thanks, > > Mario > > -- > ************************************************************************ > * Mario Albrecht (Office telephone: ++49 (0)2241-14-2806)* > * Address: Am Jesuitenhof 3, App. 1363 / 53117 Bonn / GERMANY * > * (Home: Lortzingstr. 5 / 92665 Altenstadt / GERMANY) * > * Telephone: ++49 (0)228-9675049 (Home: ++49 (0)9602-4231) * > * E-mail: mario@albrecht.net, mario.albrecht@gmx.de * > ************************************************************************ > -- Marvin R. Paule Professor Department of Biochemistry and Molecular Biology Colorado State University Fort Collins, CO 80523-1870 phone: 970-491-6748 FAX: 970-491-0494 email: mpaule@lamar.colostate.edu internet: http://www.bmb.colostate.edu/faculty_detailed.cfm?lastname=Paule&firstname=Marvin ----------------------------------------------------------------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 in linux w/ WINE? Date: Mon, 01 Apr 2002 12:57:53 -0500 To: rasmol@lists.umass.edu Has anyone tried running Chime under WINE in linux (or any other flavor of unix)? http://www.winehq.com I'd be very interested in the results, particularly whether Protein Explorer (PE) can be run under WINE. For other solutions, please see http://molvis.sdsc.edu/protexpl/platform.htm They include Win4Lin, VMWare, and Citrix Metaframe (known to support PE), and Codeweaver's Crossover (uncertain). -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), 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 (X11; U; Linux i686; en-US; rv:0.9.9) Gecko/20020313 X-Accept-Language: en-us, en References: <200204011759.g31HxA224910@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Ron Worthington, Ph.D." Subject: Re: Chime in linux w/ WINE? Date: Mon, 01 Apr 2002 12:06:01 -0600 To: rasmol@lists.umass.edu Hi, Chime works great under RedHat-7.2: Linux worms 2.4.9-31smp #1 SMP Tue Feb 26 05:55:20 EST 2002 i686 unknown after installation using the crossover software from Code Weavers. Protein Explorer works with the plug-in then running under WINE, but tends to hang more often than on Macintosh OS 9.2.2. -Ron Eric Martz wrote: >Has anyone tried running Chime under WINE in linux (or any other flavor of >unix)? http://www.winehq.com > >I'd be very interested in the results, particularly whether Protein >Explorer (PE) can be run under WINE. >For other solutions, please see http://molvis.sdsc.edu/protexpl/platform.htm >They include Win4Lin, VMWare, and Citrix Metaframe (known to support PE), >and Codeweaver's Crossover (uncertain). > >-Eric > > >/* - - - - - - - - - - - - - - - - - - - - - - - - - - - >The Protein Explorer: http://proteinexplorer.org >Workshops: http://www.umass.edu/molvis/workshop >World Index of Molecular Visualization Resources: http://molvisindex.org >PDB Lite molecule finder: http://pdblite.org >Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > >Eric Martz, Professor (Immunology), 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: agc Subject: Re: Chime in linux w/ WINE? Date: Mon, 01 Apr 2002 13:41:24 -0500 (EST) To: rasmol@lists.umass.edu I have used wine for running chime, I use under windows netscape 4.7, my linux box is SUSE 7.3, I have seen it is a little bit slower than usual but works fine. On Mon, 1 Apr 2002, Eric Martz wrote: > Date: Mon, 01 Apr 2002 12:57:53 -0500 > From: Eric Martz > To: rasmol@lists.umass.edu > Subject: Chime in linux w/ WINE? > > Has anyone tried running Chime under WINE in linux (or any other flavor of > unix)? http://www.winehq.com > > I'd be very interested in the results, particularly whether Protein > Explorer (PE) can be run under WINE. > For other solutions, please see http://molvis.sdsc.edu/protexpl/platform.htm > They include Win4Lin, VMWare, and Citrix Metaframe (known to support PE), > and Codeweaver's Crossover (uncertain). > > -Eric > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > The Protein Explorer: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > PDB Lite molecule finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), 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 (X11; U; Linux i686; en-US; rv:0.9.2) Gecko/20010726 Netscape6/6.1 X-Accept-Language: en-us ++++------+------+------+------+------+------+------+------+------+------+ From: WZocher@t-online.de (Wolfgang Zocher) Subject: 24-bit display Date: Mon, 08 Apr 2002 19:34:45 +0200 To: rasmol@lists.umass.edu Hi all, I'm trying to get rasmol-2.7 running on a laptop with a 24-bit display (under SuSE Linux 7.2) and it won't work. There are no colours and kind of weird structures on the screen - did anyone have success in trying the same?? Thanks in advance, Wolfgang Zocher ----------------------------------------------------------------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 V6.0.5762.3 Thread-Topic: MacOSX and chime Thread-Index: AcHfNkBZgRnvv973EcG3FCLjfaqk3A== Content-Class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: "Campbell, Malcolm" Subject: MacOSX and chime Date: Mon, 08 Apr 2002 15:47:44 -0400 To: rasmol@lists.umass.edu RasMol Readers: I am new to the list but I did not see any answers when I checked the archives. Are there any fixes for Mac Users who want to use chime running OSX without having to boot Classic OS 9.2? Thanks, Malcolm ------------------------------------------------------ A. Malcolm Campbell, Ph.D. Associate Professor of Biology Director of the Genome Consortium for Active Teaching (http://www.bio.davidson.edu/GCAT) Biology Department P. O. Box 7118 (US Mail) 225 Concord Rd (Shipping) Davidson, NC 28036 USA macampbell@davidson.edu http://www.bio.davidson.edu/campbell 704-894-2692 (voice) 704-894-2512 (fax) ----------------------------------------------------------------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-- <20020408163118-r01050000-9475FE7C-4B2F-11D6-880C-003065DFD8FC-1013-010c@192.168.1.13> ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: MacOSX and chime Date: Mon, 08 Apr 2002 16:31:17 -0400 To: rasmol@lists.umass.edu here's what Campbell, Malcolm (macampbell@davidson.edu) said on 04.08.02 (3:47 PM): > RasMol Readers: > I am new to the list but I did not see any answers when I checked the archives. > > Are there any fixes for Mac Users who want to use chime running OSX without having to boot Classic OS 9.2? > > Thanks, > Malcolm > unfortunately, there is not, although Chime in the Classic environment runs as well as it does in stand-alone OS 9. IOW, there are no new bugs ;-) OS X is known to run many unix programs without problems; I'm reaching a bit, but it makes me think there could be a linux solution. for a starting point, try Eric Martz's doc at . I have no direct experience with running linux software under OS X, though, so YMMV. if you do discover a work-around, I'm sure that the list would be interested in hearing of it. hth, tim -- molvisions - 3D molecular visualization waltham, ma usa ----------------------------------------------------------------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-- <"20020408163118-r01050000-9475FE7C-4B2F-11D6-880C-003065DFD 8FC-1013-010c"@192.168.1.13> References: <4AE8AED63DA0244FA26B3EE309675DD40148BBB9@lola.davidson.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: MacOSX and chime Date: Mon, 08 Apr 2002 18:23:44 -0400 To: rasmol@lists.umass.edu At 4/8/02, Tim Driscoll wrote: >OS X is known to run many unix programs without problems; I'm reaching a bit, but >it makes me think there could be a linux solution. for a starting point, try Eric >Martz's doc at . I have no idea what IOW and YMMV are, but for a more recently updated list of linux options for Chime, please see http://molvis.sdsc.edu/protexpl/platform.htm -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), 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-- <20020408193524-r01050000-4CDCF7F2-4B49-11D6-880C-003065DFD8FC-1013-010c@192.168.1.13> ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: MacOSX and chime Date: Mon, 08 Apr 2002 19:35:24 -0400 To: rasmol@lists.umass.edu here's what Eric Martz (emartz@microbio.umass.edu) said on 04.08.02 (6:23 PM): > At 4/8/02, Tim Driscoll wrote: > >OS X is known to run many unix programs without problems; I'm reaching a > bit, but > >it makes me think there could be a linux solution. for a starting point, > try Eric > >Martz's doc at . > > I have no idea what IOW and YMMV are, but for a more recently updated list > of linux options for Chime, please see > http://molvis.sdsc.edu/protexpl/platform.htm > > -Eric > > er, sorry. YMMV - your mileage may vary; IOW = in other words. -tim -- molvisions - 3D molecular visualization waltham, ma usa ----------------------------------------------------------------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 (X11; U; Linux i586; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: de, en-us References: <3CB1D4B5.7010208@t-online.de> ++++------+------+------+------+------+------+------+------+------+------+ From: Karl Sarnow Subject: Re: 24-bit display Date: Tue, 09 Apr 2002 09:17:37 +0200 To: rasmol@lists.umass.edu Wolfgang Zocher wrote: > Hi all, > > I'm trying to get rasmol-2.7 running on a laptop with a 24-bit display > (under SuSE Linux 7.2) and it won't work. There are no colours and kind > of weird structures on the screen - did anyone have success in trying > the same?? > > Thanks in advance, > > Wolfgang Zocher > Since SuSE 7.2 there should be no problem. If you get it started without an error message, this is OK. But the version distributed with SuSE 7.2 is compiled for a 16 Bit display. At least it is this what I am reading when I start it. CU Karl Sarnow -- Dr. Karl Sarnow Teacher at Gymnasium Isernhagen German national co-ordinator of the European Schools Project e-Mail: karl@dadoka.h.ni.schule.de URL: http://www.shuttle.schule.de/h/dadoka ----------------------------------------------------------------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-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Todd Carlson Subject: sprout hydrogens in Chime Date: Wed, 10 Apr 2002 16:27:12 -0400 To: rasmol@lists.umass.edu Hi I wanted to use the sprout hydrogens feature in a Chime page. The mouse menu button works, but the embed tag: options3d=hydrogen which I got from the MDL support site doesn't work. However, other option3d tags: options3d={dots|hetero|hydrogen|labels|shadows|slab|specular|stereo} do work. Is there any way to do this? A sript command maybe? Thanks Todd Carlson ----------------------------------------------------------------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-Accept-Language: en References: <3CB4A01F.75EC7E00@gvsu.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Marv Paule Subject: Re: sprout hydrogens in Chime Date: Wed, 10 Apr 2002 17:25:50 -0600 To: rasmol@lists.umass.edu Did you try "sprout hydrogens" ? Todd Carlson wrote: > Hi > > I wanted to use the sprout hydrogens feature in a Chime page. The mouse > menu button works, but the embed tag: > > options3d=hydrogen > > which I got from the MDL support site doesn't work. However, other > option3d tags: > > options3d={dots|hetero|hydrogen|labels|shadows|slab|specular|stereo} > > do work. Is there any way to do this? A sript command maybe? > > Thanks > > Todd Carlson > -- Marvin R. Paule Professor Department of Biochemistry and Molecular Biology Colorado State University Fort Collins, CO 80523-1870 phone: 970-491-6748 FAX: 970-491-0494 email: mpaule@lamar.colostate.edu internet: http://www.bmb.colostate.edu/faculty_detailed.cfm?lastname=Paule&firstname=Marvin ----------------------------------------------------------------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 ++++------+------+------+------+------+------+------+------+------+------+ From: Todd Carlson Subject: Re: sprout hydrogens in Chime Date: Thu, 11 Apr 2002 08:52:42 -0400 To: rasmol@lists.umass.edu Yes, I tried that. Todd >>> mpaule@lamar.colostate.edu 04/10/02 07:25PM >>> Did you try "sprout hydrogens" ? Todd Carlson wrote: > Hi > > I wanted to use the sprout hydrogens feature in a Chime page. The mouse > menu button works, but the embed tag: > > options3d=hydrogen > > which I got from the MDL support site doesn't work. However, other > option3d tags: > > options3d={dots|hetero|hydrogen|labels|shadows|slab|specular|stereo} > > do work. Is there any way to do this? A sript command maybe? > > Thanks > > Todd Carlson > -- Marvin R. Paule Professor Department of Biochemistry and Molecular Biology Colorado State University Fort Collins, CO 80523-1870 phone: 970-491-6748 FAX: 970-491-0494 email: mpaule@lamar.colostate.edu internet: http://www.bmb.colostate.edu/faculty_detailed.cfm?lastname=Paule&firstname=Marvin ----------------------------------------------------------------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: selecting residues with insertion codes Date: Sat, 13 Apr 2002 13:14:08 -0400 To: rasmol@lists.umass.edu Dear RasMolluscs and Chimeleons (especially RasMolluscs familiar with the source code): The residues in some PDB files are numbered to match a related reference molecule. Inserted residues are then often numbered with the SAME number as the previous residue, distinguished only by a so-called insertion code or iCode letter following the residue number, e.g. 82, 82A, 82B, etc. An example is 1IGY. (In Protein Explorer, click Molecule Information/Mol Info, then Sequences to see the inserted residues highlighted in green.) Fabian Glaser and Nir Ben-Tal have recently pointed out to me 1UCY. It has inserted residues before residue 1. In some cases, authors give these negative and zero residue numbers, then continuing with 1 (e.g. 1AVQ). However in 1UCY, the leading inserted residues are numbered with an alternative scheme, 1H, 1G, 1F, 1E, 1D, 1C, 1B, 1A, and 1 (in reverse alphabetical order). [Protein Explorer assumes the letters are in alphabetical order and does NOT display these residue iCodes correctly, as they appear in the ATOM records of 1UCY.] Insertions after residue 1 are coded in alphabetical order in 1UCY. Finally, the questions: 1. In RasMol 2.6b2a, 'show residue' omits the iCodes. In Chime, neither 'show sequence' nor 'show residue' includes the iCode. I suspect RasMol and Chime are ignoring iCodes when they read ATOM records. ***Confirmation of this by someone familiar with the RasMol source code would be appreciated.*** 2. In RasMol or Chime, is there any way to select a single inserted residue, for example, Thr14B in 1UCY? 'select thr14b' doesn't work, nor 'select 14b'. The first residue (lacking an iCode) can be selected, e.g. 'select asp14', provided there are no other thr's numbered 14. 'select 1' selects all residues numbered one including all inserted residues with that number. You can select gln14a with 'select gln14 and :l' because it is the only gln numbered 14 in chain L. However, since there are 3 glu's inserted after 14 (14C, 14E, 14H), you get all 3 with 'select glu14 and :l'. Of course you could use the atom serial numbers but that would be very cumbersome. [Presently, Protein Explorer's Seq3D interface (where a click on a residue selects it) fails to work for inserted residues.] /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), 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-- <20020413163616-r01050000-1A757D54-4F1E-11D6-8BA4-003065DFD8FC-1013-010c@192.168.1.13> ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Chime animations to video? Date: Sat, 13 Apr 2002 16:36:16 -0400 To: "LIST: rasmol" hello all, I'm interested in converting Chime animations to standard video format (mov, mpg, avi, whatever). I imagine it would require some software capable of capturing desktop events - akin to Grab or Screen Capture, but able to capture at some decent fps. has anyone ever done this, or know of software that might handle the task? thanks, tim -- molvisions - 3D molecular visualization waltham, ma usa ----------------------------------------------------------------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: <200204131714.g3DHEL222216@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: selecting residues with insertion codes Date: Sat, 13 Apr 2002 19:27:37 -0400 To: rasmol@lists.umass.edu At present the only significant use that RasMol makes of the insertion code is to start a new residue when the insertion code (or the residue number) changes. When you pick an atom, the insertion code is displayed (at least in the current version). RasMol can be changed to make more use of the insertion code, if there is a need. I will try work up a reasonable, upwards compatible syntax for selection by insertion code. Until and unless Chime becomes open source, I cannot make the equivalent change in Chime. -- Herbert At 1:14 PM -0400 4/13/02, Eric Martz wrote: >Dear RasMolluscs and Chimeleons (especially RasMolluscs familiar with the >source code): > >The residues in some PDB files are numbered to match a related reference >molecule. Inserted residues are then often numbered with the SAME number as >the previous residue, distinguished only by a so-called insertion code or >iCode letter following the residue number, e.g. 82, 82A, 82B, etc. An >example is 1IGY. (In Protein Explorer, click Molecule Information/Mol Info, >then Sequences to see the inserted residues highlighted in green.) > >Fabian Glaser and Nir Ben-Tal have recently pointed out to me 1UCY. It has >inserted residues before residue 1. In some cases, authors give these >negative and zero residue numbers, then continuing with 1 (e.g. 1AVQ). >However in 1UCY, the leading inserted residues are numbered with an >alternative scheme, 1H, 1G, 1F, 1E, 1D, 1C, 1B, 1A, and 1 (in reverse >alphabetical order). [Protein Explorer assumes the letters are in >alphabetical order and does NOT display these residue iCodes correctly, as >they appear in the ATOM records of 1UCY.] Insertions after residue 1 are >coded in alphabetical order in 1UCY. > >Finally, the questions: > >1. In RasMol 2.6b2a, 'show residue' omits the iCodes. In Chime, neither >'show sequence' nor 'show residue' includes the iCode. I suspect RasMol and >Chime are ignoring iCodes when they read ATOM records. ***Confirmation of >this by someone familiar with the RasMol source code would be appreciated.*** > >2. In RasMol or Chime, is there any way to select a single inserted >residue, for example, Thr14B in 1UCY? 'select thr14b' doesn't work, nor >'select 14b'. The first residue (lacking an iCode) can be selected, e.g. >'select asp14', provided there are no other thr's numbered 14. 'select 1' >selects all residues numbered one including all inserted residues with that >number. You can select gln14a with 'select gln14 and :l' because it is the >only gln numbered 14 in chain L. However, since there are 3 glu's inserted >after 14 (14C, 14E, 14H), you get all 3 with 'select glu14 and :l'. Of >course you could use the atom serial numbers but that would be very >cumbersome. [Presently, Protein Explorer's Seq3D interface (where a click >on a residue selects it) fails to work for inserted residues.] > > >/* - - - - - - - - - - - - - - - - - - - - - - - - - - - >The Protein Explorer: http://proteinexplorer.org >Workshops: http://www.umass.edu/molvis/workshop >World Index of Molecular Visualization Resources: http://molvisindex.org >PDB Lite molecule finder: http://pdblite.org >Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > >Eric Martz, Professor (Immunology), 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 020 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-- <20020413163616-r01050000-1A757D54-4F1E-11D6-8BA4-003065DFD8FC-1013-010c@192.168.1.13> References: <20020413163616-r01050000-1A757D54-4F1E-11D6-8BA4-003065DFD8FC-1013-010c@192.168.1.13> ++++------+------+------+------+------+------+------+------+------+------+ From: "William F. Coleman" Subject: Re: Chime animations to video? Date: Sat, 13 Apr 2002 20:09:03 -0400 To: rasmol@lists.umass.edu I do this using SnagIt (version 6) from www.techsmith.com - it does an very good job of capturing screen motion - adjustable capture rates etc. The default is to avi and I then usually go into either something like Animation Shop if I want it as an animated gif or Flix2, if I want it in Flash format. Hope this helps, Flick William F. Coleman (a.k.a. Flick Coleman) Professor of Chemistry Wellesley College Wellesley, MA 02481 for the period 12/01-7/02 Visiting Professor of Chemistry Department of Chemistry University of Wisconsin - Madison 1101 University Avenue Madison WI 53706 608-262-1511 email: wcoleman@wellesley.edu web: www.wellesley.edu/Chemistry/colemanw.html ----------------------------------------------------------------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-- <20020414082339-r01050000-737F17E2-4FA2-11D6-B26D-003065DFD8FC-1013-010c@192.168.1.13> ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Chime animations to video? Date: Sun, 14 Apr 2002 08:23:39 -0400 To: rasmol@lists.umass.edu William F. Coleman at said: > I do this using SnagIt (version 6) from www.techsmith.com - it does an > very good job of capturing screen motion - adjustable capture rates etc. > The default is to avi and I then usually go into either something like > Animation Shop if I want it as an animated gif or Flix2, if I want it in > Flash format. > > Hope this helps, > > Flick > > > I wrote: > > > > hello all, > > > > I'm interested in converting Chime animations to standard video format > > (mov, mpg, avi, whatever). I imagine it would require some software > > capable of capturing desktop events - akin to Grab or Screen Capture, > > but able to capture at some decent fps. > > > > has anyone ever done this, or know of software that might handle the > > task? > > > > thanks, > > > > tim hi Flick, thanks for responding. unfortunately, SnagIt only captures still images, and it is limited to Win. I'm trying to capture animations (movies), and I'm on a Mac (sorry - I should have said that in the beginning). TechSmith's Camtasia does capture video from the desktop but it is $$$, fairly high-end, and Win platform only. I can get around 1 and 2, but not 3. do you know of a Mac-side relative? regards, tim -- molvisions - 3D molecular visualization waltham, ma usa ----------------------------------------------------------------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-- <20020414082339-r01050000-737F17E2-4FA2-11D6-B26D-003065DFD8FC-1013-010c@192.168.1.13> <20020414114654-r01050000-D87BE4BA-4FBE-11D6-A8D6-003065DFD8FC-1013-010c@192.168.1.13> ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Chime animations to video? Date: Sun, 14 Apr 2002 11:46:54 -0400 To: rasmol@lists.umass.edu Timothy Driscoll at said: > William F. Coleman at said: > > > I do this using SnagIt (version 6) from www.techsmith.com - it does an > > very good job of capturing screen motion - adjustable capture rates etc. > > The default is to avi and I then usually go into either something like > > Animation Shop if I want it as an animated gif or Flix2, if I want it in > > Flash format. > > > > Hope this helps, > > > > Flick > > > > > > I wrote: > > > > > > hello all, > > > > > > I'm interested in converting Chime animations to standard video format > > > (mov, mpg, avi, whatever). I imagine it would require some software > > > capable of capturing desktop events - akin to Grab or Screen Capture, > > > but able to capture at some decent fps. > > > > > > has anyone ever done this, or know of software that might handle the > > > task? > > > > > > thanks, > > > > > > tim > > hi Flick, > > thanks for responding. unfortunately, SnagIt only captures still images, > and it is limited to Win. I'm trying to capture animations (movies), and > I'm on a Mac (sorry - I should have said that in the beginning). > > TechSmith's Camtasia does capture video from the desktop but it is $$$, > fairly high-end, and Win platform only. I can get around 1 and 2, but not > 3. do you know of a Mac-side relative? > > regards, > > tim hello again, 1. Flick, my apologies for contradicting you so blatantly, and somewhat rudely. I plead pre-coffee fog, and ask forgiveness. what I meant to say was that I am confused. I do know about SnagIt but, as far as I could tell from their Web site, it only captures screenshots and not video. can it capture desktop events directly as video (as distinct from video imported from a digital camcorder, for example)? if so, is it a straight capture, like a screen grab, or do you have to catch frame-by-frame? I do have access to a Win machine, but it's a last resort for me ;-) again, my apologies for being rude - I hope you find this response a bit more respectful. 2. for those interested, an answer to my own question about a Mac version. there is a program called SnapzPro ( that advertises the ability to capture desktop events to QT. I've read through their site, but there is little in the way of details about this feature. but it is only $50 so may be worth the leap. this thread may seem a bit OT; after all, converting Chime into QT is a step backward, in my estimation (you lose all the interactivity). however, QTed Chimes make for great teaser material, since almost everyone is set up to view movies. in addition, it would provide one possible method (albeit kludgy) for combining Chime material with other formats (Flash, Director, etc.). regards, tim (now suitably caffienated) -- molvisions - 3D molecular visualization waltham, ma usa ----------------------------------------------------------------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-- <20020414114654-r01050000-D87BE4BA-4FBE-11D6-A8D6-003065DFD8FC-1013-010c@192.168.1.13> References: <20020414114654-r01050000-D87BE4BA-4FBE-11D6-A8D6-003065DFD8FC-1013-010c@192.168.1.13> ++++------+------+------+------+------+------+------+------+------+------+ From: rbeaver@tsud.edu Subject: Re: Chime animations to video? Date: Sun, 14 Apr 2002 11:17:01 -0500 To: rasmol@lists.umass.edu > >2. for those interested, an answer to my own question about a Mac version. >there is a program called SnapzPro ( that >advertises the ability to capture desktop events to QT. I've read through >their site, but there is little in the way of details about this feature. >but it is only $50 so may be worth the leap. > Snapz Pro is great. The download is free for thirty days (and even after continues to work, albeit with a nag screen, so you can give it a thorough testing). It can capture a window, a selected portion of the screen, or the whole screen, and allows total control over frame rate, compression, and lots of other stuff. There are a bunch of QuickTime Photoshop tutorials (with narration) at the Apple web site (url below) that illustrate what Snapz Pro can do (I am not certain that they were created with SnapZ Pro, but I would bet on it, and they are exactly what Snapz Pro is capable of doing and they look really good). http://www.apple.com/creative/resources/ttphotoshop/ ----------------------------------------------------------------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-- <20020413163616-r01050000-1A757D54-4F1E-11D6-8BA4-003065DFD8FC-1013-010c@192.168.1.13> References: <20020413163616-r01050000-1A757D54-4F1E-11D6-8BA4-003065DFD8FC-1013-010c@192.168.1.13> ++++------+------+------+------+------+------+------+------+------+------+ From: Dave Hurley Subject: Re: Chime animations to video? Date: Mon, 15 Apr 2002 09:34:02 -0700 To: rasmol@lists.umass.edu I did this a few times and ended up using a combination of AppleScript, Prefab Player (which enables AppleScript to drive mouse movement and menu choices) and SwissPDBviewer to grab single frames and then I used Quicktime Player Pro (although Graphic Converter will also do the job) to assemble the frames into a movie. It sounds laborious but it's not that bad. If you are using Rasmol then you probably won't need Prefab Player. I have a web site that describes the basic process at http://www.biology.washington.edu/molecular/ Let me know if you have any further questions. Dave Hurley Senior Computer Specialist (a biologist in disguise) University of Washington Biology Program 220 Hitchcock Hall Box 355320 Seattle, WA 98195-5320 phone: 206-685-8038 fax: 206-543-4649 >hello all, > >I'm interested in converting Chime animations to standard video format (mov, >mpg, avi, whatever). I imagine it would require some software capable of >capturing desktop events - akin to Grab or Screen Capture, but able to >capture at some decent fps. > >has anyone ever done this, or know of software that might handle the task? > >thanks, > >tim >-- >molvisions - 3D molecular visualization >waltham, ma usa > > -- ----------------------------------------------------------------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 <"20020413163616-r01050000-1A757D54-4F1E-11D6-8BA4-003065DFD 8FC-1013-010c"@192.168.1.13> X-UCL-MailScanner: Found to be clean ++++------+------+------+------+------+------+------+------+------+------+ From: Mike Porter Subject: Re: Chime animations to video? Date: Mon, 15 Apr 2002 18:27:02 +0100 To: rasmol@lists.umass.edu Tim, I've not done this in Chime, but it's OK to do in Rasmol. You can write a script file which goes rotate y 2 save gif image1.gif rotate y 2 save gif image2.gif and so on up to image180.gif - of course, you can make the rotations bigger and the file smaller if you want! You now need a bit of software which can convert a series of gifs into a movie - I've used Corel PhotoPaint, but I'm sure there's plenty around. Finally, delete the several MB of gifs clogging up your hard drive... Mike At 21:36 13/04/02, you wrote: >hello all, > >I'm interested in converting Chime animations to standard video format (mov, >mpg, avi, whatever). I imagine it would require some software capable of >capturing desktop events - akin to Grab or Screen Capture, but able to >capture at some decent fps. > >has anyone ever done this, or know of software that might handle the task? > >thanks, > >tim >-- >molvisions - 3D molecular visualization >waltham, ma usa > > _________________________________________________________ Dr M J Porter Lecturer in Organic Chemistry Department of Chemistry Email: m.j.porter@ucl.ac.uk UCL (University College London) Tel: +44 20 7679 4710 20 Gordon Street Fax: +44 20 7679 7463 London WC1H 0AJ, UK http://www.chem.ucl.ac.uk/people/porter/index.html ----------------------------------------------------------------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 ++++------+------+------+------+------+------+------+------+------+------+ From: Todd Carlson Subject: Re: Chime animations to video? Date: Mon, 15 Apr 2002 16:52:27 -0400 To: rasmol@lists.umass.edu I'll answer for Tim The RasMol save command doesn't function in Chime. Also, the move command in chime is more complex than just rotate y, etc. You are rotating x, y and z simultaneously and they have to be done in the correct order to get the right results. Todd >>> m.j.porter@ucl.ac.uk 04/15/02 01:27PM >>> Tim, I've not done this in Chime, but it's OK to do in Rasmol. You can write a script file which goes rotate y 2 save gif image1.gif rotate y 2 save gif image2.gif and so on up to image180.gif - of course, you can make the rotations bigger and the file smaller if you want! You now need a bit of software which can convert a series of gifs into a movie - I've used Corel PhotoPaint, but I'm sure there's plenty around. Finally, delete the several MB of gifs clogging up your hard drive... Mike At 21:36 13/04/02, you wrote: >hello all, > >I'm interested in converting Chime animations to standard video format (mov, >mpg, avi, whatever). I imagine it would require some software capable of >capturing desktop events - akin to Grab or Screen Capture, but able to >capture at some decent fps. > >has anyone ever done this, or know of software that might handle the task? > >thanks, > >tim >-- >molvisions - 3D molecular visualization >waltham, ma usa > > _________________________________________________________ Dr M J Porter Lecturer in Organic Chemistry Department of Chemistry Email: m.j.porter@ucl.ac.uk UCL (University College London) Tel: +44 20 7679 4710 20 Gordon Street Fax: +44 20 7679 7463 London WC1H 0AJ, UK http://www.chem.ucl.ac.uk/people/porter/index.html ----------------------------------------------------------------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-Accept-Language: en References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Mark J. Biscone" Subject: POVRay, altering PDB's etc. Date: Mon, 15 Apr 2002 20:20:37 -0400 To: rasmol@lists.umass.edu Hey all, 1. Does anyone have a step by step instruction on how to use POVRay 3 to boost the resolution of a RasMol generated .pov script? I am really not getting anywhere and never can focus the imported rendering to contain my whole molecule image. 2. Can .pdb files be combined for when structures of different portions are solved by altering the pdb file in text editor. For example, I am trying to make the structure of HIV-1 integrase using 1ex4 and 1k6y by deleting one of the dimer pairs in each and then cutting and pasting to make a new pdb file. What needs to be preserved from each file to make this work (if it can be done)? Thank you very much for your help in these matters. Sincerely, Mark Biscone University of Pennsylvania ----------------------------------------------------------------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 V5.50.4522.1200 X-MSMail-priority: Normal References: <3CBB6E55.177E87FD@mail.med.upenn.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: POVRay, altering PDB's etc. Date: Tue, 16 Apr 2002 09:06:04 +0200 To: rasmol@lists.umass.edu Mark, 1) I have currently RasTop installed and maybe it formats differently the pov file. Send me an example file please. What you want is easy, but the direction, angle etc of the camera can be expressed in diffeent ways. Probably you need to change the camera viewing angle only. 2) What you want can be done manually too, provided the atom numbering of the two portions, chains do not overlap. You need all ATOM and HETATM records, a simple TER between the chains, finishing with END. Do not deal with CONECT records, they complicate things, and most programs do not require them. ATOM 1 ...... ATOM n ...... TER ATOM m ... ATOM z... END If atom numberings overlap, you need some auxuliary program to merge the files and re-edit, for example Mol2Mol. regards Tama ----------------------- Dr. Tamas E. Gunda Research Group for Antibiotics Hungarian Academy of Sciences University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tamasgunda@tigris.klte.hu ----- Original Message ----- Sent: Tuesday, April 16, 2002 02:20 From: "Mark J. Biscone" Subject: POVRay, altering PDB's etc. To: > Hey all, > > 1. Does anyone have a step by step instruction on how to use POVRay 3 to boost the resolution of a RasMol generated .pov script? I am really not getting anywhere and never can focus the imported rendering to contain my whole molecule image. > > 2. Can .pdb files be combined for when structures of different portions are solved by altering the pdb file in text editor. For example, I am trying to make the structure of HIV-1 integrase using 1ex4 and 1k6y by deleting one of the dimer > pairs in each and then cutting and pasting to make a new pdb file. What needs to be preserved from each file to make this work (if it can be done)? > > Thank you very much for your help in these matters. > > Sincerely, > Mark Biscone > University of Pennsylvania > > > ----------------------------------------------------------------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 X-UCL-MailScanner: Found to be clean ++++------+------+------+------+------+------+------+------+------+------+ From: Mike Porter Subject: Re: Chime animations to video? Date: Tue, 16 Apr 2002 08:55:23 +0100 To: rasmol@lists.umass.edu Todd,

I'm aware that the save command doesn't work in Chime, and that the Chime move command is more complex than simply rotating about the y axis.  I wasn't for a moment suggesting that this method would work in Chime.  All I was saying is that, if you want to generate a movie that looks like Chime, using RasMol with a script is a possibility!

Mike

At 21:52 15/04/02, you wrote:
I'll answer for Tim

The RasMol save command doesn't function in Chime.  Also, the move command in chime is more complex than just rotate y, etc.  You are rotating x, y and z simultaneously and they have to be done in the correct order to get the right results.

Todd


>>> m.j.porter@ucl.ac.uk 04/15/02 01:27PM >>>
Tim,

I've not done this in Chime, but it's OK to do in Rasmol.  You can write a
script file which goes

rotate y 2
save gif image1.gif
rotate y 2
save gif image2.gif


and so on up to image180.gif - of course, you can make the rotations bigger
and the file smaller if you want!

You now need a bit of software which can convert a series of gifs into a
movie - I've used Corel PhotoPaint, but I'm sure there's plenty
around.  Finally, delete the several MB of gifs clogging up your hard drive...

Mike


_________________________________________________________
Dr M J Porter
Lecturer in Organic Chemistry
Department of Chemistry                         Email: m.j.porter@ucl.ac.uk
UCL (University College London)           Tel: +44 20 7679 4710
20 Gordon Street                                 Fax: +44 20 7679 7463
London
WC1H 0AJ, UK

http://www.chem.ucl.ac.uk/people/porter/index.html ----------------------------------------------------------------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-- <20020416083254-r01050000-13687325-5136-11D6-B8AE-003065DFD8FC-1013-010c@192.168.1.13> ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Chime animations to video? Date: Tue, 16 Apr 2002 08:32:54 -0400 To: rasmol@lists.umass.edu Mike Porter at said: > Todd, > > I'm aware that the save command doesn't work in Chime, and that the Chime > move command is more complex than simply rotating about the y axis.  I > wasn't for a moment suggesting that this method would work in Chime.  All > I was saying is that, if you want to generate a movie that looks like > Chime, using RasMol with a script is a possibility! > > Mike > > > At 21:52 15/04/02, Todd Carlson wrote: > > > > I'll answer for Tim > > > > The RasMol save command doesn't function in Chime.  Also, the move > > command in chime is more complex than just rotate y, etc.  You are > > rotating x, y and z simultaneously and they have to be done in the > > correct order to get the right results. > > > > Todd > > > > > > > m.j.porter@ucl.ac.uk 04/15/02 01:27PM >>> > > > Tim, > > > > > > I've not done this in Chime, but it's OK to do in Rasmol.  You can > > > write a script file which goes > > > > > > rotate y 2 save gif image1.gif rotate y 2 save gif image2.gif > > > > > > > > > and so on up to image180.gif - of course, you can make the rotations > > > bigger and the file smaller if you want! > > > > > > You now need a bit of software which can convert a series of gifs > > > into a movie - I've used Corel PhotoPaint, but I'm sure there's > > > plenty around.  Finally, delete the several MB of gifs clogging up > > > your hard drive... > > > > > > Mike hi Mike, I agree; this is one way to generate animated gifs from RasMol "movies" and a method I've used in the past. and I do have software that will take gifs and string them all together. but it is a prohibitive amount of work, with results of dubious quality, and let's face it - I'm lazy (er, I mean, I need to be efficient with my time - yeah, that's it). and Todd is correct in pointing out that it is very difficult to reproduce a Chime movement in RasMol, unless it is very simple. I spent a long time struggling with this very thing and eventually gave up (I mean, I found a work-around). what I want to do is turn existing Chime animations into quicktime movies. in fact, it may be more accurate to call them Chime-based presentations; some of them run for 20-30 seconds or more, and they include complex 3D movements, transitions, color changes, textual elements, etc. - and not just Chime events. so I'm looking for something that is similar to capturing input from a camcorder. only in this case, the video feed originates on my desktop, and not an external device. SnapZ Pro for the Mac seems to be a decent choice - though I have not been able to test it yet, so it may lack the quality output that I need. I'll certainly post to the list when I have results, in case there is some interest. in the meantime, if anyone is running OS X and has experience with volumes that refuse to mount, could you please email me off-list? I can't get the SnapZ Pro disk image to show up on my desktop! (or any other disk images, or CDs, or DVDs.) thanks. regards, tim -- molvisions - 3D molecular visualization waltham, ma usa ----------------------------------------------------------------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 ++++------+------+------+------+------+------+------+------+------+------+ From: Todd Carlson Subject: one button, two images? Date: Tue, 16 Apr 2002 15:29:51 -0400 To: rasmol@lists.umass.edu Hi Is it possible to have one chime button execute two scripts for different chime images without using javascript? Thanks Todd ----------------------------------------------------------------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-- <20020416191153-r01050000-56AAA2F6-518F-11D6-AE02-003065DFD8FC-1013-010c@192.168.1.13> ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: one button, two images? Date: Tue, 16 Apr 2002 19:11:52 -0400 To: rasmol@lists.umass.edu Todd Carlson at said: > Hi > > Is it possible to have one chime button execute two scripts for different > chime images without using javascript? > hi Todd, I don't believe it's possible, though someone is more than welcome to prove me wrong ;-) why can't you use javascript? have the button send a script to plug-in instance 1, and also trigger the creation of a second, invisible, immediate-mode button that sends a second script to plug-in instance 2. that gets around LiveConnect, and I think it uses only standard javascript syntax (I'd have to try the code to know for sure). hth, tim -- molvisions - 3D molecular visualization waltham, ma usa ----------------------------------------------------------------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-Accept-Language: en References: <3CBB6E55.177E87FD@mail.med.upenn.edu> <003d01c1e515$2da13ca0$3b8506c1@cthulhu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Mark J. Biscone" Subject: Re: POVRay, altering PDB's etc. Date: Wed, 17 Apr 2002 00:03:21 -0400 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_N0rNcsXnm7i1jKeTmuj6vQ) Hi Tamas, Thanks for your help and suggestions. 1) Attached is an example file (just pasted in a powerpoint file - JPEG or TIFF formatted picture) that I wanted to import into POVRay and then export to boost resolution. I am not familiar with RasTop either but am trying to get know a bunch of these programs now. 2) I was able to cut and paste the ATOM and HETATM portions to create a new pdb file of subsets of proteins and that was pretty neat. I have tried to combine different proteins in a new pdb file but so far haven't had any luck - (some are predicted structures and are rather strange) Thanks again for the help! Cheers, Mark > Mark, > > 1) > I have currently RasTop installed and maybe it formats differently the pov > file. Send me an example file please. > What you want is easy, but the direction, angle etc of the camera can be > expressed in diffeent ways. > Probably you need to change the camera viewing angle only. > > 2) > What you want can be done manually too, provided the atom numbering of the > two portions, chains do not overlap. > You need all ATOM and HETATM records, a simple TER between the chains, > finishing with END. > Do not deal with CONECT records, they complicate things, and most programs > do not require them. > > ATOM 1 ...... > ATOM n ...... > TER > ATOM m ... > ATOM z... > END > > If atom numberings overlap, you need some auxuliary program to merge the > files and re-edit, for example Mol2Mol. > > regards > > Tama > ----------------------- > > > Hey all, > > > > 1. Does anyone have a step by step instruction on how to use POVRay 3 to > boost the resolution of a RasMol generated .pov script? I am really not > getting anywhere and never can focus the imported rendering to contain my > whole molecule image. > > > > 2. Can .pdb files be combined for when structures of different portions > are solved by altering the pdb file in text editor. For example, I am > trying to make the structure of HIV-1 integrase using 1ex4 and 1k6y by > deleting one of the dimer > > pairs in each and then cutting and pasting to make a new pdb file. What > needs to be preserved from each file to make this work (if it can be done)? > > > > Thank you very much for your help in these matters. > > > > Sincerely, > > Mark Biscone > > University of Pennsylvania > > > > > > > ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: POVRay, altering PDB's etc. Date: Thu, 18 Apr 2002 11:41:33 +0200 To: rasmol@lists.umass.edu Dear Mark, In the pov file you should find the camera object, should look something similar such as: camera { orthographic location <0.954505, 0.332051, -40> look_at <0.954505, 0.332051, 0.598872> up <0, -1.74, 0> right <2.032, 0, 0> } The use of orthographic camera complicates manual trimming, so comment out "orthographic, up, right" and add angle 50: camera { //orthographic location <0.954505, 0.332051, -40> look_at <0.954505, 0.332051, 0.598872> angle 50 //up <0, -1.74, 0> //right <2.032, 0, 0> } If you run the script now, the molecule will probably look very small. Therefore: You should move the camera toward the molecule - decrease the z-distance e.g. from -40 to -20 (the negative z axis points toward you(=camera) ), and/or you can change the camera lens angle. Hope this helps, regards Tamas -------- Dr. Tamas E. Gunda Research Group for Antibiotics Hungarian Academy of Sciences University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tamasgunda@tigris.klte.hu ----- Original Message ----- Sent: Wednesday, April 17, 2002 06:03 From: "Mark J. Biscone" Subject: Re: POVRay, altering PDB's etc. To: > Hi Tamas, > > Thanks for your help and suggestions. > > 1) Attached is an example file (just pasted in a powerpoint file - JPEG or TIFF > formatted picture) that I wanted to import into POVRay and then export to boost > resolution. I am not familiar with RasTop either but am trying to get know a > bunch of these programs now. > > 2) I was able to cut and paste the ATOM and HETATM portions to create a new pdb > file of subsets of proteins and that was pretty neat. I have tried to combine > different proteins in a new pdb file but so far haven't had any luck - (some are > predicted structures and are rather strange) > > Thanks again for the help! > > Cheers, > Mark > > > > Mark, > > > > 1) > > I have currently RasTop installed and maybe it formats differently the pov > > file. Send me an example file please. > > What you want is easy, but the direction, angle etc of the camera can be > > expressed in diffeent ways. > > Probably you need to change the camera viewing angle only. > > > > 2) > > What you want can be done manually too, provided the atom numbering of the > > two portions, chains do not overlap. > > You need all ATOM and HETATM records, a simple TER between the chains, > > finishing with END. > > Do not deal with CONECT records, they complicate things, and most programs > > do not require them. > > > > ATOM 1 ...... > > ATOM n ...... > > TER > > ATOM m ... > > ATOM z... > > END > > > > If atom numberings overlap, you need some auxuliary program to merge the > > files and re-edit, for example Mol2Mol. > > > > regards > > > > Tama > > ----------------------- > > > > > Hey all, > > > > > > 1. Does anyone have a step by step instruction on how to use POVRay 3 to > > boost the resolution of a RasMol generated .pov script? I am really not > > getting anywhere and never can focus the imported rendering to contain my > > whole molecule image. > > > > > > 2. Can .pdb files be combined for when structures of different portions > > are solved by altering the pdb file in text editor. For example, I am > > trying to make the structure of HIV-1 integrase using 1ex4 and 1k6y by > > deleting one of the dimer > > > pairs in each and then cutting and pasting to make a new pdb file. What > > needs to be preserved from each file to make this work (if it can be done)? > > > > > > Thank you very much for your help in these matters. > > > > > > Sincerely, > > > Mark Biscone > > > University of Pennsylvania > > > > > > > > > > > > ----------------------------------------------------------------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: rasmol and OS X Date: Fri, 19 Apr 2002 15:55:33 -0400 To: "LIST: rasmol" hi, has anyone had success compiling and running rasmol in OS X? I downloaded the files from and tried to follow the directions for a standard unix build, but I couldn't get it to work (I'm mostly unfamiliar with unix). I reached "make" but it told me that "rasmol is up-to-date," which is okay, but now I can't find any executable. any takers? thanks, tim -- molvisions - 3D molecular visualization waltham, ma usa ----------------------------------------------------------------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: Mengjuei Hsieh Subject: Re: rasmol and OS X Date: Mon, 22 Apr 2002 04:17:56 -0700 To: rasmol@lists.umass.edu Did you install an X server? I believe that you should have one before you start. If you don't have one, try http://sourceforge.net/projects/xonx/ for more information. For this case, all you need is to "make install" instead of "make". But you have to be a root when you are running this command. There is no "Aqua" Window for RasMol so far. Perhaps somebody in this maillist is working on it. :-) Best, MJ On Friday, April 19, 2002, at 12:55 PM, Timothy Driscoll wrote: > has anyone had success compiling and running rasmol in OS X? I > downloaded the > files from and tried to follow the > directions for a standard unix build, but I couldn't get it to work > (I'm mostly > unfamiliar with unix). I reached "make" but it told me that "rasmol is > up-to-date," which is okay, but now I can't find any executable. > any takers? ----------------------------------------------------------------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-- <20020408163118-r01050000-9475FE7C-4B2F-11D6-880C-003065DFD8FC-1013-010c@192.168.1.13> ++++------+------+------+------+------+------+------+------+------+------+ From: Mengjuei Hsieh Subject: Re: MacOSX and chime Date: Mon, 22 Apr 2002 04:24:22 -0700 To: rasmol@lists.umass.edu Well, I think the only option to run i386 linux software so far is to install a PC emulator like VPC or bochs. I prefer running classic version of netscape with chime plugin. Best, MJ On Monday, April 8, 2002, at 01:31 PM, Timothy Driscoll wrote: >I have no direct experience with running linux software under OS X, though >YMMV. if you do discover a work-around, I'm sure that the list would be >interested in hearing of it. ----------------------------------------------------------------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: How to avoid breaking Chime in IE Date: Wed, 24 Apr 2002 15:13:00 -0400 To: rasmol@lists.umass.edu For the past couple of months, I've been struggling with an obscure bug that causes many Chime sites designed for Internet Explorer (IE) to fail to work in IE, including my Protein Explorer 1.922, Demers' MOI, and Pillot's MoLUSC (URL's are at http://molvisindex.org). (This concerns Windows only since Chime is not supported for IE on the Mac.) After an exhausting amount of work, I've finally discovered that this damaged-Chime state of IE is caused when the very first installation of Chime on a Windows system is directed to Netscape only (by unchecking IE in the installer). It occurs only when the IE on the system is IE5.0, but once it happens, upgrading afterwards to IE 5.5 or 6 won't fix it. It occurs in Win98, Win98SE, and Win2000. It occurs both with the Chime 2.0.3 and Chime 2.6SP3 installers. If the very first installation of Chime is done before Netscape is installed, or is left in the default mode of installing Chime in both browsers, or is directed to IE only, the problem does NOT occur. Or if you upgrade to IE5.5SP2 BEFORE you first install Chime, it doesn't happen regardless of where you direct the first Chime installation. So that's how to avoid it. The bad news is that so far I don't know any way to fix the problem, short of reformatting your hard disk and reinstalling Windows. I'm working on a more practical fix and will report it here if I succeed. Upgrading, repairing, or reinstalling IE, reverting to a previously installed version of IE, and uninstalling/reinstalling Chime don't fix it. A simple test to find out if your Chime/IE installation has this problem: in IE, go to http://www.umass.edu/microbio/chime/quizzer/index.htm (or a local downloaded copy of this site). Click on the large link to start the Amino Acid Quizzer -- when it loads you will see a wireframe protein (assuming Chime has been installed in IE). Enter a number in the slot, e.g. "1". If it FAILS to render the number-specified residue in bright green spacefill, you have the damaged state. (The green spacefilled residue ALWAYS appears in Netscape.) Specifically, what fails is the only mechanism known in IE for javascript to send a command string to Chime ("immediate mode button in invisible frame"). A more detailed account of this saga is available on request. In the end, I had to use virtual machines (www.vmware.com) in order to do the diagnosis at a practical pace. I have conveyed my detailed findings directly to the Chime Team at MDL. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), 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: FW: How to avoid breaking Chime in IE Date: Wed, 24 Apr 2002 21:37:55 -0400 To: rlight@chemmail.chem.fsu.edu Cc: rasmol@lists.umass.edu At 4/24/02, rlight wrote: > >Eric, > >Have you otherwise gotten chime to work in IE 6? (under windows XP)? > >Robley Yes. Provided the problem I described today is avoided, Protein Explorer 1.922 alpha (my acid test for Chime function in IE) appears to work just fine in IE 6.0. I have no WinXP systems at my disposal for testing. I am not aware of any Chime or browser-specific problems in XP. As far as I know, there are still multiple serious bugs in Netscape 6 (and Mozilla) that prevent Chime scripting from working. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), 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: YOU, too, could be unwittingly unsubscribed Date: Wed, 24 Apr 2002 21:49:08 -0400 To: rasmol@lists.umass.edu Just a reminder -- of the 600 subscribers to this list (seems to have reached a steady state), I have to unsubscribe several each week because their mail bounces with the message "user unknown" or "account discontinued" or "unable to deliver for 3 days" or somesuch. I try to avoid unsubscribing mail that bounces due to overfilled mailboxes, temporary server outages, "unable to deliver for 1 day" and so forth, but after a few days of receiving and having to scrutinize each of dozens of those bounces my patience runs out on those too, and they get unsubscribed to save my sanity. So if you have temporary email problems, be aware you may get unsubscribed and simply need to resubscribe. Instructions are at the bottom of EVERY message you receive from this list -- please use them. (File a copy of this email where you can find it in case one day you feel something is missing in your life.) -Eric (list manager) 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:0.9.4.1) Gecko/20020314 Netscape6/6.2.2 X-Accept-Language: en-us References: <200204241912.g3OJCN228699@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: T & S Carlson Subject: Re: How to avoid breaking Chime in IE Date: Thu, 25 Apr 2002 00:01:14 -0400 To: rasmol@lists.umass.edu Eric What a remarkable piece of debugging. Hats off to you. I saw a note at the Chime site that says they are working to make Chime less dependent on browser features, and thus more portable. Let's hope they succeede. Todd Eric Martz wrote: > For the past couple of months, I've been struggling with an obscure bug > that causes many Chime sites designed for Internet Explorer (IE) to fail to > work in IE, including my Protein Explorer 1.922, Demers' MOI, and Pillot's > MoLUSC (URL's are at http://molvisindex.org). (This concerns Windows only > since Chime is not supported for IE on the Mac.) > > After an exhausting amount of work, I've finally discovered that this > damaged-Chime state of IE is caused when the very first installation of > Chime on a Windows system is directed to Netscape only (by unchecking IE in > the installer). It occurs only when the IE on the system is IE5.0, but once > it happens, upgrading afterwards to IE 5.5 or 6 won't fix it. It occurs in > Win98, Win98SE, and Win2000. It occurs both with the Chime 2.0.3 and Chime > 2.6SP3 installers. > > If the very first installation of Chime is done before Netscape is > installed, or is left in the default mode of installing Chime in both > browsers, or is directed to IE only, the problem does NOT occur. Or if you > upgrade to IE5.5SP2 BEFORE you first install Chime, it doesn't happen > regardless of where you direct the first Chime installation. So that's how > to avoid it. The bad news is that so far I don't know any way to fix the > problem, short of reformatting your hard disk and reinstalling Windows. I'm > working on a more practical fix and will report it here if I succeed. > Upgrading, repairing, or reinstalling IE, reverting to a previously > installed version of IE, and uninstalling/reinstalling Chime don't fix it. > > A simple test to find out if your Chime/IE installation has this problem: > in IE, go to http://www.umass.edu/microbio/chime/quizzer/index.htm (or a > local downloaded copy of this site). Click on the large link to start the > Amino Acid Quizzer -- when it loads you will see a wireframe protein > (assuming Chime has been installed in IE). Enter a number in the slot, e.g. > "1". If it FAILS to render the number-specified residue in bright green > spacefill, you have the damaged state. (The green spacefilled residue > ALWAYS appears in Netscape.) > > > Specifically, what fails is the only mechanism known in IE for javascript > to send a command string to Chime ("immediate mode button in invisible > frame"). A more detailed account of this saga is available on request. In > the end, I had to use virtual machines (www.vmware.com) in order to do the > diagnosis at a practical pace. > > I have conveyed my detailed findings directly to the Chime Team at MDL. > > -Eric > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > The Protein Explorer: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > PDB Lite molecule finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), 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 V6.00.2600.0000 X-MSMail-priority: Normal References: <200204250137.g3P1bJ209397@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Chime in Netscape 6.2 and Mozilla Date: Thu, 25 Apr 2002 08:37:36 +0200 To: rasmol@lists.umass.edu Eric, thanks again for the work done. I use Netscape 6.2.1, and I tried Mozlla 9.8. Both of them work with chime, untill you did install the Chime files in their plug-in directory. Unfortunately Opera 6.0 could work but is too much unstable. I succeed to make the IMBIF method work in these browser, for my project MolUSc. An update will be soon available so that you could test it. For people interested in writing cross-browser javascript for chime, here is the code I use : The function to send scripts to Chime : function do_cmds(cmds) { if (document.getElementById) { html= ""; html += ""; document.getElementById("invisible").innerHTML = '"' + html + '"'; } else top.f_vis.document.molecule.executeScript(cmds); } and in the body, at the bottom of the page : document.getElementById is an Internet Explorer, and a Netscape 6 function. As it doesn't exist in Communicator, the test is false in this last browser. Paul Pillot ----- Original Message ----- Sent: Thursday, April 25, 2002 3:37 AM From: "Eric Martz" Subject: Re: FW: How to avoid breaking Chime in IE To: Cc: > At 4/24/02, rlight wrote: > > > >Eric, > > > >Have you otherwise gotten chime to work in IE 6? (under windows XP)? > > > >Robley > > Yes. Provided the problem I described today is avoided, Protein Explorer > 1.922 alpha (my acid test for Chime function in IE) appears to work just > fine in IE 6.0. > > I have no WinXP systems at my disposal for testing. I am not aware of any > Chime or browser-specific problems in XP. > > As far as I know, there are still multiple serious bugs in Netscape 6 (and > Mozilla) that prevent Chime scripting from working. > ----------------------------------------------------------------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: <200204250137.g3P1bJ209397@marlin.bio.umass.edu> <001101c1ec23$b0573400$0100a8c0@zig> ++++------+------+------+------+------+------+------+------+------+------+ From: Jean Richelle Subject: Re: Chime in Netscape 6.2 and Mozilla Date: Thu, 25 Apr 2002 09:17:59 +0200 To: rasmol@lists.umass.edu Dear Paul, I suppose you are running under Windows ? >I use Netscape 6.2.1, and I tried Mozlla 9.8. Both of them work with chime, >untill you did install the Chime files in their plug-in directory. >Unfortunately Opera 6.0 could work but is too much unstable. Jean ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-MSMail-priority: Normal References: <200204250137.g3P1bJ209397@marlin.bio.umass.edu> <001101c1ec23$b0573400$0100a8c0@zig> ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re: Chime in Netscape 6.2 and Mozilla Date: Thu, 25 Apr 2002 09:32:48 +0200 To: rasmol@lists.umass.edu Forgive me for this imprecision : I'm effectively running under windows, and I haven't the possibility to make tests under MacOs... Paul Pillot ----- Original Message ----- Sent: Thursday, April 25, 2002 9:17 AM From: "Jean Richelle" Subject: Re: Chime in Netscape 6.2 and Mozilla To: > Dear Paul, > > I suppose you are running under Windows ? > > >I use Netscape 6.2.1, and I tried Mozlla 9.8. Both of them work with chime, > >untill you did install the Chime files in their plug-in directory. > >Unfortunately Opera 6.0 could work but is too much unstable. > > Jean > > ----------------------------------------------------------------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: <200202042146.g14Lk9225264@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Michael H. Patrick" Subject: Re: What are they learning from Chime? Date: Thu, 25 Apr 2002 07:59:32 -0500 To: rasmol@lists.umass.edu I have been reading with great interest the postings on "what are they learning from Chime", since we are in the midst of a large NSF-funded project to evaluate the integrated use of accurate physical modelis and computer visulaization (RasMol, Chime, PE) in undergrad classes ranging from introductory chemistry to honors sophomore biology to upper level biochemistry. We also have been developing and testing approaches with high school teachers as part of our NIH professional development program. We hope to have the results of this study analyzed within the year, but I can share some preliminary findings. First, we, like others, find RasMol-based learning helps students understand protein structure, but this is more pronounced at the advanced courses than the introductory level. Second, we find that Chime tutorials are very popular and are excellent adjuncts to text and/or lecture, but they are basically passive.....and so, students in introductory courses aren't helped a great deal. It seems to call for a degree of "chemspeak" that most don't (yet) have. The same seems to be true for PE. We find that having them spend time getting up to speed on RasMol commands then undergo guided exploration is so far the best learning mode. I have a feeling, however, that there will not be a definitive evaluation since the whole thing is too confounded with the background and abilities of the instructor on the use of computer visualization as an educational vehicle. Probably the most interesting thing we find is how very important physical models are in helping students understand biomolecular structure and function. Over the past several years, we have developed rapid prototyping models of biomolecules using as the ultimate data source, the same pdb file that used in RasMol. The three dimensionality and simple tactile nature of these models seems to make a great deal of difference in student understanding at all levels. However, there are aspects and features that physical models can not do and computer modeling can. So, our conclusion thus far....at all levels....is that no one modeling platform is sufficient, but when integrated they can be very powerful. We are always looking for facutly interested in becoming part of this evaluation project. If you wish to find out more, please let me or my colleague, Tim Herman, know. Meanwhile, you can get a glimpse of some of this on our website, www.rpc.msoe.edu/cbm (now undergoing major reconstruction). We are also in the process of preparing CDs that describe the approach we use in detail. -- Michael H. Patrick, Ph.D. Adjunct Professor and Co-Director: Center for BioMolecular Modeling, Milwaukee School of Engineering Wisconsin Teacher Enhancement Program, University of Wisconsin-Madison Campus: 104 Genetcs 445 Henry Mall Madison, WI. 53706 Ph. (608)265-4564 Fx (608)262-2976 Home Office: E3130 Saxeville Rd. Pine River, WI. 54965 Ph. (715) 258-5141 Fx. (715) 258-5041 mpatrick@facstaff.wisc.edu or models@execpc.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-- X-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: Chime in Netscape 6.2 and Mozilla Date: Thu, 25 Apr 2002 10:04:51 -0500 (CDT) To: rasmol@lists.umass.edu Hi, Under Linux, CodeWeaver's CrossOver plugin version 1.1.0 will now directly install Chime (you have to first download the Windows version of the Chime installer and then use the pluginsetup in advanced mode). CodeWeaver's actually made changes in CrossOver for Chime eventhough it is not a plugin they support. I have not updated my browsers in a while but Chime works in these Linux versions: Netscape 4.78 Mozilla 0.9.4 - there is now a version 1 release candidate Galeon 0.12.1 - now over version 1. I have not tried to get my version of Konqueror to recognize the crossover plugins yet. I have not tried Opera on Linux. Codeweavers also have their CrossOver Office that allows you to run Microsoft Office on Linux. While Word, Excel and Powerpoint run well, Internet Explorer crashes but it appears that CodeWeavers may get it to run also. Regards, Bruce On Thu, 25 Apr 2002, Paul Pillot wrote: > Forgive me for this imprecision : I'm effectively running under windows, and > I haven't the possibility to make tests under MacOs... > Paul Pillot > ----- Original Message ----- > From: "Jean Richelle" > To: > Sent: Thursday, April 25, 2002 9:17 AM > Subject: Re: Chime in Netscape 6.2 and Mozilla > > > > Dear Paul, > > > > I suppose you are running under Windows ? > > > > >I use Netscape 6.2.1, and I tried Mozlla 9.8. Both of them work with > chime, > > >untill you did install the Chime files in their plug-in directory. > > >Unfortunately Opera 6.0 could work but is too much unstable. > > > > Jean > > > > > > ----------------------------------------------------------------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-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Repairing "broken Chime" in IE Date: Thu, 25 Apr 2002 12:13:50 -0700 To: rasmol@lists.umass.edu This message pertains to Windows 98, 98SE, 2000, and most likely other versions of Windows (but not to Macs). Below, I review how the Chime installer can damage your Windows system, rendering many IE-compatible Chime sites inoperable on your computer, and I provide a procedure that I believe will repair the damage. My testing of the repair procedure has been limited, so I would greatly appreciate hearing from those of you who find you have the damaged state. Please let me know whether the procedure corrected it, and mention the version of IE (Help, About IE) and version of Windows (right click on My Computer, then click Properties). Most if not all Chime sites work in Netscape. If you can use Netscape for Chime sites, you probably don't need to repair IE's ability to work with Chime. In some institutions and teaching computer labs, it is not permitted to install Netscape -- in these cases, the repair procedure below should allow you to use all IE-compatible Chime sites. (Many older Chime sites were developed for Netscape and have not been upgraded to work in IE, including many that I authored.) THE PROBLEM Yesterday I reported that if the very first installation of Chime on a Windows system is directed into Netscape only (not Internet Explorer, IE), while IE 5.0 is present, IE's ability to communicate command scripts to Chime (after Chime is subsequently installed into IE) is permanently broken. Upgrading IE, uninstalling/reinstalling Chime, repairing or reinstalling IE all fail to correct this "damaged IE" condition, which prevents the operation of Protein Explorer in IE as well as many other IE-compatible Chime sites. For further details, consult yesterday's message in the list history at ftp://marlin.bio.umass.edu/pub/shareware/rasmol/email-history/00ReadMe.html (click on "current", wait for all of it to load, and go to the bottom). DETECTION OF THE PROBLEM The "damaged IE" condition can be detected by going to http://www.umass.edu/microbio/chime/quizzer/index.htm, and clicking on the link "Amino Acid Quizzer". If, despite Chime having been installed into IE, you see a white rectangle in the left frame with a "missing plugin" icon, and no molecule displays, you have the damaged state. (You can confirm that Chime was installed for IE: Start, Settings, Control Panel, Add/Remove Software: if "Chime for IE" appears on the list, it was installed.) If a black rectangle appears in the Amino Acid Quizzer, and a wireframe protein molecule displays automatically, then proceed to enter the number "1" into the slot. If, after pressing the Enter key, a spacefilled bright green residue does NOT appear, you have the damaged state. If the green spacefilled residue appears, your system is OK. REPAIR PROCEDURE Caution: this procedure involves editing the Windows Registry, and though unlikely if the procedure is followed carefully, could possibly render your computer unbootable. Backup critical files first, and be sure you have a bootable rescue diskette (on Windows 98, Start, Settings, Control Panel, Add/Remove Programs, then click the Startup Disk tab; can someone please tell me how to create one on Win2000? Microsoft hasn't made it easy to find!). PROCEED AT YOUR OWN RISK. If you are not comfortable doing this procedure, seek help from someone more familiar with the technical side of Windows. 1. Start, Settings, Control Panel, Add/Remove Software. 2. Uninstall Chime for IE, and if present, any other Chime installations such as Chime for Netscape. All Chime's should be uninstalled. 3. Start, Run, and enter "regedit" into the slot, then click OK. The Registry Editor will open. 4. In the Registry Editor, click Help, Help Topics, Restore the Registry. Right click the help text that appears and print it, just in case. I have never had to do this, but better safe than sorry. 5. In the Registry Editor, click the [+] next to each of the following in the hierarchy of keys. Each click will open the keys encompassed by the parent key, enabling you to find the next key to open. HKEY_LOCAL_MACHINE Software Microsoft Internet Explorer Plugins Extension Highlight the last entry, "Extension", and Edit, Delete, confirm deletion. The following (or something similar) subsumed under Extension will thereby be deleted. These keys appear to be responsible for the problem. "Content Type"="chemical/x-pdb" "Version"="2, 6, 0, 8" @="Chemscape Chime 2.6 SP3" "Location"="C:\\NAVIGATO\\PROGRAM\\PLUGINS\\npchime.dll" Close the Registry Editor (Registry, Exit, or simply click on the X at the upper right corner). 6. Install Chime into IE (and also in Netscape if you have it). (Run the Chime installer downloadable from http://www.mdlchime.com) Repeat the test above for detection of the damaged state. Your IE should be repaired, the green spacefilled residue should appear, and Protein Explorer 1.922 alpha and other IE-compatible Chime sites should now operate on your computer. -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-- Content-return: allowed boundary="Boundary_(ID_ENZyAHEpGdkefLs/FzwifQ)" ++++------+------+------+------+------+------+------+------+------+------+ From: Joel Dudley Subject: rasmol rendering core Date: Thu, 25 Apr 2002 10:07:51 -0700 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_ENZyAHEpGdkefLs/FzwifQ) I am trying to isolate the rasmol rendering core such that I can place it in a DLL (or .so on Linux) and load the library into a Delphi/Kylix application so I can provide a rasmol rendering window inside my app. Does anyone have experience isolating the rasmol rendering core or know of any source code documentation that would aid my efforts? Thank you for reading my post. - Joel --Boundary_(ID_ENZyAHEpGdkefLs/FzwifQ) rasmol rendering core

I am trying to isolate the rasmol rendering core such that I can place it in a DLL (or .so on Linux) and load the library into a Delphi/Kylix application so I can provide a rasmol rendering window inside my app. Does anyone have experience isolating the rasmol rendering core or know of any source code documentation that would aid my efforts? Thank you for reading my post.

- Joel

--Boundary_(ID_ENZyAHEpGdkefLs/FzwifQ)-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 boundary="Boundary_(ID_oGtwHgVvvSRwHaPIcuGAdQ)" X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: Re: rasmol rendering core Date: Tue, 23 Apr 2002 23:25:21 -0700 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_oGtwHgVvvSRwHaPIcuGAdQ) rasmol rendering coreDear Joel, It is relatively simple and you may want to have a look at rastop source code at www.geneinfinity.org/rastop, especially the set of c files which isolates the rasmol rendering core that you mentioned. You may also want to read the license, which probably prevents you to do that unless your application becomes under the same license. You can use rasmol 2.6.4 source, which is totally free, but is becoming a little old and is full of known bugs. Good luck, Philippe --------------------------- *** RasTop *** --------------------------- Philippe Valadon P.O. Box 13014, La Jolla, CA 92039, USA. rastop@geneinfinity.org ----- Original Message ----- From: Joel Dudley To: 'rasmol@lists.umass.edu' Sent: Thursday, April 25, 2002 10:07 AM Subject: rasmol rendering core I am trying to isolate the rasmol rendering core such that I can place it in a DLL (or .so on Linux) and load the library into a Delphi/Kylix application so I can provide a rasmol rendering window inside my app. Does anyone have experience isolating the rasmol rendering core or know of any source code documentation that would aid my efforts? Thank you for reading my post. - Joel --Boundary_(ID_oGtwHgVvvSRwHaPIcuGAdQ) rasmol rendering core
Dear Joel,
 
It is relatively simple and you may want to have a look at rastop source code at www.geneinfinity.org/rastop, especially the set of c files which isolates the rasmol rendering core that you mentioned. You may also want to read the license, which probably prevents you to do that unless your application becomes under the same license. You can use rasmol 2.6.4 source, which is totally free, but is becoming a little old and is full of known bugs.
 
Good luck,
Philippe
 
---------------------------
   *** RasTop ***  
---------------------------
Philippe Valadon
P.O. Box 13014, La Jolla, CA 92039, USA.
rastop@geneinfinity.org

 
----- Original Message -----
Sent: Thursday, April 25, 2002 10:07 AM
Subject: rasmol rendering core

I am trying to isolate the rasmol rendering core such that I can place it in a DLL (or .so on Linux) and load the library into a Delphi/Kylix application so I can provide a rasmol rendering window inside my app. Does anyone have experience isolating the rasmol rendering core or know of any source code documentation that would aid my efforts? Thank you for reading my post.

- Joel

--Boundary_(ID_oGtwHgVvvSRwHaPIcuGAdQ)-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 X-MSMail-priority: Normal References: <3CC8556E.8A07A7D6@microbio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: Repairing "broken Chime" in IE Date: Fri, 26 Apr 2002 10:00:50 +0200 To: rasmol@lists.umass.edu Emergency backup diskette & registry backup in Win2000: > Caution: this procedure involves editing the Windows Registry, and > though unlikely if the procedure is followed carefully, could possibly > render your computer unbootable. Backup critical files first, and be > sure you have a bootable rescue diskette (on Windows 98, Start, > Settings, Control Panel, Add/Remove Programs, then click the Startup > Disk tab; can someone please tell me how to create one on Win2000? > Microsoft hasn't made it easy to find!). > In Start Menu, open Program | Accessories | System Tools |Backup; In the Backup dialog select from the main menu Tools | Create emergency backup diskette; Put an empty diskette into A: Check the Also backup registry checkbox, and OK. To restore a "dead" registry, you have to start-up the PC from the Win2000 CD-ROM, and follow the instructions. Best regards Tamas Gunda ---------------- Dr. Tamas E. Gunda Research Group for Antibiotics Hungarian Academy of Sciences University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tamasgunda@tigris.klte.hu ----------------------------------------------------------------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: Karen Ocorr Subject: Re: Repairing "broken Chime" in IE Date: Fri, 26 Apr 2002 14:39:20 -0400 To: rasmol@lists.umass.edu THANKS!! Karen At 12:13 PM 4/25/2002 -0700, you wrote: >This message pertains to Windows 98, 98SE, 2000, and most likely other >versions of Windows (but not to Macs). Below, I review how the Chime >installer can damage your Windows system, rendering many IE-compatible >Chime sites inoperable on your computer, and I provide a procedure that >I believe will repair the damage. > >My testing of the repair procedure has been limited, so I would greatly >appreciate hearing from those of you who find you have the damaged >state. Please let me know whether the procedure corrected it, and >mention the version of IE (Help, About IE) and version of Windows (right >click on My Computer, then click Properties). > >Most if not all Chime sites work in Netscape. If you can use Netscape >for Chime sites, you probably don't need to repair IE's ability to work >with Chime. In some institutions and teaching computer labs, it is not >permitted to install Netscape -- in these cases, the repair procedure >below should allow you to use all IE-compatible Chime sites. (Many older >Chime sites were developed for Netscape and have not been upgraded to >work in IE, including many that I authored.) > >THE PROBLEM > >Yesterday I reported that if the very first installation of Chime on a >Windows system is directed into Netscape only (not Internet Explorer, >IE), while IE 5.0 is present, IE's ability to communicate command >scripts to Chime (after Chime is subsequently installed into IE) is >permanently broken. Upgrading IE, uninstalling/reinstalling Chime, >repairing or reinstalling IE all fail to correct this "damaged IE" >condition, which prevents the operation of Protein Explorer in IE as >well as many other IE-compatible Chime sites. For further details, >consult yesterday's message in the list history at >ftp://marlin.bio.umass.edu/pub/shareware/rasmol/email-history/00ReadMe.html > >(click on "current", wait for all of it to load, and go to the bottom). > >DETECTION OF THE PROBLEM > >The "damaged IE" condition can be detected by going to >http://www.umass.edu/microbio/chime/quizzer/index.htm, and clicking on >the link "Amino Acid Quizzer". If, despite Chime having been installed >into IE, you see a white rectangle in the left frame with a "missing >plugin" icon, and no molecule displays, you have the damaged state. (You >can confirm that Chime was installed for IE: Start, Settings, Control >Panel, Add/Remove Software: if "Chime for IE" appears on the list, it >was installed.) If a black rectangle appears in the Amino Acid Quizzer, >and a wireframe protein molecule displays automatically, then proceed to >enter the number "1" into the slot. If, after pressing the Enter key, a >spacefilled bright green residue does NOT appear, you have the damaged >state. If the green spacefilled residue appears, your system is OK. > >REPAIR PROCEDURE > >Caution: this procedure involves editing the Windows Registry, and >though unlikely if the procedure is followed carefully, could possibly >render your computer unbootable. Backup critical files first, and be >sure you have a bootable rescue diskette (on Windows 98, Start, >Settings, Control Panel, Add/Remove Programs, then click the Startup >Disk tab; can someone please tell me how to create one on Win2000? >Microsoft hasn't made it easy to find!). > >PROCEED AT YOUR OWN RISK. If you are not comfortable doing this >procedure, seek help from someone more familiar with the technical side >of Windows. > >1. Start, Settings, Control Panel, Add/Remove Software. > >2. Uninstall Chime for IE, and if present, any other Chime installations >such as Chime for Netscape. All Chime's should be uninstalled. > >3. Start, Run, and enter "regedit" into the slot, then click OK. The >Registry Editor will open. > >4. In the Registry Editor, click Help, Help Topics, Restore the >Registry. Right click the help text that appears and print it, just in >case. I have never had to do this, but better safe than sorry. > >5. In the Registry Editor, click the [+] next to each of the following >in the hierarchy of keys. Each click will open the keys encompassed by >the parent key, enabling you to find the next key to open. > >HKEY_LOCAL_MACHINE > Software > Microsoft > Internet Explorer > Plugins > Extension > >Highlight the last entry, "Extension", and Edit, Delete, confirm >deletion. >The following (or something similar) subsumed under Extension will >thereby be deleted. These keys appear to be responsible for the problem. > > "Content Type"="chemical/x-pdb" > "Version"="2, 6, 0, 8" > @="Chemscape Chime 2.6 SP3" > "Location"="C:\\NAVIGATO\\PROGRAM\\PLUGINS\\npchime.dll" > >Close the Registry Editor (Registry, Exit, or simply click on the X at >the upper right corner). > >6. Install Chime into IE (and also in Netscape if you have it). (Run the >Chime installer downloadable from http://www.mdlchime.com) > >Repeat the test above for detection of the damaged state. Your IE should >be repaired, the green spacefilled residue should appear, and Protein >Explorer 1.922 alpha and other IE-compatible Chime sites should now >operate on your computer. > >-Eric Martz > > > _________________________________________________________________________ Karen Ocorr, Ph.D. Biology Department University of Michigan Ann Arbor, MI. 48109-1048 Phone: 734/ 647-2470 Fax: 734/ 647-0884 E-mail: kocorr@umich.edu Home Page: http://biology.lsa.umich/~www/bio310/kohome.html Web Sites: http://biology.lsa.umich.edu/~www/bio310 http://biology.lsa.umich.edu/~www/bio225Winter/ http://biology.lsa.umich.edu/~www/bio100 _________________________________________________________________________ ----------------------------------------------------------------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: "Peter C. McCluskey" Subject: Re: rasmol rendering core Date: Fri, 26 Apr 2002 12:02:02 -0700 (PDT) To: rasmol@lists.umass.edu Joel.Dudley@DevelopOnline.com (Joel Dudley) writes: >I am trying to isolate the rasmol rendering core such that I can place it in >a DLL (or .so on Linux) and load the library into a Delphi/Kylix application >so I can provide a rasmol rendering window inside my app. Does anyone have >experience isolating the rasmol rendering core or know of any source code >documentation that would aid my efforts? Thank you for reading my post. I modified Rasmol 2.6 to make a fair amount of the functionality available in a library form. I didn't end up using it much, and haven't looked at it for about 1.5 years, so I don't recall clearly how well it was working. You can find it in the rasmolapi directory of: ftp://ftp.openchem.org/openchem0.0.8.tar.gz -- ------------------------------------------------------------------------------ Peter McCluskey | Free Jon Johansen! http://www.rahul.net/pcm | ----------------------------------------------------------------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_ZToLapuJLKaGedT8roMwjQ)" ++++------+------+------+------+------+------+------+------+------+------+ From: Joel Dudley Subject: RE: rasmol rendering core Date: Fri, 26 Apr 2002 12:16:03 -0700 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_ZToLapuJLKaGedT8roMwjQ) Peter, I actually had found the openchem source prior to my post. I had hoped that I could use large portions of your RasMol DLL code but when I used dumpbin.exe on your DLL I found that it only exported a single function. Regardless I was able to get a good idea of which files I needed to include in my own library which was helpful. I currently have the entire core (2.6) wrapped up in a DLL. Using Raswin.c as a reference I am creating a Delphi interface to the library and trying to replace Win32 specific GDI interactions where I can. Thanks again for replying to my post. - Joel -----Original Message----- Sent: Friday, April 26, 2002 12:02 PM From: Peter C. McCluskey [mailto:pcm@rahul.net] Subject: Re: rasmol rendering core To: rasmol@lists.umass.edu Joel.Dudley@DevelopOnline.com (Joel Dudley) writes: >I am trying to isolate the rasmol rendering core such that I can place it in >a DLL (or .so on Linux) and load the library into a Delphi/Kylix application >so I can provide a rasmol rendering window inside my app. Does anyone have >experience isolating the rasmol rendering core or know of any source code >documentation that would aid my efforts? Thank you for reading my post. I modified Rasmol 2.6 to make a fair amount of the functionality available in a library form. I didn't end up using it much, and haven't looked at it for about 1.5 years, so I don't recall clearly how well it was working. You can find it in the rasmolapi directory of: ftp://ftp.openchem.org/openchem0.0.8.tar.gz -- ---------------------------------------------------------------------------- -- Peter McCluskey | Free Jon Johansen! http://www.rahul.net/pcm | --Boundary_(ID_ZToLapuJLKaGedT8roMwjQ) RE: rasmol rendering core

Peter,
  I actually had found the openchem source prior to my post. I had hoped that I could use large portions of your RasMol DLL code but when I used dumpbin.exe on your DLL I found that it only exported a single function. Regardless I was able to get a good idea of which files I needed to include in my own library which was helpful. I currently have the entire core (2.6) wrapped up in a DLL. Using Raswin.c as a reference I am creating a Delphi interface to the library and trying to replace Win32 specific GDI interactions where I can. Thanks again for replying to my post.

- Joel

-----Original Message-----
From: Peter C. McCluskey [mailto:pcm@rahul.net]
Sent: Friday, April 26, 2002 12:02 PM
To: rasmol@lists.umass.edu
Subject: Re: rasmol rendering core


 Joel.Dudley@DevelopOnline.com (Joel Dudley) writes:
>I am trying to isolate the rasmol rendering core such that I can place it in
>a DLL (or .so on Linux) and load the library into a Delphi/Kylix application
>so I can provide a rasmol rendering window inside my app. Does anyone have
>experience isolating the rasmol rendering core or know of any source code
>documentation that would aid my efforts? Thank you for reading my post.

 I modified Rasmol 2.6 to make a fair amount of the functionality
available in a library form. I didn't end up using it much, and haven't
looked at it for about 1.5 years, so I don't recall clearly how well it
was working.
 You can find it in the rasmolapi directory of:
ftp://ftp.openchem.org/openchem0.0.8.tar.gz
--
------------------------------------------------------------------------------
Peter McCluskey          | Free Jon Johansen!
http://www.rahul.net/pcm |

--Boundary_(ID_ZToLapuJLKaGedT8roMwjQ)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Phillip Barak Subject: Re: Repairing "broken Chime" in IE Date: Fri, 26 Apr 2002 15:12:20 -0500 To: rasmol@lists.umass.edu At 12:13 PM 4/25/2002 -0700, you wrote: >This message pertains to Windows 98, 98SE, 2000, and most likely other >versions of Windows (but not to Macs). Below, I review how the Chime >installer can damage your Windows system, rendering many IE-compatible >Chime sites inoperable on your computer, and I provide a procedure that >I believe will repair the damage. > >My testing of the repair procedure has been limited, so I would greatly >appreciate hearing from those of you who find you have the damaged >state. Please let me know whether the procedure corrected it, and >mention the version of IE (Help, About IE) and version of Windows (right >click on My Computer, then click Properties). FYI: My computer is running IE5.5 sp2, Wink2000 and had Chime 2.6 sp1 installed, and so the Registry indicated. I uninstalled Chime (both NS and IE) using "Add/Remove Program" from the Control Panel. Downloaded Chime 2.6 sp3 from mdlchime and installed for both NS and IE, and checked your AminoAcidQuizzer and it was _not_ broken with IE, according to your suggested tests. I doublechecked the Registry and it still says that what is installed is Chime 2.6 sp1, even after reboot, etc.! And the "about" Chime confirms that it is running sp3. So, even though not functionally "damaged" in IE, it would still appear to have a "sticky" Registry key! It's a sunny Friday afternoon...Should I fix the Registry key if the plug-in is working? Phillip Barak Assoc. Prof., Soil Science Dept of Soil Science University of Wisconsin-Madison 1525 Observatory Dr. Madison, WI 53706-1299 tel: 608-263-5450 fax: 608-265-2595 e-mail: pwbarak@facstaff.wisc.edu web: http://www.soils.wisc.edu/~barak/ Virtual Museum of Minerals and Molecules: http://www.soils.wisc.edu/virtual_museum/ ========================================= ----------------------------------------------------------------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: <3CC8556E.8A07A7D6@microbio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Repairing "broken Chime" in IE Date: Fri, 26 Apr 2002 18:07:10 -0400 To: rasmol@lists.umass.edu Cc: pwbarak@facstaff.wisc.edu At 4/26/02, Phillip Barak wrote: >So, even though not functionally "damaged" in IE, it would still appear to have a "sticky" >Registry key! > >It's a sunny Friday afternoon...Should I fix the Registry key if the plug-in is working? No. I don't recommend messing with the registry unless you are compelled to do so. The "broken Chime in IE" problem is very frustrating when it happens: Protein Explorer, MoLUSC, MOI, and many other Chime sites cannot work at all in IE, and the usual fixing maneuvers don't correct it. Therefore I resorted to changing the registry, and thankfully it fixed this problem. I'm not aware that the sticky keys cause any other problems. I subscribe to the notion "Don't fix what isn't broken". By the way, so far I haven't had a single report from someone who DID have the "broken Chime" in IE problem who has applied the fix. Again, if you have the problem and do the fix, please tell me (not the list): 1. Did the procedure correct the problem? 2. What is your version number of IE (Help, About IE)? 3. Version of Windows (right click on My Computer, then click Properties) -- (95, 98, 98SE, 2000, Me, XP, etc.)? -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: IEEE Vis2002 Meeting/Boston Date: Mon, 29 Apr 2002 11:05:32 -0400 To: rasmol@lists.umass.edu Here is a meeting on visualization that may be of interest. http://vis.computer.org/vis2002/ It is in Boston MA in late October. Some of the submission deadlines have already passed. The theme is biomedical and bioinformatics visualization. It is held jointly with the Information Visualization and Volume Visualization groups within IEEE. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), 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: CASP5 announcement Date: Mon, 06 May 2002 16:21:31 -0400 To: rasmol@lists.umass.edu pdb-l ----------------------------------------------------------------------- Dear CASP5 Registrant: Attached is a public announcement of the CASP5 experiment. We would appreciate your help in disseminating the information as widely as possible. So please forward the message to any colleagues or relevant email lists. Thanks, CASP5 organizers. ---------------------------------------------------------------------- Announcing the Fifth Community Wide ------------------------------------ Experiment on the Critical Assessment of ---------------------------------------- Techniques for Protein Structure Prediction ------------------------------------------- (CASP5) ------- Introduction ------------ CASP experiments aim at establishing the current state of the art in protein structure prediction, identifying what progress has been made, and highlighting where future effort may be most productively focused. There have been four previous experiments, in 1994, 1996, 1998 and 2000. Full details of these may be found at the CASP web site, http://PredictionCenter.llnl.gov/, and in the special issues of the journal PROTEINS: 23(5), 1995; Suppl 1, 1997, Suppl 3, 1999 and Suppl 5, 2001. In CASP4, 163 prediction groups from all around the world took part. We now announce the fifth experiment. As before, the goal is to obtain an in-depth and objective assessment of our current abilities and inabilities in this area. To this end, participants will predict as much as possible about a set of soon to be known structures. These will be true predictions, not 'post-dictions' made on already known structures. Full details will be available at http://predictioncenter.llnl.gov/casp5. The experiment will begin in May 2002, when the first prediction targets will be made available. The prediction season will run through August. There will be a meeting at the Asilomar Conference Center in California December 1 - 5th, to discuss the results. In more detail: =============== Scope of CASP5 and Related Experiments -------------------------------------- As in earlier CASPs, all types of methods for predicting protein structure will be considered, ranging from comparative modeling through fold recognition and 'new fold' prediction. Most emphasis will be on tertiary structure prediction but secondary structure and contact prediction methods will also be included. A new category, prediction of disordered regions in proteins, will be introduced. In addition, there will be additional activities included in CASP5, which will extend the scope substantially: CAFASP3: In the era of genome sequencing, rapid protein structure modeling methods have a critical role to play. This experiment, led by Dani Fischer, will evaluate automatic methods of predicting protein structure, using the CASP targets. All targets will be processed through prediction servers that register for the experiment. Models will be evaluated by the same numerical criteria as used for CASP5, as well as the CAFASP criteria, and a session at the CASP5 meeting will compare performance through the servers with that obtained when full human participation is allowed. Further details of this experiment may be found at: http://www.cs.bgu.ac.il/~dfischer/CAFASP3/ Large scaling benchmarking: It is hoped that the results of well run benchmarking experiments such as EVA and LIVEBENCH will also be included in the CASP meeting and publications. Ten Most Wanted: Results of the community effort to produce useful models of ten proteins of particular biological or medical interest will also be discussed at the meeting. Experiment ---------- The broad goals of the CASP5 experiment are to address the following questions about the current state of the art in protein structure prediction: 1. Are the models produced similar to the corresponding experimental structure? 2. Is the mapping of the target sequence onto the proposed structure (i.e. the alignment) correct? 3. Have similar structures that a model can be based on been identified? 4. Are the details of the models correct? 5. Has there been progress from the earlier CASPs? 6. What methods are most effective? 7. Where can future effort be most productively focused? In addition, CASP5 will focus particularly on areas of prediction that previous CASPs have shown to be current bottlenecks to progress. Suggested problem areas are: 1. Alignment of a sequence onto a template fold. 2. Model refinement - improving the accuracy of an initial model. 3. Accurately modeling regions of insertion and deletion relative to a template structure. 4. Improved fold recognition, particularly for analogous, analogous/new fold targets. 5. Improved New Fold methods. 6. Bold new methods aimed at removing one of the current bottlenecks to progress. To facilitate progress in some of these areas, partly built models will provided where necessary, for example, correct alignment as a starting point for loop building, and full approximate models as a starting point for refinement. The MD community is encouraged to participate, making use of these starting points. The set of problem areas may be revised, following discussion with the consultancy groups. Participants are advised to check for revisions. Prediction Targets ------------------ For the experiment to succeed, it is essential that we obtain the help of the experimental community. As in previous CASPs, we will invite protein crystallographers and NMR spectroscopists to provide details of structures they expect to have made public before 1st October 2002, using the target submission form available at http://PredictionCenter.llnl.gov/casp5. Prediction targets will be made available through the web site. All targets will be assigned an expiry date, and predictions must be received and accepted before that expiration date. Participation ------------- Participation is open to all. Intending CASP predictors must register at the web site: http://PredictionCenter.llnl.gov/casp5 Those interested in receiving mailings concerning progress of the experiment may also register as 'observers'. CAFASP predictors must register at that web site. Participation in both experiments (initial submission of server generated models to CAFASP and subsequent submission of models based on human interaction to CASP) is encouraged. Note that separate registrations are required for CASP and CAFASP participation. Assessment of Predictions ------------------------- As in previous CASPs, independent assessors will evaluate the predictions. There will be three assessors, representing expertise in the comparative modeling, fold recognition and new fold prediction areas. Assessors will be provided with the results of numerical evaluation of the predictions, and will judge the results primarily on that basis. They will be asked to focus particularly on the effectiveness of different methods. As CASP has grown, the work of the assessors has become more and more demanding. To help them with their task, predictors and target submitters will be asked to assist in the evaluation of models. Numerical evaluation criteria will as far as possible be very similar to those used in CASP4, although the assessors may be permitted to introduce some additional ones. Appropriate members of the prediction community will be asked to develop methods of assessing the statistical significance of performance ranking, a controversial area in the past. Release of Results ------------------ 1. All CASP predictions and evaluations will be made available through this web site, shortly before the meeting. 2. The proceedings of the meeting will be published. In recent CASPs, the large number of predictors together with the limited number of published predictor papers has been one of the main causes of excessive focus on winners and losers. To combat that, the mix of papers in the special issue will altered. There will not be a predefined number of 'winner' group papers. Instead, papers that focus on problem areas and solutions will be included. 3. In a further change to increase recognition of the contributions of more predictors, a new web site will be developed, allowing all participants to report their work if they wish, and encouraging vigorous discussion of the results. Meeting ------- A meeting will be held 1-5 December, 2002 at Asilomar, California, USA to evaluate the results of the prediction experiment. The meeting will be limited to about 200 participants and precedence will be given to active predictors. It is hoped that some financial assistance will be available for the more successful predictors. It is expected that the format of the meeting will be changed from previous CASPs, concentrating more on progress in problem areas, rather than the best performers in each section, irrespective of whether there has been a significant change since last time. Organizing Committee -------------------- John Moult CARB, UMBI, USA jmoult@tunc.org Krzysztof Fidelis Lawrence Livermore National Laboratory, USA fidelis@llnl.gov Adam Zemla Lawrence Livermore National Laboratory, USA adamz@llnl.gov Tim Hubbard Sanger Centre, Hinxton, UK th@sanger.ac.uk Support ------- The organizers gratefully acknowledge support for the CASP5 experiment from the NIH and the Department of Energy. Additional industrial support is being sought. More Information ---------------- Further details will be available at the web site (http://PredictionCenter.llnl.gov/casp5) Please address any questions or queries to casp5@PredictionCenter.llnl.gov *********************************************************************** Adam Zemla, Ph.D. | E-mail: adamz@llnl.gov Biology and Biotechnology Research Program | Phone: (925) 423-5571 Lawrence Livermore National Laboratory, L-448 | Fax: (925) 422-2282 7000 East Ave., Livermore, CA 94550, USA | Bldg: 3751, Room: 109 *********************************************************************** ----------------------------------------------------------------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-Accept-Language: es ++++------+------+------+------+------+------+------+------+------+------+ From: Jordi Oliver Subject: About mol files Date: Wed, 08 May 2002 10:22:42 -0500 To: rasmol Hi, Is it possible to view a mol file embedded in a html page or open the file in a script? I try to do this and it work when I open the html page from my computer locally but when I upload the page and script in an Apache server (Linux) it doesn't work. I define the mol extension in the mime.type configuration (chemical/x-mdl-molfile mol) of the apache server but the problem persist. Thanks in advance, Jordi Oliver Lab. Biochemistry and Molecular Biology University of Balearic Island E07071 - Palma de Mallorca http://palou.uib.es/roolpi/docencia/moleculas/ http://palou.uib.es/roolpi/docencia/tbp/tbp.htm ----------------------------------------------------------------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: About mol files Date: Thu, 09 May 2002 12:50:34 -0400 To: rasmol@lists.umass.edu At 5/8/02, you wrote: >Hi, > >Is it possible to view a mol file embedded in a html page or open the >file in a script? >I try to do this and it work when I open the html page from my computer >locally but when I upload the page and script in an Apache server >(Linux) it doesn't work. >I define the mol extension in the mime.type configuration >(chemical/x-mdl-molfile mol) of the apache server but the problem >persist. > >Thanks in advance, > >Jordi Oliver >Lab. Biochemistry and Molecular Biology >University of Balearic Island >E07071 - Palma de Mallorca >http://palou.uib.es/roolpi/docencia/moleculas/ >http://palou.uib.es/roolpi/docencia/tbp/tbp.htm Dear Jordi: The answer is YES. For example, try http://www.umass.edu/microbio/chime/dna/at.mol In Netscape, after the molecule appears in Chime, View Page Info, and the MIME type is confirmed. Double check your MIME setting for an error, and be sure to restart the http server! -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), 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-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Wetzel, Ron B." Subject: fatal error message / PE 1.922 alpha / IE 5.5 Date: Thu, 09 May 2002 17:25:24 -0400 To: "'rasmol@lists.umass.edu'" Eric, As directed here is a message report of a fatal error occurring in the alpha PE version for IE. You don't actually request info on what I was doing at the time of the crash, but here it is if it will help. I'm running on IE 5.5 in Windows 2000. I had my molecule displayed as a backbone and messing around trying to figure out how to change the color of the molecule and background. I think I had the molecule color set to 'color->amino acid'. I then chose 'select->change color to->blue' and got the crash. I just repeated the operation and it went ok, so I don't know what happened to cause the failure. I still can't figure out how to change background color - pasting into powerpoint looks much nicer if the background isn't white. Is this possible? I looked in the documentation but can't find any hints on this. Thanks. (love the software!) Ron Wetzel ------------------- Scrambled message report (after Fatal Error): Error is: [ERROR: Msg 2 neither a new gap nor fits an existing gap!] Message is [Chime script completed.] [debug_unscramble_tape is disabled] --------------------- ----------------------------------------------------------------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: fatal error message / PE 1.922 alpha / IE 5.5 Date: Thu, 09 May 2002 17:46:21 -0400 To: rasmol@lists.umass.edu At 5/9/02, you wrote: >Eric, >As directed here is a message report of a fatal error occurring in the alpha >PE version for IE. > >You don't actually request info on what I was doing at the time of the >crash, but here it is if it will help. I'm running on IE 5.5 in Windows >2000. I had my molecule displayed as a backbone and messing around trying >to figure out how to change the color of the molecule and background. I >think I had the molecule color set to 'color->amino acid'. I then chose >'select->change color to->blue' and got the crash. I just repeated the >operation and it went ok, so I don't know what happened to cause the >failure. Thanks, but crashes that can't be reproduced are untraceable and can't be debugged. This one is probably a subtle timing problem -- several people have reported it. I'll increase a time delay in the next release by maybe 0.l sec and hopefully it will happen even less often. >I still can't figure out how to change background color - pasting into >powerpoint looks much nicer if the background isn't white. Is this >possible? I looked in the documentation but can't find any hints on this. >Thanks. Press the button labeled [Bkg] to toggle white to black or back to white. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), 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: "Herbert J. Bernstein" Subject: HPUX RasMol Binaries for HP computers Date: Thu, 09 May 2002 22:48:30 -0400 (EDT) To: rasmol@lists.umass.edu, pdb-l@rcsb.org We are pleased to announce the availability of compiled versions of RasMol 2.7.1.1 (latest stable release) and RasMol 2.7.2.1 (next test version) for HP computers running HPUX 11. Both PARISC and IA64 system are supported. Our thanks to Gabriele Rearick of Hewlett Packard for her assistance and for making HP computers available for the builds. Gabriele has also provided a script, hp_supported.ksh, that may be used to identify the correct version of RasMol (PARISC or IA64) to run under HPUX on your system. For more information and download links, see the OpenRasmol page (http://www.OpenRasMol.org) or go directly to: http://www.bernstein-plus-sons.com/software/RasMol_2.7.1.1 and http://www.bernstein-plus-sons.com/software/RasMol_2.7.2.1 Work supported in part by the National Science Foundation under grant #DBI-0203064. ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 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: "Herbert J. Bernstein" Subject: Solaris 2.5.1 RasMol Binaries for older Sun computers Date: Thu, 09 May 2002 23:03:35 -0400 (EDT) To: rasmol@lists.umass.edu, pdb-l@rcsb.org We are pleased to announce the availability of compiled versions of RasMol 2.7.1.1 (latest stable release) and RasMol 2.7.2.1 (next test version) for older Sun computers running Solaris 2.5.1, using gcc as the compiler. These compilations were created under the auspices of the Accessible Retired Computers in Biology (ARCiB) project at Dowling College. The compilations were done using the Solaris 2.5.1 release from the Solaris Freeware Project (http://www.sunfreeware.com). If your Sun system does not have gcc, you may need to download the libraries to run this release of RasMol. Our thanks to Edward Hawrot of Brown University for donation of a Sparcserver 670 MP to the ARCiB project. The Sparcserver was used to compile the Solaris 2.5.1 binaries. For more information and download links, see the OpenRasmol page (http://www.OpenRasMol.org) or go directly to: http://www.bernstein-plus-sons.com/software/RasMol_2.7.1.1 and http://www.bernstein-plus-sons.com/software/RasMol_2.7.2.1 Work supported in part by the National Science Foundation under grant #DBI-0203064. ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 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: "Herbert J. Bernstein" Subject: OpenVMS 6.2 and 7.1 RasMol Binaries Date: Thu, 09 May 2002 23:10:20 -0400 (EDT) To: rasmol@lists.umass.edu, pdb-l@rcsb.org We are pleased to announce the availability of compiled versions of RasMol 2.7.2.1 RasMol 2.7.2.1 (next test version) for DEC/Compaq computers running OpenVMS 6.2 (VAX) or OpenVMS 7.1 (AXP) using the DECC compiler. These compilations were created under the auspices of the Accessible Retired Computers in Biology (ARCiB) project at Dowling College. Our thanks to David Atkinson of Boston University both for remote access to his AXP system which was used to compile the OpenVMS 7.1 binaries and for the donation of two VAXStations to the ARCiB project. The VAXStations were used to compile the OpenVMS 6.2 binaries. For more information and download links, see the OpenRasmol page (http://www.OpenRasMol.org) or go directly to: http://www.bernstein-plus-sons.com/software/RasMol_2.7.1.1 and http://www.bernstein-plus-sons.com/software/RasMol_2.7.2.1 Work supported in part by the National Science Foundation under grant #DBI-0203064. ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 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 V5.50.4522.1200 X-MSMail-priority: Normal References: <200106142206.f5EM6Q325732@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Chemical drawing program review Date: Sat, 11 May 2002 17:35:06 +0200 To: rasmol@lists.umass.edu Hello everybody, Those who are interested in chemical drawing programs, my comparative review on 5 applications (ISIS/Draw, ChemDraw, ChemWindow, ChemSketch and Chemistry 4-D Draw) has been updated and is available at: http://dragon.klte.hu/~gundat/rajzprogramok/dprog.html Tamas E. Gunda ----------------- Dr Tamas E. Gunda Research Group for Antibiotics Hungarian Academy of Sciences University of Debrecen, POB 36 H-4010 Debrecen Hungary tamasgunda@tigris.klte.hu ----------------------------------------------------------------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: bookmark/favorites should use "http:molvisindex.org" Date: Sat, 11 May 2002 13:49:22 -0400 To: rasmol@lists.umass.edu Due to server upgrades in progress, the domain name http://molvisindex.org is temporarily going to a different URL. The service is fully functional, but if you have bookmarked the old URL (http://molvis.sdsc.edu/visres) it will not work. If you configure your bookmark to go to http://molvisindex.org, it will work now, and (hopefully) at all future times. This is a good idea in general for domain names such as http://proteinexplorer.org and http://pdblite.org: edit the bookmark to specify the domain name rather than the URL to which it takes you. The advantage of domain names is that they can be redirected when servers have to change. In Windows, Netscape: Bookmarks, Edit, left-click to select bookmark, right-click and select Bookmark Properties. Edit the location slot to contain the domain name. In Windows, IE: Favorites, Organize Favorites, left-click on the favorite, right-click on the favorite and then click on Properties. Edit the URL slot to contain the domain name. On Macintosh, Netscape: Same as Windows except once you select the Bookmark, Apple-I gives you access to the editor dialog (if I remember correctly). Sorry if anyone has had problems accessing the site in the past few days, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), 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: temporary problems accessing Protein Explorer Date: Sun, 12 May 2002 14:04:17 -0400 To: rasmol@lists.umass.edu Due to a server configuration error, and other unlikely but coincidental problems, the address http://proteinexplorer.org is temporarily not working. Until these can be fixed, you can access Protein Explorer at http://nucleus.sdsc.edu:8079/molvis/protexpl/index.htm If you don't have a downloaded copy of PE, this would be a good time to download if you plan to use it in the next few days. The download link at the above address (3rd link from bottom in the right-most gray box) will download 1.901 beta. The IE Compatible Upgrade link there goes to 1.922 alpha, where the download link gives you 1.922 alpha. I recommend 1.922 alpha because it has several improvements over 1.901 and works well in both Netscape and IE. Windows users: don't put the downloaded files (protexpl.exe and shared.exe) on your desktop! Follow the instructions provided at the download site. Inadvertantly executing these files on a Windows desktop will create a major cleanup problem. I hope to provide a better installer in the next release. (This problem does not affect Macs.) The present temporary misconfigurations also cause the link to the UMass copy of 1.901 beta to be hidden. It can be accessed directly at http://www.umass.edu/microbio/chime/explorer/ This server has a slower link to the Internet, which is why the SDSC URL is recommended. Until they are fixed, the present misconfigurations will cause a small number of links within Protein Explorer (e.g. to some example PDB files) to fail. Sorry for any problems you may have encountered, -Eric ---- Eric Martz, Professor (Immunology), Dept Microbiology Morrill IVN 203, U Mass, Amherst MA US 01003-5720 http://www.umass.edu/molvis/martz 413-545-2325/FAX 413-545-2532 emartz@microbio.umass.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 Exchange V6.0.5762.3 Thread-Topic: Spectra standards Thread-Index: AcH5aam350YwHwkBSLKkGZLqiBteOQBE404w content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: Mitch Barker Subject: Spectra standards Date: Mon, 13 May 2002 09:05:05 -0400 To: rasmol@lists.umass.edu We're developing an application which will need to display a variety of spectra. We're developing based on our experience with EZ-Chrom but I'm wondering if there is a more general vendor neutral approach. I found JCAMP. Is that still actively used or developed? (The apparently main JCAMP website hadn't been updated since 1998). How about XML formats? Anyone use or know about CMLSpect? Are any of these ready for use by a commercial package? Thanks. Mitch ----------------------------------------------------------------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: Question Date: Mon, 13 May 2002 16:57:49 -0400 To: Brian White Cc: rasmol@lists.umass.edu, chime-team@mdli.com At 5/13/02, you wrote: >Eric - > I remember that you once showed me a chime (?) interface on the PC >that allowed you to bend & twist a structure & see the various >attractions & repulsions. Does this ring a bell? Is it somewhere on >the rasmol home page? > >THANKS > >Brian >-- >Prof. Brian White >Biology Department >University of Massachusetts, Boston >100 Morrissey Blvd >Boston MA 02125 >(617) 287-6630 >fax:(617) 287-6650 >brian.white@umb.edu >http://omega.cc.umb.edu/~bwhite/ Hi, Brian, You are probably remembering Sculpt, an energy minimization program acquired a few years ago by MDL and now sold by them. Free Chime has a free Sculpt "teaser" built-in. It isn't very functional because it has only mouse dragging to control it, and you can't save a reconfigured coordinate file. But is pretty to look at, and could be useful in an educational setting. For example, load something small like 1AL1. Click on MDL, then Sculpt Mode. Now, if you click and drag an atom, it will "pull" on it while doing dynamic energy minimization. If you click on an atom in the middle of the structure, and jiggle back and forth, you can minimize the whole structure, sort of. There is no option in Chime to just turn on minimization and let it run, like there is in the commercial version of Sculpt. MDL used to have an example on their Chime website, but I can't find any examples there anymore, or in fact any mention of Sculpt (if you use MDL's search, you find nothing). My recollection is that red baskets represent steric clashes, red dots represent repulsions, and cyan dots represent attractions. MDL has a commercial Sculpt site (http://www.mdl.com/products/sculpt.html) with tutorials and some screenshots and movies. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), 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 V6.0.5762.3 Thread-Topic: Lightweight mol file rendering software Thread-Index: AcH+6ru92T9VHEvZTsOC1dFr+ty+nwBE8EfA content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: Mitch Barker Subject: Lightweight mol file rendering software Date: Mon, 20 May 2002 09:05:46 -0400 To: rasmol@lists.umass.edu Can anyone point me to some example source code for simple display of mol files. I just need the basics. Language doesn't matter since we'll probably port to c#. I'm just looking for a simple fast display, not intended for "visualization", but a simple graphical representation of a chemical. Thanks. Mitch ----------------------------------------------------------------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 V5.50.4807.1700 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Karen Ocorr Subject: RE: Repairing "broken Chime" in IE Date: Mon, 20 May 2002 13:51:18 -0400 To: rasmol@lists.umass.edu -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Karen Ocorr Sent: Friday, April 26, 2002 2:39 PM From: owner-rasmol@lists.umass.edu Subject: Re: Repairing "broken Chime" in IE To: rasmol@lists.umass.edu THANKS!! Karen At 12:13 PM 4/25/2002 -0700, you wrote: >This message pertains to Windows 98, 98SE, 2000, and most likely other >versions of Windows (but not to Macs). Below, I review how the Chime >installer can damage your Windows system, rendering many IE-compatible >Chime sites inoperable on your computer, and I provide a procedure that >I believe will repair the damage. > >My testing of the repair procedure has been limited, so I would greatly >appreciate hearing from those of you who find you have the damaged >state. Please let me know whether the procedure corrected it, and >mention the version of IE (Help, About IE) and version of Windows (right >click on My Computer, then click Properties). > >Most if not all Chime sites work in Netscape. If you can use Netscape >for Chime sites, you probably don't need to repair IE's ability to work >with Chime. In some institutions and teaching computer labs, it is not >permitted to install Netscape -- in these cases, the repair procedure >below should allow you to use all IE-compatible Chime sites. (Many older >Chime sites were developed for Netscape and have not been upgraded to >work in IE, including many that I authored.) > >THE PROBLEM > >Yesterday I reported that if the very first installation of Chime on a >Windows system is directed into Netscape only (not Internet Explorer, >IE), while IE 5.0 is present, IE's ability to communicate command >scripts to Chime (after Chime is subsequently installed into IE) is >permanently broken. Upgrading IE, uninstalling/reinstalling Chime, >repairing or reinstalling IE all fail to correct this "damaged IE" >condition, which prevents the operation of Protein Explorer in IE as >well as many other IE-compatible Chime sites. For further details, >consult yesterday's message in the list history at >ftp://marlin.bio.umass.edu/pub/shareware/rasmol/email-history/00ReadMe.html > >(click on "current", wait for all of it to load, and go to the bottom). > >DETECTION OF THE PROBLEM > >The "damaged IE" condition can be detected by going to >http://www.umass.edu/microbio/chime/quizzer/index.htm, and clicking on >the link "Amino Acid Quizzer". If, despite Chime having been installed >into IE, you see a white rectangle in the left frame with a "missing >plugin" icon, and no molecule displays, you have the damaged state. (You >can confirm that Chime was installed for IE: Start, Settings, Control >Panel, Add/Remove Software: if "Chime for IE" appears on the list, it >was installed.) If a black rectangle appears in the Amino Acid Quizzer, >and a wireframe protein molecule displays automatically, then proceed to >enter the number "1" into the slot. If, after pressing the Enter key, a >spacefilled bright green residue does NOT appear, you have the damaged >state. If the green spacefilled residue appears, your system is OK. > >REPAIR PROCEDURE > >Caution: this procedure involves editing the Windows Registry, and >though unlikely if the procedure is followed carefully, could possibly >render your computer unbootable. Backup critical files first, and be >sure you have a bootable rescue diskette (on Windows 98, Start, >Settings, Control Panel, Add/Remove Programs, then click the Startup >Disk tab; can someone please tell me how to create one on Win2000? >Microsoft hasn't made it easy to find!). > >PROCEED AT YOUR OWN RISK. If you are not comfortable doing this >procedure, seek help from someone more familiar with the technical side >of Windows. > >1. Start, Settings, Control Panel, Add/Remove Software. > >2. Uninstall Chime for IE, and if present, any other Chime installations >such as Chime for Netscape. All Chime's should be uninstalled. > >3. Start, Run, and enter "regedit" into the slot, then click OK. The >Registry Editor will open. > >4. In the Registry Editor, click Help, Help Topics, Restore the >Registry. Right click the help text that appears and print it, just in >case. I have never had to do this, but better safe than sorry. > >5. In the Registry Editor, click the [+] next to each of the following >in the hierarchy of keys. Each click will open the keys encompassed by >the parent key, enabling you to find the next key to open. > >HKEY_LOCAL_MACHINE > Software > Microsoft > Internet Explorer > Plugins > Extension > >Highlight the last entry, "Extension", and Edit, Delete, confirm >deletion. >The following (or something similar) subsumed under Extension will >thereby be deleted. These keys appear to be responsible for the problem. > > "Content Type"="chemical/x-pdb" > "Version"="2, 6, 0, 8" > @="Chemscape Chime 2.6 SP3" > "Location"="C:\\NAVIGATO\\PROGRAM\\PLUGINS\\npchime.dll" > >Close the Registry Editor (Registry, Exit, or simply click on the X at >the upper right corner). > >6. Install Chime into IE (and also in Netscape if you have it). (Run the >Chime installer downloadable from http://www.mdlchime.com) > >Repeat the test above for detection of the damaged state. Your IE should >be repaired, the green spacefilled residue should appear, and Protein >Explorer 1.922 alpha and other IE-compatible Chime sites should now >operate on your computer. > >-Eric Martz > > > _________________________________________________________________________ Karen Ocorr, Ph.D. Biology Department University of Michigan Ann Arbor, MI. 48109-1048 Phone: 734/ 647-2470 Fax: 734/ 647-0884 E-mail: kocorr@umich.edu Home Page: http://biology.lsa.umich/~www/bio310/kohome.html Web Sites: http://biology.lsa.umich.edu/~www/bio310 http://biology.lsa.umich.edu/~www/bio225Winter/ http://biology.lsa.umich.edu/~www/bio100 _________________________________________________________________________ ----------------------------------------------------------------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: Mutant Proteins Date: Thu, 23 May 2002 19:14:37 -0400 To: Buzz Hoagland Cc: rasmol@lists.umass.edu At 5/22/02, Buzz Hoagland wrote: >Eric, > >I am looking for a mutant protein to help students visualize the central >dogma of molecular biology. I have used normal beta globin and sickle >globin, but now I am searching for a protein that has a mutation which >dramatically alters its structure. Of course there also needs to be a pdb >file of both the normal and mutated version of the protein. Do you know of >any proteins that meet these criteria? > >Thanks for any help you can offer. > >Buzz Hoagland >Westfield State College > Hi, Buzz, I looked for such a case a few years ago and found none. I think it is quite rare for a mutation to dramatically alter 3D structure. In lysozyme, every residue has been mutated, and few if any have dramatic effects on structure (see review publications of Brian Matthews). So I gave up and settled for normal vs. sickle hemoglobin (where the big effect is protein chain formation thru a hydrophobic surface residue). If you find such a case, let me know! I'm copying this to the MolVis Freeware/RasMol list in case someone has suggestions. If nothing turns up, I suggest posting your question on the PDB list (see Discussions at http://molvisindex.org). Regards, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), 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: Sydney Shall Subject: RE: Mutant Proteins Date: Fri, 24 May 2002 15:07:44 +0100 To: "'rasmol@lists.umass.edu'" --Boundary_(ID_rxZ1Lyg6kx8EmmBgGnQ67g) Perhaps you could try the ras protein. I have not myself checked that the mutant structure is in the pdb files, but it may well be. You need to look for the mutant at residue 13, which has a dramatic, but secondary effect on the active site, via an intervening alpha helix. Good luck Sydney Professor Sydney Shall. Department of Molecular Medicine, GKT [King's College] School of Medicine, The Rayne Institute, 123 Coldharbour Lane, London, SE5 9NU, LONDON. Tel:+44 0207 848 5901. Sydney.shall@kcl.ac.uk -----Original Message----- Sent: Friday, May 24, 2002 12:15 AM From: Eric Martz [SMTP:emartz@microbio.umass.edu] Subject: Re: Mutant Proteins To: Buzz Hoagland Cc: rasmol@lists.umass.edu At 5/22/02, Buzz Hoagland wrote: >Eric, > >I am looking for a mutant protein to help students visualize the central >dogma of molecular biology. I have used normal beta globin and sickle >globin, but now I am searching for a protein that has a mutation which >dramatically alters its structure. Of course there also needs to be a pdb >file of both the normal and mutated version of the protein. Do you know of >any proteins that meet these criteria? > >Thanks for any help you can offer. > >Buzz Hoagland >Westfield State College > Hi, Buzz, I looked for such a case a few years ago and found none. I think it is quite rare for a mutation to dramatically alter 3D structure. In lysozyme, every residue has been mutated, and few if any have dramatic effects on structure (see review publications of Brian Matthews). So I gave up and settled for normal vs. sickle hemoglobin (where the big effect is protein chain formation thru a hydrophobic surface residue). If you find such a case, let me know! I'm copying this to the MolVis Freeware/RasMol list in case someone has suggestions. If nothing turns up, I suggest posting your question on the PDB list (see Discussions at http://molvisindex.org). Regards, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ++++------+------+------+------+------+------+------+------+------+------+ From: cxhedg Subject: RCPT: RE: Mutant Proteins Date: Fri, 24 May 2002 10:18:21 -0500 To: rasmol@lists.umass.edu *** Confirmation of Registered Mail *** Your message sent to cxhedg has been read. Return Receipt Notification --------------------------- Perhaps you could try the ras protein. I have not myself checked that the mutant structure is in the pdb files, but it may well be. You need to look for the mutant at residue 13, which has a dramatic, but secondary effect on the active site, via an intervening alpha helix. Good luck Sydney Professor Sydney Shall. Department of Molecular Medicine, GKT [King's College] School of Medicine, The Rayne Institute, 123 Coldharbour Lane, London, SE5 9NU, LONDON. Tel:+44 0207 848 5901. Sydney.shall@kcl.ac.uk -----Original Message----- From: Eric Martz [SMTP:emartz@microbio.umass.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 ++++------+------+------+------+------+------+------+------+------+------+ From: Todd Carlson Subject: IE problems Date: Fri, 24 May 2002 14:42:22 -0400 To: rasmol@lists.umass.edu Hi all I put together this page, taking care to make sure it works even if the buttons are pressed in the wrong order. It works fine in Netscape 4.x. It even works in IE, if you push the buttons in the correct order. But if you push the buttons in the wrong order in IE, none of the scripts work. Reloading the page doesn't fix it. I have to close IE and open it again for it to work. Any suggestion? Thanks Todd Carlson Grand Valley State University ----------------------------------------------------------------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: ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re: IE problems Date: Sat, 25 May 2002 06:19:33 +0200 To: rasmol@lists.umass.edu Is it possible to know the adress of "this page" or to know which commands are being used in the scripts ? Such errors might occur in IE when chime requests for a file that doesn't exists, or that it can't find. The only solution is then to close IE and open it again. Paul Pillot ----- Original Message ----- Sent: Friday, May 24, 2002 8:42 PM From: "Todd Carlson" Subject: IE problems To: > Hi all > > I put together this page, taking care to make sure it works even if the buttons are pressed in the wrong order. It works fine in Netscape 4.x. It even works in IE, if you push the buttons in the correct order. > But if you push the buttons in the wrong order in IE, none of the scripts work. Reloading the page doesn't fix it. I have to close IE and open it again for it to work. > > Any suggestion? > > Thanks > > Todd Carlson > Grand Valley State University > > > ----------------------------------------------------------------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: IE problems Date: Sat, 25 May 2002 14:47:40 -0400 To: rasmol@lists.umass.edu At 5/24/02, you wrote: >Hi all > >I put together this page, taking care to make sure it works even if the buttons are pressed in the wrong order. It works fine in Netscape 4.x. It even works in IE, if you push the buttons in the correct order. >But if you push the buttons in the wrong order in IE, none of the scripts work. Reloading the page doesn't fix it. I have to close IE and open it again for it to work. > >Any suggestion? > >Thanks > >Todd Carlson >Grand Valley State University Dear Todd: I have documented many of the peculiarities and bugs in the IE-Chime interaction in my new IE-compatible version of PE, http://www.umass.edu/microbio/chime/beta/pe_alpha/protexpl/ For the complete list, see http://www.umass.edu/microbio/chime/beta/pe_alpha/protexpl/ie.htm In particular, IE stalls whenever a script FILE (not a javascript string containing a script) accesses another file (with a 'load' or 'script' command); or uses a move or delay command. These commands do work when they are sent by the IMBIF mechanism as a javascript string variable, but load and script commands must be issued one at a time, not followed by other commands in the same script. See the above document for details. There are lots of other "gotchas" in IE that aren't a problem in Netscape. Please see the above document for details. Once I identified, understood, and worked around the many Chime-IE pecularities, Protein Explorer works robustly and speedily in IE. (It took me a full-time month, last December!) -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), 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:0.9.4.1) Gecko/20020314 Netscape6/6.2.2 X-Accept-Language: en-us References: <001d01c203a3$5fc9abc0$4ed70b50@zig> ++++------+------+------+------+------+------+------+------+------+------+ From: T & S Carlson Subject: Re: IE problems Date: Sat, 25 May 2002 16:14:16 -0400 To: rasmol@lists.umass.edu Sorry, I forgot to give you the link. It is http://faculty.gvsu.edu/carlsont/mm/1234/1234.html As for the scripts, they are in separate script files, http://faculty.gvsu.edu/carlsont/mm/1234/primary.spt http://faculty.gvsu.edu/carlsont/mm/1234/secondary.spt http://faculty.gvsu.edu/carlsont/mm/1234/ribbon.spt http://faculty.gvsu.edu/carlsont/mm/1234/turns.spt http://faculty.gvsu.edu/carlsont/mm/1234/tertiary.spt http://faculty.gvsu.edu/carlsont/mm/1234/quaternary.spt Todd Paul Pillot wrote: > Is it possible to know the adress of "this page" or to know which commands > are being used in the scripts ? > Such errors might occur in IE when chime requests for a file that doesn't > exists, or that it can't find. The only solution is then to close IE and > open it again. > > Paul Pillot > ----- Original Message ----- > From: "Todd Carlson" > To: > Sent: Friday, May 24, 2002 8:42 PM > Subject: IE problems > > > >>Hi all >> >>I put together this page, taking care to make sure it works even if the >> > buttons are pressed in the wrong order. It works fine in Netscape 4.x. It > even works in IE, if you push the buttons in the correct order. > >>But if you push the buttons in the wrong order in IE, none of the scripts >> > work. Reloading the page doesn't fix it. I have to close IE and open it > again for it to work. > >>Any suggestion? >> >>Thanks >> >>Todd Carlson >>Grand Valley State University >> >> >> >> > > > > ----------------------------------------------------------------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:0.9.4.1) Gecko/20020314 Netscape6/6.2.2 X-Accept-Language: en-us References: <200205251844.g4PIiF214647@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: T & S Carlson Subject: Re: IE problems Date: Sat, 25 May 2002 16:21:24 -0400 To: rasmol@lists.umass.edu Thanks Eric I'm sure it my liberal use of delay and move commands, as you can see in the links I just posted. I will check your notes to see if I can work out the fix. Todd Eric Martz wrote: > At 5/24/02, you wrote: > >>Hi all >> >>I put together this page, taking care to make sure it works even if the >> > buttons are pressed in the wrong order. It works fine in Netscape 4.x. It > even works in IE, if you push the buttons in the correct order. > >>But if you push the buttons in the wrong order in IE, none of the scripts >> > work. Reloading the page doesn't fix it. I have to close IE and open it > again for it to work. > >>Any suggestion? >> >>Thanks >> >>Todd Carlson >>Grand Valley State University >> > > Dear Todd: > > I have documented many of the peculiarities and bugs in the IE-Chime > interaction in my new IE-compatible version of PE, > http://www.umass.edu/microbio/chime/beta/pe_alpha/protexpl/ > > For the complete list, see > http://www.umass.edu/microbio/chime/beta/pe_alpha/protexpl/ie.htm > > In particular, IE stalls whenever a script FILE (not a javascript string > containing a script) accesses another file (with a 'load' or 'script' > command); or uses a move or delay command. > > These commands do work when they are sent by the IMBIF mechanism as a > javascript string variable, but load and script commands must be issued one > at a time, not followed by other commands in the same script. See the above > document for details. > > There are lots of other "gotchas" in IE that aren't a problem in Netscape. > Please see the above document for details. > > Once I identified, understood, and worked around the many Chime-IE > pecularities, Protein Explorer works robustly and speedily in IE. (It took > me a full-time month, last December!) > > -Eric > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > The Protein Explorer: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > PDB Lite molecule finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), 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 V6.00.2600.0000 X-MSMail-priority: Normal References: <001d01c203a3$5fc9abc0$4ed70b50@zig> <3CEFF098.1030908@gvsu.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re: IE problems Date: Sun, 26 May 2002 00:19:14 +0200 To: rasmol@lists.umass.edu Todd, there are two commands incompatible with external scripts in IE, in your scripts : delay move The best solution is to copy the scripts and paste them directly into your html file, as parameters of script="" in your embeded buttons. I tried this with your project and it works perfectly in IE (nice scripts ;-). I'll send you personally the 1234.htm file I made. Paul PS : I can't figure out why it worked when buttons are being pushed in right order and not in reverse order... ----- Original Message ----- Sent: Saturday, May 25, 2002 10:14 PM From: "T & S Carlson" Subject: Re: IE problems To: > Sorry, I forgot to give you the link. It is > > http://faculty.gvsu.edu/carlsont/mm/1234/1234.html > > As for the scripts, they are in separate script files, > > http://faculty.gvsu.edu/carlsont/mm/1234/primary.spt > http://faculty.gvsu.edu/carlsont/mm/1234/secondary.spt > http://faculty.gvsu.edu/carlsont/mm/1234/ribbon.spt > http://faculty.gvsu.edu/carlsont/mm/1234/turns.spt > http://faculty.gvsu.edu/carlsont/mm/1234/tertiary.spt > http://faculty.gvsu.edu/carlsont/mm/1234/quaternary.spt > > > Todd > > > > Paul Pillot wrote: > > > Is it possible to know the adress of "this page" or to know which commands > > are being used in the scripts ? > > Such errors might occur in IE when chime requests for a file that doesn't > > exists, or that it can't find. The only solution is then to close IE and > > open it again. > > > > Paul Pillot > > ----- Original Message ----- > > From: "Todd Carlson" > > To: > > Sent: Friday, May 24, 2002 8:42 PM > > Subject: IE problems > > > > > > > >>Hi all > >> > >>I put together this page, taking care to make sure it works even if the > >> > > buttons are pressed in the wrong order. It works fine in Netscape 4.x. It > > even works in IE, if you push the buttons in the correct order. > > > >>But if you push the buttons in the wrong order in IE, none of the scripts > >> > > work. Reloading the page doesn't fix it. I have to close IE and open it > > again for it to work. > > > >>Any suggestion? > >> > >>Thanks > >> > >>Todd Carlson > >>Grand Valley State University > >> > >> > >> > >> > > > > > > > > > > > > ----------------------------------------------------------------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:0.9.4.1) Gecko/20020314 Netscape6/6.2.2 X-Accept-Language: en-us References: <001d01c203a3$5fc9abc0$4ed70b50@zig> <3CEFF098.1030908@gvsu.edu> <001d01c2043a$3476a440$4ed70b50@zig> ++++------+------+------+------+------+------+------+------+------+------+ From: T & S Carlson Subject: Re: IE problems Date: Mon, 27 May 2002 00:08:13 -0400 To: rasmol@lists.umass.edu Thanks Paul One of the reasons I used external scripts was that the quotes in the label commands (label "helix") are a problem inside the script="....." quotes. I know Eric had some information on quotes I will look up. But this is a holiday weekend and I'm trying not to do too much work ;-) Todd Paul Pillot wrote: > Todd, > there are two commands incompatible with external scripts in IE, in your > scripts : > delay > move > > The best solution is to copy the scripts and paste them directly into your > html file, as parameters of script="" in your embeded buttons. > I tried this with your project and it works perfectly in IE (nice scripts > ;-). I'll send you personally the 1234.htm file I made. > > Paul > > PS : I can't figure out why it worked when buttons are being pushed in right > order and not in reverse order... > > ----- Original Message ----- > From: "T & S Carlson" > To: > Sent: Saturday, May 25, 2002 10:14 PM > Subject: Re: IE problems > > > >>Sorry, I forgot to give you the link. It is >> >>http://faculty.gvsu.edu/carlsont/mm/1234/1234.html >> >>As for the scripts, they are in separate script files, >> >>http://faculty.gvsu.edu/carlsont/mm/1234/primary.spt >>http://faculty.gvsu.edu/carlsont/mm/1234/secondary.spt >>http://faculty.gvsu.edu/carlsont/mm/1234/ribbon.spt >>http://faculty.gvsu.edu/carlsont/mm/1234/turns.spt >>http://faculty.gvsu.edu/carlsont/mm/1234/tertiary.spt >>http://faculty.gvsu.edu/carlsont/mm/1234/quaternary.spt >> >> >>Todd >> >> >> >>Paul Pillot wrote: >> >> >>>Is it possible to know the adress of "this page" or to know which >>> > commands > >>>are being used in the scripts ? >>>Such errors might occur in IE when chime requests for a file that >>> > doesn't > >>>exists, or that it can't find. The only solution is then to close IE and >>>open it again. >>> >>>Paul Pillot >>>----- Original Message ----- >>>From: "Todd Carlson" >>>To: >>>Sent: Friday, May 24, 2002 8:42 PM >>>Subject: IE problems >>> >>> >>> >>> >>>>Hi all >>>> >>>>I put together this page, taking care to make sure it works even if the >>>> >>>> >>>buttons are pressed in the wrong order. It works fine in Netscape 4.x. >>> > It > >>>even works in IE, if you push the buttons in the correct order. >>> >>> >>>>But if you push the buttons in the wrong order in IE, none of the >>>> > scripts > >>>work. Reloading the page doesn't fix it. I have to close IE and open >>> > it > >>>again for it to work. >>> >>> >>>>Any suggestion? >>>> >>>>Thanks >>>> >>>>Todd Carlson >>>>Grand Valley State University >>>> >>>> >>>> >>>> >>>> >>> >>> >>> >> >> >> > > > > ----------------------------------------------------------------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: <001d01c203a3$5fc9abc0$4ed70b50@zig> <3CEFF098.1030908@gvsu.edu> <001d01c2043a$3476a440$4ed70b50@zig> <3CF1B12D.4040302@gvsu.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re: IE problems Date: Mon, 27 May 2002 07:03:45 +0200 To: rasmol@lists.umass.edu Todd, to label your helices, you don't need any quotes : just use label helix Paul ----- Original Message ----- Sent: Monday, May 27, 2002 6:08 AM From: "T & S Carlson" Subject: Re: IE problems To: > Thanks Paul > > One of the reasons I used external scripts was that the quotes in the > label commands (label "helix") are a problem inside the script="....." > quotes. I know Eric had some information on quotes I will look up. But > this is a holiday weekend and I'm trying not to do too much work ;-) > > > Todd > > > Paul Pillot wrote: > > > Todd, > > there are two commands incompatible with external scripts in IE, in your > > scripts : > > delay > > move > > > > The best solution is to copy the scripts and paste them directly into your > > html file, as parameters of script="" in your embeded buttons. > > I tried this with your project and it works perfectly in IE (nice scripts > > ;-). I'll send you personally the 1234.htm file I made. > > > > Paul > > > > PS : I can't figure out why it worked when buttons are being pushed in right > > order and not in reverse order... > > > > ----- Original Message ----- > > From: "T & S Carlson" > > To: > > Sent: Saturday, May 25, 2002 10:14 PM > > Subject: Re: IE problems > > > > > > > >>Sorry, I forgot to give you the link. It is > >> > >>http://faculty.gvsu.edu/carlsont/mm/1234/1234.html > >> > >>As for the scripts, they are in separate script files, > >> > >>http://faculty.gvsu.edu/carlsont/mm/1234/primary.spt > >>http://faculty.gvsu.edu/carlsont/mm/1234/secondary.spt > >>http://faculty.gvsu.edu/carlsont/mm/1234/ribbon.spt > >>http://faculty.gvsu.edu/carlsont/mm/1234/turns.spt > >>http://faculty.gvsu.edu/carlsont/mm/1234/tertiary.spt > >>http://faculty.gvsu.edu/carlsont/mm/1234/quaternary.spt > >> > >> > >>Todd > >> > >> > >> > >>Paul Pillot wrote: > >> > >> > >>>Is it possible to know the adress of "this page" or to know which > >>> > > commands > > > >>>are being used in the scripts ? > >>>Such errors might occur in IE when chime requests for a file that > >>> > > doesn't > > > >>>exists, or that it can't find. The only solution is then to close IE and > >>>open it again. > >>> > >>>Paul Pillot > >>>----- Original Message ----- > >>>From: "Todd Carlson" > >>>To: > >>>Sent: Friday, May 24, 2002 8:42 PM > >>>Subject: IE problems > >>> > >>> > >>> > >>> > >>>>Hi all > >>>> > >>>>I put together this page, taking care to make sure it works even if the > >>>> > >>>> > >>>buttons are pressed in the wrong order. It works fine in Netscape 4.x. > >>> > > It > > > >>>even works in IE, if you push the buttons in the correct order. > >>> > >>> > >>>>But if you push the buttons in the wrong order in IE, none of the > >>>> > > scripts > > > >>>work. Reloading the page doesn't fix it. I have to close IE and open > >>> > > it > > > >>>again for it to work. > >>> > >>> > >>>>Any suggestion? > >>>> > >>>>Thanks > >>>> > >>>>Todd Carlson > >>>>Grand Valley State University > >>>> > >>>> > >>>> > >>>> > >>>> > >>> > >>> > >>> > >> > >> > >> > > > > > > > > > > > > ----------------------------------------------------------------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-Accept-Language: es References: <001d01c203a3$5fc9abc0$4ed70b50@zig> ++++------+------+------+------+------+------+------+------+------+------+ From: Gabriel Pons Subject: problems with IE and protein explorer Date: Mon, 27 May 2002 10:27:20 +0200 To: rasmol@lists.umass.edu Dear All: I downloaded the 1.922 alpha version of PE : I used Internet explorer, version 5.5 but every time I try to start PE it says that I don´t have the right browser. I thought that IE 5.5 worked with PE 1.922alpha. IE 5.5 seems to work fine with other chime sites. Any help? 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-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 X-MSMail-priority: Normal References: <001d01c203a3$5fc9abc0$4ed70b50@zig> <3CEFF098.1030908@gvsu.edu> <001d01c2043a$3476a440$4ed70b50@zig> ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: IE problems of scripts Date: Mon, 27 May 2002 11:44:58 +0200 To: rasmol@lists.umass.edu Exactly. I had also struggled with the same problems concerning script files, but I gave up. I simply put the full script(s) into the html files, and they work perfectly. Tamas Dr. Tamas E. Gunda Research Group for Antibiotics Hungarian Academy of Sciences University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tamasgunda@tigris.klte.hu ----- Original Message ----- Sent: Sunday, May 26, 2002 00:19 From: "Paul Pillot" Subject: Re: IE problems To: > Todd, > there are two commands incompatible with external scripts in IE, in your > scripts : > delay > move > > The best solution is to copy the scripts and paste them directly into your > html file, as parameters of script="" in your embeded buttons. > I tried this with your project and it works perfectly in IE (nice scripts > ;-). I'll send you personally the 1234.htm file I made. > > Paul > > PS : I can't figure out why it worked when buttons are being pushed in right > order and not in reverse order... > > ----- Original Message ----- > From: "T & S Carlson" > To: > Sent: Saturday, May 25, 2002 10:14 PM > Subject: Re: IE problems > > > > Sorry, I forgot to give you the link. It is > > > > http://faculty.gvsu.edu/carlsont/mm/1234/1234.html > > > > As for the scripts, they are in separate script files, > > > > http://faculty.gvsu.edu/carlsont/mm/1234/primary.spt > > http://faculty.gvsu.edu/carlsont/mm/1234/secondary.spt > > http://faculty.gvsu.edu/carlsont/mm/1234/ribbon.spt > > http://faculty.gvsu.edu/carlsont/mm/1234/turns.spt > > http://faculty.gvsu.edu/carlsont/mm/1234/tertiary.spt > > http://faculty.gvsu.edu/carlsont/mm/1234/quaternary.spt > > > > > > Todd > > > > > > > > Paul Pillot wrote: > > > > > Is it possible to know the adress of "this page" or to know which > commands > > > are being used in the scripts ? > > > Such errors might occur in IE when chime requests for a file that > doesn't > > > exists, or that it can't find. The only solution is then to close IE and > > > open it again. > > > > > > Paul Pillot > > > ----- Original Message ----- > > > From: "Todd Carlson" > > > To: > > > Sent: Friday, May 24, 2002 8:42 PM > > > Subject: IE problems > > > > > > > > > > > >>Hi all > > >> > > >>I put together this page, taking care to make sure it works even if the > > >> > > > buttons are pressed in the wrong order. It works fine in Netscape 4.x. > It > > > even works in IE, if you push the buttons in the correct order. > > > > > >>But if you push the buttons in the wrong order in IE, none of the > scripts > > >> > > > work. Reloading the page doesn't fix it. I have to close IE and open > it > > > again for it to work. > > > > > >>Any suggestion? > > >> > > >>Thanks > > >> > > >>Todd Carlson > > >>Grand Valley State University > > >> > > >> > > >> > > >> > > > > > > > > > > > > > > > > > > > > > > > ----------------------------------------------------------------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: <001d01c203a3$5fc9abc0$4ed70b50@zig> X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id g4REx2202494 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: problems with IE and protein explorer Date: Mon, 27 May 2002 11:00:31 -0400 To: rasmol@lists.umass.edu Cc: gpons@bell.ub.es At 5/27/02, Gabriel Pons wrote: >Dear All: >I downloaded the 1.922 alpha version of PE : I used Internet explorer, version >5.5 but every time I try to start PE it says that I don´t have the right >browser. I thought that IE 5.5 worked with PE 1.922alpha. IE 5.5 seems to work >fine with other chime sites. >Any help? >Thanks PE 1.922 works only with IE 5.5SP2 (or later, e.g. IE6), on Windows (Mac IE is not supported). SP2 means Service Pack 2. If you are using 5.5SP1 or plain 5.5, it will not work. This is due to a change Microsoft made in SP2 concerning plugins. If you are using IE that needs to be upgraded to 5.5SP2, the instructions are at the top of the page that reports the problem, namely http://www.umass.edu/microbio/chime/beta/pe_alpha/protexpl/needbrow.htm?too_ old Gabriel, if this is not the problem you are having, please be more explicit and detailed about exactly what error message you are getting. It is a common misconception that because bare Chime (various versions) works with IE (various versions), so should PE. It isn't that simple! PE has more lines of code now than does RasMol! It is not a priority for me to support older versions of IE or Chime -- it took me a full-time month to get IE5.5SP2 to work in most respects. I think it is more important to provide new features in PE. It is easy enough to upgrade your browser or Chime if you want to use PE. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), 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: "Herbert J. Bernstein" Subject: New RasMol 2.7.2.1 PC binary Date: Mon, 27 May 2002 22:57:12 -0400 To: rasmol@lists.umass.edu, pdb-l@rcsb.org The PC (MS Windows) binary for RasMol version 2.7.2.1 (the best test version) has been recompiled with a patch to correct the handling of mouse right-click and drag. This action was supposed to produce a shift of the molecule proportionate to the mouse motion. Until this patch, the PC version of RasMol 2.7.2.1 was shifting the molecule off-screen. With this patch the PC version of RasMol 2.7.2.1 should handle the mouse right-click and drag correctly. No change has been made to the Unix or Mac versions. They did not have this bug. No change has been made to the RasMol 2.7.1.1 production release. Our apologies for the long delay in finding and correcting this bug. The updated binary and source of the patch are available on the http://www.bernstein-plus-sons.com/software/RasMol_2.7.2.1 web page. -- H. J. Bernstein ----------------------------------------------------------------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-Accept-Language: fr,en-US References: <001d01c203a3$5fc9abc0$4ed70b50@zig> <3CEFF098.1030908@gvsu.edu> <001d01c2043a$3476a440$4ed70b50@zig> <3CF1B12D.4040302@gvsu.edu> <000801c2053b$e14e2740$4ed70b50@zig> ++++------+------+------+------+------+------+------+------+------+------+ From: Jean-Philippe Demers Subject: Re: IE problems Date: Tue, 28 May 2002 12:45:00 -0400 To: rasmol@lists.umass.edu Hello everybody, I have released a new version of the MoI (Mechanism of Interaction), which allow any web page using Chime to be compatible with Internet Explorer. As Eric said, "there are lots of other 'gotchas' in IE that aren't a problem in Netscape." The MoI manages the communication between Chime and JavaScript to avoid compatibility problems. This new version is featuring a debugger and provides a command line interface to any of your plug-in to help you develop a script. It now supports multiples instances of the same page under Internet Explorer. The MoI is available at the following address: http://www3.sympatico.ca/diane.demers/moi/ Cheers! Jean-Philippe Demers ----------------------------------------------------------------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: "Herbert J. Bernstein" Subject: Re: New RasMol 2.7.2.1 PC binary Date: Wed, 29 May 2002 14:46:28 -0400 (EDT) To: pdb-l@rcsb.org, rasmol@lists.umass.edu The new RasMol 2.7.2.1 PC binary released on 27 May 2002 has now been tested successfully on: Windows for Workgroups 3.11 with Win32S 1.3 Windows 98 Windows 2000 Our thanks to Rohit Tripathi for these reports. Reports of success (or failure) on other Windows versions would be appreciated. -- H. J. Bernstein ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 27 May 2002, Herbert J. Bernstein wrote: > > The PC (MS Windows) binary for RasMol version 2.7.2.1 (the best test version) > has been recompiled with a patch to correct the handling of mouse right-click > and drag. > ... > The updated binary and source of the patch are available on the > > http://www.bernstein-plus-sons.com/software/RasMol_2.7.2.1 > > web page. > > -- H. J. Bernstein > ----------------------------------------------------------------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: Mac >1 Gig memory/Chime conflict Date: Thu, 30 May 2002 14:24:27 -0400 To: rasmol@lists.umass.edu In January 2002, Michael Morales, Peter Walter, and James W. Caras reported here that Chime 2.6SP3 fails to work on Macintosh G4's with >= 1 gigabyte of memory when running OS 9.2. They offered two solutions. First, you can run OS X, and Chime will work properly in the Classic environment. Second, you can physically remove some of your hardware memory. My question: does Mac Chime 2.0a have the same problem? Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), 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: Mac >1 Gig memory/Chime conflict Date: Thu, 30 May 2002 17:15:52 -0400 To: rasmol@lists.umass.edu it was 2:24 PM EDT on (Thursday) 30 May 2002 when Eric Martz said: > In January 2002, Michael Morales, Peter Walter, and James W. Caras > reported here that Chime 2.6SP3 fails to work on Macintosh G4's with >= 1 > gigabyte of memory when running OS 9.2. They offered two solutions. > First, you can run OS X, and Chime will work properly in the Classic > environment. Second, you can physically remove some of your hardware > memory. > > My question: does Mac Chime 2.0a have the same problem? > hi Eric, as far as I know, Chime 2.0a is not affected by this. I'll forward your request to Mike and Peter, in case I'm wrong. -tim -- molvisions - 3D molecular visualization waltham, ma usa ----------------------------------------------------------------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: Fwd: Re: Mac >1 Gig memory/Chime conflict Date: Fri, 31 May 2002 13:45:17 -0400 To: "LIST: rasmol" ====== Forwarded Message ====== ++++------+------+------+------+------+------+------+------+------+------+ From: Michael Morales Date: 05.31.2002 10:20 AM To: timothy driscoll it was 10:20 AM EDT on (Friday) 31 May 2002 when Michael Morales said: > Actually, no. 2.0a doesn't work either. It solves an entirely different > incompatibility issue with some Macs that just can't run 2.6SP3. > > The only thing that works besides removing the memory is to run the thing > in OSX and then use the Classic mode. Go figure. > > Best, Mike > > > > > > it was 2:24 PM EDT on (Thursday) 30 May 2002 when Eric Martz said: > > > > > In January 2002, Michael Morales, Peter Walter, and James W. Caras > > > reported here that Chime 2.6SP3 fails to work on Macintosh G4's with > > > gigabyte of memory when running OS 9.2. They offered two solutions. > > > First, you can run OS X, and Chime will work properly in the Classic > > > environment. Second, you can physically remove some of your hardware > > > memory. > > > > > > My question: does Mac Chime 2.0a have the same problem? > > > > > > Thanks, -Eric > > > ====== End Forwarded Message ====== -- molvisions - 3D molecular visualization waltham, ma usa ----------------------------------------------------------------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: Joel Kowit Subject: Directions for "Three Frame for Chime" Date: Mon, 03 Jun 2002 13:20:38 -0400 To: rasmol@lists.umass.edu Hi All: I'm trying to set up a Chime tutorial that involves side by side windows so that two proteins can be viewed side by side. I have modified the file, <2-Frame> by adding a "middle" window, but the other template files aren't compatible, so buttons don't work. Can anyone point me to "How to" directions? Thanks. Joel Kowit Dept. Biology Emmanuel College Boston, MA 02421 kowitj@emmanuel.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: animated gifs in powerpoint? Date: Mon, 03 Jun 2002 13:23:15 -0400 To: rasmol@lists.umass.edu Cc: chris@bio.umass.edu Is it possible to insert animated GIF files into PowerPoint, and have them animate? For example, http://molvis.sdsc.edu/protexpl/efhandm.gif is an animated GIF. When viewed in Netscape or IE, animation is automatic. When it is saved to disk, then imported into PowerPoint (Insert, Picture, >From File), it is static, showing only the first frame. PowerPoint's Insert, Movies and Sounds, Movie from File does not accept .gif format. Can someone familiar with animations in PowerPoint please advise? Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), 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: "J. Ricky Cox" Subject: Re: animated gifs in powerpoint? Date: Mon, 03 Jun 2002 12:28:07 -0500 To: rasmol@lists.umass.edu Eric-

You should be able to insert an animated gif (as you describe below starting with insert) into a powerpoint presentation and have it activate as soon as you "view show".  I just did that successfully with the file you mentioned.  I am not sure if the version of Powerpoint is critical.  I am using the Office 2000 version.

Ricky



At 01:23 PM 6/3/2002 -0400, you wrote:
Is it possible to insert animated GIF files into PowerPoint, and have them
animate?

For example, http://molvis.sdsc.edu/protexpl/efhandm.gif
is an animated GIF. When viewed in Netscape or IE, animation is automatic.

When it is saved to disk, then imported into PowerPoint (Insert, Picture,
>From File), it is static, showing only the first frame. PowerPoint's
Insert, Movies and Sounds, Movie from File does not accept .gif format.

Can someone familiar with animations in PowerPoint please advise?

Thanks, -Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
The Protein Explorer: http://proteinexplorer.org
Workshops: http://www.umass.edu/molvis/workshop
World Index of Molecular Visualization Resources: http://molvisindex.org
PDB Lite molecule finder: http://pdblite.org
Molecular Visualization EMail List:
      http://www.umass.edu/microbio/rasmol/raslist.htm

Eric Martz, Professor (Immunology), 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-- Content-return: allowed boundary="Boundary_(ID_qbWJwefu0wvIKpx6B3RUPA)" ++++------+------+------+------+------+------+------+------+------+------+ From: David Margulies Subject: RE: animated gifs in powerpoint? Date: Mon, 03 Jun 2002 13:37:43 -0400 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_qbWJwefu0wvIKpx6B3RUPA) Eric: I just moved the movie image (on a mac) to my desktop, then imported into powerpoint (Insert, Movies and Sounds, from file). and it works. When you copy the powerpoint to a disk, you may need to keep the original *.gif in the same folder. I've done a number of anim.gif into powerpoint presentations with no trouble. Let me know if you're still having problems. david > ---------- > From: Eric Martz > Reply To: rasmol@lists.umass.edu > Sent: Monday, June 3, 2002 1:23 PM > To: rasmol@lists.umass.edu > Cc: chris@bio.umass.edu > Subject: animated gifs in powerpoint? > > Is it possible to insert animated GIF files into PowerPoint, and have them > animate? > > For example, http://molvis.sdsc.edu/protexpl/efhandm.gif > is an animated GIF. When viewed in Netscape or IE, animation is automatic. > > When it is saved to disk, then imported into PowerPoint (Insert, Picture, > >From File), it is static, showing only the first frame. PowerPoint's > Insert, Movies and Sounds, Movie from File does not accept .gif format. > > Can someone familiar with animations in PowerPoint please advise? > > Thanks, -Eric > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > The Protein Explorer: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > PDB Lite molecule finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > > --Boundary_(ID_qbWJwefu0wvIKpx6B3RUPA) RE: animated gifs in powerpoint?

Eric:

    I just moved the movie image (on a mac) to my desktop, then imported into powerpoint (Insert, Movies and Sounds, from file).  and it works.  When you copy the powerpoint to a disk, you may need to keep the original *.gif in the same folder. 

    I've done a number of anim.gif into powerpoint presentations with no trouble.  Let me know if you're still having problems.

    david
    ----------
    From:   Eric Martz
    Reply To:       rasmol@lists.umass.edu
    Sent:   Monday, June 3, 2002 1:23 PM
    To:     rasmol@lists.umass.edu
    Cc:     chris@bio.umass.edu
    Subject:        animated gifs in powerpoint?

    Is it possible to insert animated GIF files into PowerPoint, and have them
    animate?

    For example, http://molvis.sdsc.edu/protexpl/efhandm.gif
    is an animated GIF. When viewed in Netscape or IE, animation is automatic.

    When it is saved to disk, then imported into PowerPoint (Insert, Picture,
    >From File), it is static, showing only the first frame. PowerPoint's
    Insert, Movies and Sounds, Movie from File does not accept .gif format.

    Can someone familiar with animations in PowerPoint please advise?

    Thanks, -Eric
    /* - - - - - - - - - - - - - - - - - - - - - - - - - - -
    The Protein Explorer: http://proteinexplorer.org
    Workshops: http://www.umass.edu/molvis/workshop
    World Index of Molecular Visualization Resources: http://molvisindex.org
    PDB Lite molecule finder: http://pdblite.org
    Molecular Visualization EMail List:
          http://www.umass.edu/microbio/rasmol/raslist.htm

    Eric Martz, Professor (Immunology), Dept Microbiology
    U Mass, Amherst MA US  413-545-2325/FAX 413-545-2532
                  http://www.umass.edu/molvis/martz
    - - - - - - - - - - - - - - - - - - - - - - - - - - - */


--Boundary_(ID_qbWJwefu0wvIKpx6B3RUPA)-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Eric C Niederhoffer Subject: Re: Directions for "Three Frame for Chime" Date: Mon, 03 Jun 2002 12:41:01 -0500 To: rasmol@lists.umass.edu Joel: I have set up Chime presentations that allows one to view multiple windows of the same protein or different proteins on the same page. Some of these presentations use a remote control to minimize window scrolling. All the Javascript may be easily viewed for custom changes. See the following link to the presentations (also listed on Eric's worldwide directory). http://www.siu.edu/departments/biochem/chime_rasmol/instruct.htm Eric Niederhoffer >Hi All: > >I'm trying to set up a Chime tutorial that involves side by side windows >so that two proteins >can be viewed side by side. I have modified the file, <2-Frame> by >adding a "middle" window, >but the other template files aren't compatible, so buttons don't work. Can >anyone point me to "How to" directions? Thanks. > >Joel Kowit >Dept. Biology >Emmanuel College >Boston, MA 02421 >kowitj@emmanuel.edu Eric C Niederhoffer, PhD Associate Professor Biochemistry & Molecular Biology, MC 6503 600 Agriculture Drive, Rm 112 Southern Illinois University School of Medicine Carbondale, IL 62901-6503 eniederhoffer@siumed.edu 618.453.6467 (office) http://www.siu.edu/departments/biochem/faculty/Niederhoffer.html ----------------------------------------------------------------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_Dz9ygyyBQ/KzoBAR02qeCw)" ++++------+------+------+------+------+------+------+------+------+------+ From: "Gorga, Frank" Subject: RE: animated gifs in powerpoint? Date: Mon, 03 Jun 2002 14:23:15 -0400 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_Dz9ygyyBQ/KzoBAR02qeCw) PowerPoint (I currently use the "2K" version on Windows) can be a bit finicky in this regard.... As a previous correspondent mentioned using the "Insert Picture" command works, but you will not see the animation until you actually view the slide show. Unfortunately, if you drag exactly the same file into your presentation (from the desktop or a folder) you will get only a static image! Go figure! --- Frank ---------------------------------------------------------------------------- - Frank R. Gorga, Ph.D. Department of Chemical Sciences Bridgewater State College Bridgewater, MA 02325 508-531-2827 / 508-531-1785 (fax) fgorga@bridgew.edu webhost.bridgew.edu/fgorga ---------------------------------------------------------------------------- Comfort the troubled; trouble the comfortable. -- Dietrich Bonhoeffer, 1906-1945 http://www.dbonhoeffer.org/who-was-db2.htm -----Original Message----- Sent: Monday, June 03, 2002 1:38 PM From: David Margulies [mailto:DMARGULIES@niaid.nih.gov] Subject: RE: animated gifs in powerpoint? To: 'rasmol@lists.umass.edu' Eric: I just moved the movie image (on a mac) to my desktop, then imported into powerpoint (Insert, Movies and Sounds, from file). and it works. When you copy the powerpoint to a disk, you may need to keep the original *.gif in the same folder. I've done a number of anim.gif into powerpoint presentations with no trouble. Let me know if you're still having problems. david ---------- Reply To: rasmol@lists.umass.edu Sent: Monday, June 3, 2002 1:23 PM From: Eric Martz Subject: animated gifs in powerpoint? To: rasmol@lists.umass.edu Cc: chris@bio.umass.edu Is it possible to insert animated GIF files into PowerPoint, and have them animate? For example, http://molvis.sdsc.edu/protexpl/efhandm.gif is an animated GIF. When viewed in Netscape or IE, animation is automatic. When it is saved to disk, then imported into PowerPoint (Insert, Picture, >From File), it is static, showing only the first frame. PowerPoint's Insert, Movies and Sounds, Movie from File does not accept .gif format. Can someone familiar with animations in PowerPoint please advise? Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ --Boundary_(ID_Dz9ygyyBQ/KzoBAR02qeCw) RE: animated gifs in powerpoint?
PowerPoint (I currently use the "2K" version on Windows) can be a bit finicky in this regard....
 
As a previous correspondent mentioned using the "Insert Picture" command works, but you will not see the animation until you actually view the slide show.
 
Unfortunately, if you drag exactly the same file into your presentation (from the desktop or a folder) you will get only a static image! Go figure!
 
 
--- Frank
 
-----------------------------------------------------------------------------
Frank R. Gorga, Ph.D.
Department of Chemical Sciences
Bridgewater State College
Bridgewater, MA 02325
508-531-2827 / 508-531-1785 (fax)
fgorga@bridgew.edu
webhost.bridgew.edu/fgorga
----------------------------------------------------------------------------
Comfort the troubled; trouble the comfortable.
       -- Dietrich Bonhoeffer, 1906-1945
          http://www.dbonhoeffer.org/who-was-db2.htm
-----Original Message-----
From: David Margulies [mailto:DMARGULIES@niaid.nih.gov]
Sent: Monday, June 03, 2002 1:38 PM
To: 'rasmol@lists.umass.edu'
Subject: RE: animated gifs in powerpoint?

Eric:

    I just moved the movie image (on a mac) to my desktop, then imported into powerpoint (Insert, Movies and Sounds, from file).  and it works.  When you copy the powerpoint to a disk, you may need to keep the original *.gif in the same folder. 

    I've done a number of anim.gif into powerpoint presentations with no trouble.  Let me know if you're still having problems.

    david
    ----------
    From:   Eric Martz
    Reply To:       rasmol@lists.umass.edu
    Sent:   Monday, June 3, 2002 1:23 PM
    To:     rasmol@lists.umass.edu
    Cc:     chris@bio.umass.edu
    Subject:        animated gifs in powerpoint?

    Is it possible to insert animated GIF files into PowerPoint, and have them
    animate?

    For example, http://molvis.sdsc.edu/protexpl/efhandm.gif
    is an animated GIF. When viewed in Netscape or IE, animation is automatic.

    When it is saved to disk, then imported into PowerPoint (Insert, Picture,
    >From File), it is static, showing only the first frame. PowerPoint's
    Insert, Movies and Sounds, Movie from File does not accept .gif format.

    Can someone familiar with animations in PowerPoint please advise?

    Thanks, -Eric
    /* - - - - - - - - - - - - - - - - - - - - - - - - - - -
    The Protein Explorer: http://proteinexplorer.org
    Workshops: http://www.umass.edu/molvis/workshop
    World Index of Molecular Visualization Resources: http://molvisindex.org
    PDB Lite molecule finder: http://pdblite.org
    Molecular Visualization EMail List:
          http://www.umass.edu/microbio/rasmol/raslist.htm

    Eric Martz, Professor (Immunology), Dept Microbiology
    U Mass, Amherst MA US  413-545-2325/FAX 413-545-2532
                  http://www.umass.edu/molvis/martz
    - - - - - - - - - - - - - - - - - - - - - - - - - - - */


--Boundary_(ID_Dz9ygyyBQ/KzoBAR02qeCw)-- ++++------+------+------+------+------+------+------+------+------+------+ From: christian.simon@ppce.jussieu.fr (Christian Simon) Subject: Re: animated gifs in powerpoint? Date: Mon, 03 Jun 2002 20:43:37 +0200 (FRA Ete) To: rasmol@lists.umass.edu Dear Eric, What system are you running ? Windows ? > Can someone familiar with animations in PowerPoint please advise? I had the same kind of problems under Windows98, with mpeg files: the mpeg type was not appearing in the menu. I could insert it only as static image. I solved it in following the hints given at: www.iats.missouri.edu/servlets/knowledgebase/article/18926 I hope this helps. -- Christian SIMON, PhD The Center for Molecular Modeling (CMM, Rm. 141I) University of Pennsylvania, Tel: (215)-573-4773 Department of Chemistry, Box 127 Fax: (215)-573-6233 231 S. 34th St. Philadelphia, PA 19104-6323 USA ----------------------------------------------------------------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: <200206031719.g53HJ5h15265@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: animated gifs in powerpoint? Date: Mon, 03 Jun 2002 14:54:43 -0400 To: rasmol@lists.umass.edu Thanks for the quick replies to my question.

At 6/3/02, Ricky Cox wrote:
Eric-

You should be able to insert an animated gif (as you describe below starting with insert) into a powerpoint presentation and have it activate as soon as you "view show".=A0 I just did that successfully with the file you mentioned.=A0 I am not sure if the version of Powerpoint is critical.=A0 I am using the Office 2000 version.

Thanks, Ricky. Are you using Windows or Macintosh? (I use Windows.)
What version of PowerPoint are you using (run PowerPoint, pull down the Help menu, click on About Powerpoint)? I am using PowerPoint 97 SP1. I notice that one can download Office Converter Pack for Office 97 users (http://office.microsoft.com/downloads/9798/Convpack.aspx) but it doesn't mention animated GIF files so I haven't done it.

It appears that PowerPoint 2000 has direct support for animated GIFs:
http://office.microsoft.com/assistance/2000/ppanimat.asp= x

So I'm coming to the conclusion that PowerPoint 97 can't animate GIFs, but requires that they be converted to AVI format. Alternatively, one can upgrade to PP 2000.

/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
The Protein Explorer: http://proteinexplorer.org
World Index of Molecular Visualization Resources: http://molvisindex.org
PDB Lite molecule finder: http://pdblite.org
Molecular Visualization EMail List:

Eric Martz, Professor (Immunology), 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: Markus Winter Subject: Re: animated gifs in powerpoint? Date: Tue, 04 Jun 2002 09:32:14 +1200 To: rasmol@lists.umass.edu > Is it possible to insert animated GIF files into PowerPoint, and have them > animate? Seems to be version dependend - PP98 on a Mac does not animate them, PP2001 on a Mac does. Best Regards Markus -- Dr. Markus Winter Tel: 0064 (0)9 373 7599 (wait for message then type extension) 3960 ----------------------------------------------------------------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 (X11; U; Linux i686; en-US; rv:0.9.4.1) Gecko/20020314 Netscape6/6.2.2 X-Accept-Language: en-us References: <200206032127.ADY73135@mailhost-mp.auckland.ac.nz> ++++------+------+------+------+------+------+------+------+------+------+ From: mike Subject: Re: animated gifs in powerpoint? Date: Mon, 03 Jun 2002 17:30:51 -0700 To: rasmol@lists.umass.edu there is also ** pdfscreen **: http://www.ctan.org/tex-archive/macros/latex/contrib/supported/pdfscreen/manual-screen.pdf which allows embedding MPEGs etc... in v. nice presentations. Mike (new subscriber) ----------------------------------------------------------------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: Joel Kowit Subject: Re: Directions for "Three Frame for Chime" Date: Mon, 03 Jun 2002 21:40:09 -0400 To: rasmol@lists.umass.edu rasmol@lists.umass.edu writes: >Joel: > >I have set up Chime presentations that allows one to view multiple >windows of the same protein or different proteins on the same page. >Some of these presentations use a remote control to minimize window >scrolling. All the Javascript may be easily viewed for custom >changes. See the following link to the presentations (also listed on >Eric's worldwide directory). > >http://www.siu.edu/departments/biochem/chime_rasmol/instruct.htm > >Eric Niederhoffer ----------------------------------------------------------------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: prohibited boundary="Boundary_(ID_Q7CyBNzUcrMRmDnKfKCc+Q)" X-MIMETrack: Serialize by Router on USMAIL12/AM/LLY(Release 5.0.10 |March 22, 2002) at 06/04/2002 09:43:00 AM, Serialize complete at 06/04/2002 09:43:00 AM ++++------+------+------+------+------+------+------+------+------+------+ From: BRIGGS_STEPHEN_L@LILLY.COM Subject: Re: animated gifs in PowerPoint Date: Tue, 04 Jun 2002 09:43:11 -0500 To: rasmol@lists.umass.edu Cc: owner-rasmol@lists.umass.edu, rasmol@lists.umass.edu This is a multipart message in MIME format. --Boundary_(ID_Q7CyBNzUcrMRmDnKfKCc+Q) I finally got it to work. I have tried several times in the past to get these animation files to work in PowerPoint, but I always ended up with the first frame as a still. For those of us that are somewhat not in sync with the guru's I am going to show you how I did it - step by step: Using several, recent, suggestions, I created a file on the desktop- called PowerPoint. Made a shortcut from my file powerpoint.exe into the desktop file. From the web site, Animation example: http://molvis.sdsc.edu/protexpl/efhandm.gif Found the animation and saved file: as_a.gif file to the desk top PowerPoint folder. Then go to desktop folder: shortcut for powerpoint.exe My Version: Microsoft Office\Office\PowerPoint 2000 SR-1 Open PowerPoint: You get the Auto content Wizard, click next, select All, click next, Select On screen presentation, click next, enter title, click next, and finish. Then: Go to Insert, select picture, select from file It will then prompt you for file location: desk top, PowerPoint and then select the gif file, then click on INSERT You should see your first picture immediately as a still! Go to top of menu: select view, then select slide show Your program should immediately run in animation! very best, Steve christian.simon@ppce.jussieu.fr (Christian Simon) Sent by: owner-rasmol@lists.umass.edu 06/03/2002 01:43 PM Please respond to rasmol To: rasmol@lists.umass.edu cc: Subject: Re: animated gifs in powerpoint? Dear Eric, What system are you running ? Windows ? > Can someone familiar with animations in PowerPoint please advise? I had the same kind of problems under Windows98, with mpeg files: the mpeg type was not appearing in the menu. I could insert it only as static image. I solved it in following the hints given at: www.iats.missouri.edu/servlets/knowledgebase/article/18926 I hope this helps. -- Christian SIMON, PhD The Center for Molecular Modeling (CMM, Rm. 141I) University of Pennsylvania, Tel: (215)-573-4773 Department of Chemistry, Box 127 Fax: (215)-573-6233 231 S. 34th St. Philadelphia, PA 19104-6323 USA --Boundary_(ID_Q7CyBNzUcrMRmDnKfKCc+Q)
I finally got it to work.  I have tried several times in the past to get these animation files to work in PowerPoint,
but I always ended up with the first frame as a still.
For those of us that are somewhat not in sync with the guru's I am going to show you how I did it - step by step:

Using several, recent, suggestions, I created a file on the desktop- called PowerPoint.
Made a shortcut from my file powerpoint.exe into the desktop file.  From the web site,
Animation example:    http://molvis.sdsc.edu/protexpl/efhandm.gif
Found the animation and saved file:  as_a.gif file to the desk top PowerPoint folder.

Then go to desktop folder:  shortcut for powerpoint.exe
My Version: Microsoft Office\Office\PowerPoint   2000 SR-1

Open PowerPoint: You get the Auto content Wizard, click next, select All, click next,
Select On screen presentation, click next, enter title, click next, and finish.

Then:
Go to Insert, select picture, select from file
It will then prompt you for file location:  desk top, PowerPoint and then select the
gif file, then click on INSERT

You should see your first picture immediately as a still!
Go to top of menu:  select view, then select slide show

Your program should immediately run in animation!

very best,

Steve


christian.simon@ppce.jussieu.fr (Christian Simon)
Sent by: owner-rasmol@lists.umass.edu

06/03/2002 01:43 PM
Please respond to rasmol

       
        To:        rasmol@lists.umass.edu
        cc:        
        Subject:        Re: animated gifs in powerpoint?



Dear Eric,

What system are you running ? Windows ?

> Can someone familiar with animations in PowerPoint please advise?

I had the same kind of problems under Windows98, with mpeg files: the mpeg
type was not appearing in the menu. I could insert it only as static image.
I solved it in following the hints given at:

www.iats.missouri.edu/servlets/knowledgebase/article/18926

I hope this helps.
--
Christian SIMON, PhD
The Center for Molecular Modeling  (CMM, Rm. 141I)
University of Pennsylvania,        Tel: (215)-573-4773
Department of Chemistry, Box 127   Fax: (215)-573-6233
231 S. 34th St.
Philadelphia, PA 19104-6323 USA

--Boundary_(ID_Q7CyBNzUcrMRmDnKfKCc+Q)-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Gopalan Vivek Subject: XdomView-Chime tool for Protein Domain and Exon Position Visualization Date: Tue, 04 Jun 2002 14:20:25 +0800 To: rasmol@lists.umass.edu Dear all, For those of you interested in protein structure and gene evolution - I have developed a chime based visualization tool called XdomView to study protein domain and exon position correspondence. It is available at http://surya.bic.nus.edu.sg/xdom/. I'd appreciate your views and suggestions! Thanking you G.Vivek Bioinformatics Center Block MD7 #02-07 BioChemistry Department National University of Singapore Singapore 119260 http://surya.bic.nus.edu.sg/~vivek Off Tel : (65) 68744459 ----------------------------------------------------------------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 (X11; U; Linux i686; en-US; rv:0.9.9) Gecko/20020513 X-Accept-Language: en-us, en References: <200206032127.ADY73135@mailhost-mp.auckland.ac.nz> <3CFC0A3B.8090602@salk.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Douglas Kojetin Subject: chime - multiple per page Date: Tue, 04 Jun 2002 17:29:15 -0400 To: rasmol@lists.umass.edu Hello- I think this was recently posted, but I accidently erased the email. Can someone forward me the email or a website explaining how to set up multiple instances of CHIME on one page? Thanks, Doug ----------------------------------------------------------------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/10.0.0.1309 X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id g54LuGh27783 ++++------+------+------+------+------+------+------+------+------+------+ From: "James W. Caras" Subject: Chime and Macs Date: Tue, 04 Jun 2002 16:57:32 -0500 To: rasmol@lists.umass.edu Hello everyone- I have been very troubled by the dwindling browser support for Chime of late, and have been following the discussions on this list and elsewhere that relate to this very closely. While there has been a lot of talk regarding support on the Windows side, very little has been said about the Mac (besides that you must use Navigator 4, and the >1GB fiasco, if you are so lucky as to have this problem). If you are a Chime fan using a Windows PC, things are bad. If you are an avid Mac user (I know I can count myself and the ever helpful Tim Driscoll in this camp), things are downright bleak. For Chime on a PC, Chime developers such as Jean-Philippe Demers and Eric Martz have been very creative trying to work around Internet Explorer's (IE) troubles with LiveConnect, trying to maintain functionality with IE. Unfortunately, these solutions do not work in any manner for the Mac. Navigator 4 is a strict requirement for Chime modules with any scripting involved. For everyone's benefit, I have taken the time to compile what I know on the Mac side regarding browser compatibility, including non-traditional browsers such as Opera. I would appreciate anyone's input regarding the following information, and will take all comments (especially what is known on the PC side) and fill out this document and re-post it when the comments stop rolling in. You might want to email me directly, since I will be re-posting the info anyway. I would also appreciate anyone's input as to whether MDL has dropped all notions of supporting the Mac (having a strict requirement for a browser that is so old that it is barely offered for download at Netscape is not support). Here is the info-- CHIME COMPATIBILITY ++++++++++++++++++++++++++++++++++++ >>> NETSCAPE 4 <<< Mac: OS 8 (Netscape Navigator 4.08, Original Powerbook G3, PowerMac 7100)-yes OS 9 (Netscape Navigator 4.08, Original Powerbook G3)-yes OS X running in "classic mode" (Netscape Navigator 4.08, G4 tower)-yes-yes, howver once OS X is installed on computers with >1GB memory, it appears Chime only runs in Classic mode, and will not run if rebooted to OS 9 (strange) Windows: Windows 95-yes windows 98-yes Windows ME-yes Windows NT-yes Windows 2000-yes Windows XP-haven't tested, but should work? ++++++++++++++++++++++++++++++++++++ >>> NETSCAPE 6 <<< Mac: OS X (NS 6.2 OS X native, G4 tower)-No. Although people state they have gotten it to work after fixing the following problem: the installer installed the chime plug-ins inside a "plug-ins" folder, that was inside the main "plug-ins" folder. I tried moving the plug-ins into the maIn "plug-ins" folder (as other people claim success doing). Still didn't work on a simple page. I cannot even see the plug-in and file type listed in the "helper applications" of the preferences. I cannot see any other plug-ins here either, or even in the "plug-ins" folder itself, despite that I know the browser displays Flash content just fine (where is the Flash Plug-in???). it is likely using the common "Internet Plugins" in the system library (have not verified this). Windows: Doubt it works, according to everything I have read. ++++++++++++++++++++++++++++++++++++ >>> INTERNET EXPLORER <<< Mac: OS X (IE 5.1 OS X native, G4 tower)-No. The installer installed the chime plug-ins inside a "plug-ins" folder, that was inside the main "plug-ins" folder. I tried opening a PDB file from the open command and dragging into the window, but nothing happened. I then tried to view an html page with an embedded pdb, but then got the "You do not have the plug-in needed to view..." message. I quit IE, moved the three files installed by Chime up one directory, into the main "plug-ins" folder. Got the same results. I cannot even see the plug-in and file type listed in the "file helpers" of the preferences. OS X (IE 5 made for OS 9 running in "classic" mode, G4 tower)-Barely. I can load pdb files into the browser window, and they will show and the menu will kindof work (seemed OK but the display command gives me a list of files on my hard drive initially, then corrects itself later). If I try a web page with embedded chime with a small script or with no scripts at all, does not work. PDB files can be loaded directly into frames, but again, not loaded into frames within the context of an embed command on an HTML page. OS 9 (IE 5, Original G3 Powerbook)-Barely. The installer installed the chime plug-ins inside a "plug-ins" folder, that was inside the main "plug-ins" folder, whether I changed this or not had no effect on the final result. I can load pdb files into the browser window. If I try a web page with embedded chime with a small script or with no scripts at all, does not work. Windows: IE appears to have some functionality, but LiveConnect is very messy. Some javascript solutions help parse commands so that IE can be more reliable. ++++++++++++++++++++++++++++++++++++ >>> MOZILLA <<< Mac: OS X (G4 tower, Mozilla 1.0)-No. Mimics the behavior of NS6 (as you would predict). I tried moving the plug-ins into the man "plug-ins" folder (as other people claim success doing), so that it resided in (path): Mozilla/Contents/MacOS/Plug-ins. Still didn't work on a simple page. I cannot even see the plug-in and file type listed in the "helper applications" of the preferences. Windows: People state they have gotten it to work (in Windows) after fixing the following problem: the installer installed the Chime plug-ins inside a "plug-ins" folder, that was inside the main "plug-ins" folder. They simply moved the files up one directory level. (I cannot remember where I saw this). >From the Oregon chemistry 336 website (http://www.chem.orst.edu/ch336/)-Versions up to and including 6.2 and the Mozilla browser can view plugin structures.  There may be difficulties with printing. Have not verified this. ++++++++++++++++++++++++++++++++++++ >>> OPERA <<< Mac: OS X (Opera 5beta - OS X native, G4 tower)-No. When viewing a PDB file locally, simply dispays as text. I had trouble telling where plug-ins should be installed, for there was no plug-ins folder in the Opera application directory nor within the hidden package contents. Tied adding a "Plug-ins" folder to the application directory, to no avail. Then deleted this and tried to add the three Chime files added to browsers by the Chime installer to the "Internet Plug-ins" folder in the System Library (which apparently Opera uses), but got same result. Since the preferences option for Windows: Apparently, Chime will work on Opera for the PC with a strange installation process where you rename the Opera.exe file as Netscape.exe. The Chime installer will install the plugin files into Opera and it will work (haven't tested this). (from Opera's Support web page) 1. Download Chime from MDL Information Systems, Inc. 2. Close Opera and rename Opera.exe to Netscape.exe 3. Double-click the downloaded plug-in intallation file to start the installation wizard. Follow the on-screen instructions to install the program. 4. The installer will ask you what method you would like to use for finding the web browser for which Chime will be installed. You should select "Specify the location of a web browser", then click on "Next". 5. The installation program will then request that you specify the folder directly above the Plugins folder for the target browser. Click on "Browse" and find the folder "C:\Program Files\Opera". Click on "OK", then click "Next" to complete the installation. 6. Rename Netscape.exe back to Opera.exe 7. In Opera, pull down the "File" menu and choose Preferences/Plugins. Press the "Find Plugins" button. Opera will locate the plug-in and associate it with Chime files. (From Tamas E. Gunda's Chime page) Having installed Opera, you may want to recheck the use of plugins: open File | Preferences, select Plugins. Enable everything, and press the Find plugins button. In the file list box you should see the plugin folder of Netscape. If not, the opera.ini file should be modified, as written in the Help. The following line should be seen (or entered) in opera.ini (can be found in the parent Opera folder): Plugin Path=C:\Program Files\Opera\Program\Plugins;C:\PROGRAM FILES\NETSCAPE\COMMUNICATOR\PROGRAM\Plugins; ++++++++++++++++++++++++++++++++++++ >>> OTHERS (ICAB, ETC???) <<< Best Regards, Jamie ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ /|||X|||\ X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X|||/ \|||X `-' `-' `-' `-' `-' `-' `-' `-' `-' `-' Dr. James Caras Principal Science Technologies 5410 Avenue G Austin, TX 78751 jcaras@sciencetechnologies.com http://www.sciencetechnologies.com (512) 467-8842 ----------------------------------------------------------------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: Frank Johnston Subject: Re: Chime and Macs Date: Wed, 05 Jun 2002 09:41:53 -0300 To: rasmol@lists.umass.edu Dr. James Caras: ICab (OS9) works as a viewer with 2.0a and 2.7.1 plugins. 'Not recognized as compatible by protein Explorer. I use RasMol as a helper application for dowloaded files. Yours Frank Johnston Frank P. Johnston 166 Basin ST Grand Falls NB Canada E3Z 1J2 ----------------------------------------------------------------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: Chime and Macs Date: Wed, 05 Jun 2002 09:58:08 -0400 To: rasmol@lists.umass.edu it was 4:57 PM EDT on (Tuesday) 4 June 2002 when James W. Caras said: > Hello everyone- > > For everyone's benefit, I have taken the time to compile what I know on > the Mac side regarding browser compatibility, including non-traditional > browsers such as Opera. I would appreciate anyone's input regarding the > following information, and will take all comments (especially what is > known on the PC side) and fill out this document and re-post it when the > comments stop rolling in. You might want to email me directly, since I > will be re-posting the info anyway. > hi Jamie, nice doc - depressing, but nice. I generally agree with your assessment. I can add specific details about my Mac setups here if you want, but we can take that off-list. however, I've been testing Chime in iCab, a Mac-only browser, and I wanted to share some preliminary info with the list. maybe others can add to it; I will doing more testing in the near future. ************************** iCab I have iCab 2.8 with Chime 2.6SP3 installed running under OS 9.2.2. the installation went without incident. (G3, 350 MHz, 192MB RAM.) I also have all NC versions between 4.5-4.79, and IE5 installed on this machine. iCab allows an unparalleled amount of user customization. you can tell it which javascript versions to recognize, how it identifies itself to server-side queries, etc. I have it recognizing all possible JS and JScript versions, all cookies accepted, and masquerading as Netscape 4.72 to get past web site screens. under this setup, I can view pdb files in iCab via drag-and-drop, or from a web site. so far, I have not been able to run external script files successfully in iCab. I am still investigating exactly why, and where the process breaks down. Protein Explorer 1.901b (the IE-compatible version) does load, but a structure does not appear and the plug-in, while apparent, appears to be nonfunctional. I assume for now that it is related to the script problem. I will continue to test the viability of Chime scripts in iCab, and I will begin testing the OS X version, too. I will be testing the effects of various other settings on Chime use as well. ************************** > I would also appreciate anyone's input as to whether MDL has dropped all > notions of supporting the Mac (having a strict requirement for a browser > that is so old that it is barely offered for download at Netscape is not > support). > good luck. people with much, much (MUCH) bigger names than I have tried to pry open MDL for access or, at least, info. you would think they were protecting Fort Knox. no amount of compromise seems to be good enough for them - as if Chime were somehow the linchpin of their entire empire. at one point, one of my clients offered to pay a third-party developer to make several minor changes to the Chime source code, then GIVE the compiled version back to MDL with no strings attached. even this was not acceptable. the last four upgrades to Chime have been all but useless (essentially since version 2). their lack of support for Mac, UNIX, and other platforms popular with students and educators is bullsh*t. their Web site is a joke, as are the forums, and they refuse to participate in, actively monitor, or post announcements on any of the existing lists (including this one). even worse, despite repeated outcries, they refuse to address even miniscule bugs that could have a substantial effect on the usefulness of Chime - not to mention pacifying a lot of users, who want just some hint that MDL is still interested in supporting Chime. AFAIK, most if not all requests fail to even elicit a "we're aware of the problem" comment. this forces developers to implement, test, and support such laborious patches and work-arounds that the creation of new resources often grinds to a halt. (yes, personal experience.) I feel that I've been patient for a long time (as a devoted Mac user, I've learned to wait for Mac support). recently, my patience has worn quite thin. based on the past 18 months or so of observation, I've decided that either MDL doesn't care or they are incompetent. I would welcome any response from MDL, even a scathing one, that offers an alternative interpretation. go ahead and rip me to shreds, but give us a morsel. at the moment, my livelihood depends on being able to reach users on a variety of platforms. at a bare minimum, that means Mac, UNIX, LINUX, and Windows. I am disgusted with MDL but, even worse, my clients are disgusted with MDL. and so tolls the death knell for me. FWIW, I will struggle with Chime for a short while longer and then, barring a complete reversal of the current situation, I will port everything I've ever done to a different format and drop Chime like a bad habit. my apologies to the list for ranting. feel free to charge me the standard therapist's fee - split equally, of course. just put it on my tab ;-) regards, tim -- molvisions - 3D molecular visualization waltham, ma usa ----------------------------------------------------------------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 g567J9h12334 ++++------+------+------+------+------+------+------+------+------+------+ From: Jean Richelle Subject: Re: Chime and Macs Date: Thu, 06 Jun 2002 09:18:26 +0200 To: rasmol@lists.umass.edu Hello, I completely agree with the position and complaints of Timothy. Would it be possible to start an "oChime", i.e. the development of an open source rasmol plugin that would be really multiplatform ? Jean > > I would also appreciate anyone's input as to whether MDL has dropped all >> notions of supporting the Mac (having a strict requirement for a browser >> that is so old that it is barely offered for download at Netscape is not >> support). >> > >good luck. people with much, much (MUCH) bigger names than I have tried to >pry open MDL for access or, at least, info. you would think they were >protecting Fort Knox. no amount of compromise seems to be good enough for >them - as if Chime were somehow the linchpin of their entire empire. at one >point, one of my clients offered to pay a third-party developer to make >several minor changes to the Chime source code, then GIVE the compiled >version back to MDL with no strings attached. even this was not acceptable. > >the last four upgrades to Chime have been all but useless (essentially since >version 2). their lack of support for Mac, UNIX, and other platforms >popular with students and educators is bullsh*t. their Web site is a joke, >as are the forums, and they refuse to participate in, actively monitor, or >post announcements on any of the existing lists (including this one). even >worse, despite repeated outcries, they refuse to address even miniscule bugs >that could have a substantial effect on the usefulness of Chime - not to >mention pacifying a lot of users, who want just some hint that MDL is still >interested in supporting Chime. AFAIK, most if not all requests fail to >even elicit a "we're aware of the problem" comment. this forces developers >to implement, test, and support such laborious patches and work-arounds that >the creation of new resources often grinds to a halt. (yes, personal >experience.) > >I feel that I've been patient for a long time (as a devoted Mac user, I've >learned to wait for Mac support). recently, my patience has worn quite >thin. based on the past 18 months or so of observation, I've decided that >either MDL doesn't care or they are incompetent. I would welcome any >response from MDL, even a scathing one, that offers an alternative >interpretation. go ahead and rip me to shreds, but give us a morsel. > >at the moment, my livelihood depends on being able to reach users on a >variety of platforms. at a bare minimum, that means Mac, UNIX, LINUX, and >Windows. I am disgusted with MDL but, even worse, my clients are disgusted >with MDL. and so tolls the death knell for me. FWIW, I will struggle with >Chime for a short while longer and then, barring a complete reversal of the >current situation, I will port everything I've ever done to a different >format and drop Chime like a bad habit. > _____________________________________________________________________________ Jean Richelle Service de Conformation des Macromolécules Biologiques Tel: +32 02 650 3587 et de Bioinformatique - Université libre de Bruxelles FAX: +32 02 648 8954 av. F.D. Roosevelt 50 - CP160/16, B-1050 Bruxelles, Belgium _____________________________________________________________________________ ----------------------------------------------------------------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-Accept-Language: en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Hens Borkent Subject: Re: Chime Date: Thu, 06 Jun 2002 09:37:37 +0200 To: rasmol@lists.umass.edu Jean Richelle wrote: > Hello, > > I completely agree with the position and complaints of Timothy. > > Would it be possible to start an "oChime", i.e. the development of an > open source rasmol plugin that would be really multiplatform ? > > Jean > > Well, that is what Java was meant for. We made a start with a Chime replacing Java applet (codename Jaime), based on Java3D, and I'd just like to know other peoples opinion on this approach. Currently it reads multi-XYZ and MOPAC input files (no PDB yet, we are in organic chemistry), and it sports a beginning of a rasmol-like scripting mechanism. Try, if you have installed a recent Java3D, http://www.cmbi.kun.nl/~borkent/jaime/test.html Hens -- Dr. J.H. (Hens) Borkent, CMBI, University of Nijmegen P.O. Box 9010, 6500 GL Nijmegen, The Netherlands Tel 0031 24 3652137 Fax 0031 24 3652977 http://www.cmbi.kun.nl/ Centre for Molecular and Biomolecular Informatics ----------------------------------------------------------------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-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by marlin.bio.umass.edu id g569sbh13664 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Chime and Macs Date: Thu, 06 Jun 2002 05:52:07 -0400 (EDT) To: rasmol@lists.umass.edu I am fully in favor of creating a new branch of the open-source RasMol 2.7 series to work within browsers. If we do not have MDL's cooperation, then we need a volunteer to do it as a "clean-room" project. In other words, we need a person who has _never_ downloaded or used Chime, who is familiar with molecular graphics and C/C++ programming, and who has some time free to do a plug-in conversion starting from RasMol 2.7. It is important that the person do the basic plug-in conversion without looking at Chime at all. We can, as a community, worry about necessary realignment of features after we have a solid open-source base plug-in. It would be a great project for a really sharp undergraduate Computer Science or Bioinformatics student. It could even make the base for a Master's thesis. Who knows. Maybe if we go ahead and do this, and do it well, MDL will see the open-source light and decide to cooperate, but I would agree with the suggestion that it is time to go ahead without them. As part of the NSF-funded Accessible Retired Computers in Biology (ARCiB) project we are building a collection of interesting older computers at Dowling. We will be happy to cooperate in multi-platform ports and compatibility tests of a new open source RasMol Browser Plugin. Any clean-room volunteers? -- H. J. Bernstein ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 020 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Thu, 6 Jun 2002, Jean Richelle wrote: > Hello, > > I completely agree with the position and complaints of Timothy. > > Would it be possible to start an "oChime", i.e. the development of an > open source rasmol plugin that would be really multiplatform ? > > Jean > > > > I would also appreciate anyone's input as to whether MDL has dropped all > >> notions of supporting the Mac (having a strict requirement for a browser > >> that is so old that it is barely offered for download at Netscape is not > >> support). > >> > > > >good luck. people with much, much (MUCH) bigger names than I have tried to > >pry open MDL for access or, at least, info. you would think they were > >protecting Fort Knox. no amount of compromise seems to be good enough for > >them - as if Chime were somehow the linchpin of their entire empire. at one > >point, one of my clients offered to pay a third-party developer to make > >several minor changes to the Chime source code, then GIVE the compiled > >version back to MDL with no strings attached. even this was not acceptable. > > > >the last four upgrades to Chime have been all but useless (essentially since > >version 2). their lack of support for Mac, UNIX, and other platforms > >popular with students and educators is bullsh*t. their Web site is a joke, > >as are the forums, and they refuse to participate in, actively monitor, or > >post announcements on any of the existing lists (including this one). even > >worse, despite repeated outcries, they refuse to address even miniscule bugs > >that could have a substantial effect on the usefulness of Chime - not to > >mention pacifying a lot of users, who want just some hint that MDL is still > >interested in supporting Chime. AFAIK, most if not all requests fail to > >even elicit a "we're aware of the problem" comment. this forces developers > >to implement, test, and support such laborious patches and work-arounds that > >the creation of new resources often grinds to a halt. (yes, personal > >experience.) > > > >I feel that I've been patient for a long time (as a devoted Mac user, I've > >learned to wait for Mac support). recently, my patience has worn quite > >thin. based on the past 18 months or so of observation, I've decided that > >either MDL doesn't care or they are incompetent. I would welcome any > >response from MDL, even a scathing one, that offers an alternative > >interpretation. go ahead and rip me to shreds, but give us a morsel. > > > >at the moment, my livelihood depends on being able to reach users on a > >variety of platforms. at a bare minimum, that means Mac, UNIX, LINUX, and > >Windows. I am disgusted with MDL but, even worse, my clients are disgusted > >with MDL. and so tolls the death knell for me. FWIW, I will struggle with > >Chime for a short while longer and then, barring a complete reversal of the > >current situation, I will port everything I've ever done to a different > >format and drop Chime like a bad habit. > > > _____________________________________________________________________________ > Jean Richelle > Service de Conformation des Macromolécules Biologiques Tel: +32 02 650 3587 > et de Bioinformatique - Université libre de Bruxelles FAX: +32 02 648 8954 > av. F.D. Roosevelt 50 - CP160/16, B-1050 Bruxelles, Belgium > _____________________________________________________________________________ > > ----------------------------------------------------------------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: <200206031853.g53Ir8h19902@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Fwd: Re: animated gifs in powerpoint? Date: Thu, 06 Jun 2002 12:39:29 -0700 To: rasmol@lists.umass.edu Cc: Chris Woodcock At 6/5/02, Chris Woodcock wrote: >Eric, > Thanks for following up on the powerpoint question. > > As it happens, I do have ppt 2000 on a new laptop and tried the .gif files >there. Now they do indeed rotate, but the motion is so jerky (not slow) >that the impact and sense of 3D is lost. The laptop has lots of speed and >memory, so I don't think that's the problem. > > This is not a request for help - I think I can do a .gif to .avi >conversion on our SGI box - just an FYI about powerpoint 2000. > >Chris > Does anyone have any suggestions? Are there settings in PowerPoint that would affect this? Chris is comparing the motion to the way the animated GIF files run in Netscape or IE. An example of one of the images Chris is working with (about 4 megs, 300 x 300, 72 frames, created with Andreas Bohne's PDB2MGIF) is: http://www.umass.edu/microbio/chime/beta/woodcock/1aoi_2.gif Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), 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-- References: <200206031853.g53Ir8h19902@marlin.bio.umass.edu> <200206061632.g56GWhh25414@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: Re: Fwd: Re: animated gifs in powerpoint? Date: Thu, 06 Jun 2002 12:40:05 -0400 To: rasmol@lists.umass.edu Cc: Chris Woodcock At 12:39 PM -0700 6/6/02, Eric Martz wrote: >Now they do indeed rotate, but the motion is so jerky (not slow) > >that the impact and sense of 3D is lost. The laptop has lots of speed and > >memory, so I don't think that's the problem. Have you checked on how much memory is allocated to the PowerPoint application? Increasing the preferred and the minimum RAM for PowerPoint might solve the problem. On a Mac, highlight the icon for the program and press command-I to get the memory dialog. Increase the preferred first, then the minimum. Experiment with different amounts to see if a certain level of memory allocation will do the trick. I am not sure how to make this adjustment on a PC. Frieda -- Frieda S. Reichsman, Ph.D. 30 South Whitney Street Molecules In Motion Amherst MA 01002 USA Interactive Molecular Structures (413) 253-2405 http://www.MoleculesInMotion.com http://www.bio.umass.edu/biochem/mydna ----------------------------------------------------------------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: Fwd: Re: animated gifs in powerpoint? Date: Thu, 06 Jun 2002 13:04:30 -0400 To: rasmol@lists.umass.edu Cc: Chris Woodcock it was 12:40 PM EDT on (Thursday) 6 June 2002 when Frieda Reichsman said: > At 12:39 PM -0700 6/6/02, Eric Martz wrote: > >Now they do indeed rotate, but the motion is so jerky (not slow) > > that the impact and sense of 3D is lost. The laptop has lots of speed > > and memory, so I don't think that's the problem. > > Have you checked on how much memory is allocated to the PowerPoint > application? Increa