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? 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 I second Frieda's suggestion, at least for Mac OS 9.2.2 and earlier. OS X and Windows handle RAM differently, and you do not have to allocate it in this manner. of course, if you don't have enough RAM on your machine then you'll run into problems no matter your OS. sorry I can't speak to the animated gif issue directly - I don't use PowerPoint. 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-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: animated gifs in powerpoint? Date: Thu, 06 Jun 2002 13:38:16 -0700 To: rasmol@lists.umass.edu Cc: chris@bio.umass.edu [Redirected to the list to circumvent technical difficulties. -Eric Martz] >Date: Thu, 06 Jun 2002 17:59:30 +0100 >From: Andy Bates >Subject: Re: Fwd: Re: animated gifs in powerpoint? >To: rasmol@lists.umass.edu > >Folks, > >I agree with this - the file below is very jerky in PP2001 on a 933 MHz G4 >Mac with loads of RAM - can't really be anything to do with the machine. >The only control I can find is a option to allow animation of gifs or not, >nothing to do with quality. > >Andy Bates >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 > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Thu, 06 Jun 2002 12:39:42 -0500 To: rasmol@lists.umass.edu In my opinion, the fact that the file (1aoi_2.gif) is 4.3 MB is the problem.  That is an extremely large animated .gif file.  It runs slow even on a 2 GHz P4 machine (running Windows 2000) with 500 MB of RAM.

Ricky

At 01:38 PM 6/6/2002 -0700, you wrote:
[Redirected to the list to circumvent technical difficulties. -Eric Martz]

>Date: Thu, 06 Jun 2002 17:59:30 +0100
>From: Andy Bates <A.D.Bates@liverpool.ac.uk>
>Subject: Re: Fwd: Re: animated gifs in powerpoint?
>To: rasmol@lists.umass.edu
>
>Folks,
>
>I agree with this - the file below is very jerky in PP2001 on a 933 MHz G4
>Mac with loads of RAM - can't really be anything to do with the machine.
>The only control I can find is a option to allow animation of gifs or not,
>nothing to do with quality.
>
>Andy Bates

>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
>

----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: animated gifs in powerpoint? Date: Thu, 06 Jun 2002 13:46:24 -0400 To: rasmol@lists.umass.edu hi Eric, have you thought about converting your PP slides to HTML instead? that would solve your animated gif problems, and give you more control over layout, distribution, portability, etc. my apologies; I usually find that sort of suggestion unhelpful myself; and I would guess that you have good reasons for using PP. OTOH, I tried both PP and HTML for presentations in grad school and found HTML superior. thought it might help here. 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: <200206061731.g56HVUh27591@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: Re: animated gifs in powerpoint? Date: Thu, 06 Jun 2002 14:17:55 -0400 To: rasmol@lists.umass.edu Cc: chris@bio.umass.edu >the file below is very jerky in PP2001 on a 933 MHz G4 > >Mac with loads of RAM - can't really be anything to do with the machine. >>The only control I can find is a option to allow animation of gifs or not, >>nothing to do with quality. >> >>Andy Bates I found that after I allow the file to finish downloading fully, it plays quite smoothly in Netscape 4.7 on a G3 PowerBook with 320 MB RAM. While the downloading is occurring (in the background) the gif plays quite choppily. Frieda > >>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 >> > -- 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-- User-Agent: Microsoft-Entourage/10.0.0.1309 ++++------+------+------+------+------+------+------+------+------+------+ From: "James W. Caras" Subject: Re: IE problems of scripts Date: Thu, 06 Jun 2002 14:15:41 -0500 To: rasmol@lists.umass.edu Hi all- Since my little email regarding Macs, I have gotten a number of responses addressing Chime support for Macs, which I will compile when I get enough information. However, I figured that while we are on the subject, I could follow up on a fairly recent (1 week) ago topic that also concerns the differences (and troubles) of cross-platform Chime scripting: The messages below deal with IE on windows and troubles that occur when using script files that are called. The solution presented was to put the scripts directly in the HTML. I have run into similar problems with Chime tutorials that I have developed, but this time it was the Mac that has the troubles, and the solution was exactly the opposite described below for the Windows IE pages. In IE 5 on Mac OS 9, Chime tutorials produced for the Boyer Concepts in Biochemistry textbook (www.boyerbiochem.com) work remarkably well, even though they call external scripts and use LiveConnect (note: IE5.1 running native on OSX fails miserably...this is probably where they abandoned plug-in support??). However, one of the tutorials, developed by someone who liked to place their scripts in the html, does not function on Mac IE5, and I am fairly sure that the failure occurs because the scripts were not sent to the plug-in through external files, though I have not thoroughly and meticulously investigated this. (For the site we simply state that Netscape is required for Chime, so were able to move past this problem). Note that this phenomenon is exactly the opposite of the fix that was prescribed for IE on Windows. For those of us who have to be cross-platform compliant, things are very sticky. We generally stock up on Midol. I hear you, Tim. Do not exceed 3 pills in a 4 hour period. One thing that does need to be explained that many people are not aware of is that IE on the Mac is very different than IE on Windows, for the Microsoft development team that produces Mac software works fairly independently from the Windows teams. This is true for Word, Excel, etc. as well. One example of this is plug-in detection. For Windows IE, you cannot access the navigator.plug-ins array for simple javascript plug-in detection, and have to detect using Visual Basic or other tricks. However, on the Mac, detecting Chime in IE5 is as easy as it is in Netscape Navigator. Jamie On 5/27/02 4:44 AM, "Tamas E. Gunda" wrote: > 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 ----- > From: "Paul Pillot" > To: > Sent: Sunday, May 26, 2002 00:19 > Subject: Re: IE problems > > >> 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 >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> >>> >>> >>> >>> >> >> >> > > > ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. /|||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-- References: <200206061731.g56HVUh27591@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: Re: animated gifs in powerpoint? Date: Thu, 06 Jun 2002 15:24:36 -0400 To: rasmol@lists.umass.edu Cc: chris@bio.umass.edu At 2:17 PM -0400 6/6/02, Frieda Reichsman wrote: > >I found that after I allow the file to finish downloading fully, it >plays quite smoothly in Netscape 4.7 on a G3 PowerBook with 320 MB >RAM. While the downloading is occurring (in the background) the gif >plays quite choppily. Sorry, I misunderstood Andy's comment on first reading, so my reply (above) is quite irrelevant. However, I still think the amount of memory specifically allocated to PowerPoint (as opposed to the RAM on the system) is relevant on a Mac. >> >>>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 >>> >> > > >-- >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 > -- 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: agc Subject: Re: Fwd: Re: animated gifs in powerpoint? Date: Thu, 06 Jun 2002 15:36:31 -0400 (EDT) To: rasmol@lists.umass.edu one option is to generate the animated gif file with different parameters, for example it is possible to speed up the frame transition (generating the gif animated file with gif construction set) another possible solution would be to generate the animation with flash more information about this may be found at http://www.macromedia.com/support/flash/ts/documents/flash_powerpoint.htm On Thu, 6 Jun 2002, Eric Martz wrote: > Date: Thu, 06 Jun 2002 12:39:29 -0700 > From: Eric Martz > To: rasmol@lists.umass.edu > Cc: Chris Woodcock > Subject: Re: Fwd: Re: animated gifs in powerpoint? > > 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-- 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: <5.1.0.14.0.20020606123637.026e4c30@murraystate.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: mike Subject: Re: animated gifs in powerpoint? Date: Thu, 06 Jun 2002 12:51:49 -0700 To: rasmol@lists.umass.edu > In my opinion, the fact that the file (1aoi_2.gif) is 4.3 MB is the > problem. That is an extremely large animated .gif file. It runs slow > even on a 2 GHz P4 machine (running Windows 2000) with 500 MB of RAM. size can be dealt with by making mpegs instead of gifs. animated gifs can be converted to mpegs rather easily using ImageMagick to defoliate the gif and then using mpeg2encode to create the mpeg. for example, a 25 Mb gif flip-book animation that I created from running rasmol with a Tcl script was only 2 Mb when I defoliated it and ran mpeg2encode on it (at maximum mpeg-1 bit rate). size can also be dealt with by making a pdf presentation (really slick) with embedded movies in this case a memory efficient, user specified external application run the gif/mpeg/.... http://www.imagemagick.org/ http://www.mpeg.org/MSSG/ http://www.ctan.org/tex-archive/help/Catalogue/entries/pdfscreen.html Mike ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <002301c20563$2a30af10$3b8506c1@cthulhu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: IE problems of scripts Date: Thu, 06 Jun 2002 16:03:27 -0700 To: rasmol@lists.umass.edu Dear James (Caras) and others struggling with Chime in IE: These comments pertain to Windows IE 5.5SP3/Chime 2.6SP3. I have no experience with Mac IE. As Paul Pillot pointed out in his original email to you, when Chime scripts access disk files (with "load" or "script" commands) in IE, scripts halt execution and various bizzare things happen. This is true even when the command script containing the file-referencing commands was sent to Chime via the IMBIF* method as a javascript string. Actually I don't know whether it is still true if the command script is a string within a Chime button embed tag. So, there are two layers of problems. If a disk file containing a script (.spt file) is sent to Chime in IE, and if it contains "load" or "script" commands, the problems appear too serious to work around. This first layer can be avoided by sending scripts to Chime via IMBIF or embed tag buttons (what you call "html" but actually the scripts are javascript character string variables, or character strings within embed tags). Avoiding the first layer, now we still have the second layer problem of "load" and "script" commands. I have succeeded with a button that loads a new PDB file and renders/colors it by sending the load command as a one-line script, waiting for Chime to report (via messageCallback) that the script is completed, then automaticaly sending a second script containing the rendering and coloring commands. If the second script contains no load, script, delay or move commands, it CAN be a .spt file. If it contains delay or move commands, it will work fine as long as it is sent via IMBIF. It won't work reliably if it contains load or script commands. (It may work the first time thru, but bizzare things happen later due to unexecuted commands buffered up within Chime that get executed later, triggered by subsequent scripts!) Again, my findings about IE vs. Chime are all detailed at http://www.umass.edu/microbio/chime/beta/pe_alpha/protexpl/ie.htm I am currently well along towards the goal of making my 1996 nonlinear DNA tutorial work in IE (on Windows) as well as Netscape (Windows and Mac). I will announce it here when it is released. I'd like to remind people starting to build new Chime resources that Jean-Philippe Demers, a college student in Montreal CA, has kindly provided a free Chime template that will work in both Netscape and IE, http://www3.sympatico.ca/diane.demers/moi/ Also he might be persuaded to convert existing Chime sites to work in IE if suitable compensation were offered. -Eric -------------- * IMBIF = Immediate Mode chime Button in Invisible Frame. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: animated gifs in powerpoint? Date: Thu, 06 Jun 2002 16:06:36 -0700 To: rasmol@lists.umass.edu Hi, Tim,

I personally do all my own slides in HTML -- but then my slides are mostly Chime pages! The question of animated GIFs arose because a colleague wishes to use them in PowerPoint, and because I'd like to document how to do it in the forthcoming revision of Protein Explorer's Help/Index/Glossary. It is a FAQ!

-Eric

At 6/6/02, you wrote:
>hi Eric,
>
>have you thought about converting your PP slides to HTML instead?=A0 that
>would solve your animated gif problems, and give you more control over
>layout, distribution, portability, etc.
>
>my apologies; I usually find that sort of suggestion unhelpful myself; and I
>would guess that you have good reasons for using PP.=A0 OTOH, I tried both PP
>and HTML for presentations in grad school and found HTML superior.=A0 thought
>it might help here.
>
>regards,
>
>tim
>--
>molvisions - 3D molecular visualization
>waltham, ma=A0 usa
><http://www.molvisions.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: <200206061731.g56HVUh27591@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: animated gifs in powerpoint? Date: Thu, 06 Jun 2002 16:22:07 -0700 To: rasmol@lists.umass.edu Cc: chris@bio.umass.edu OK, Ricky makes a good point about the 4 mB size of the original animated GIF I offered.
So, here is an animated GIF that weighs in at a measley 0.1 megabyte (100 kB).
http://www.umass.edu/microbio/chime/beta/pdb/gifs/an_dna3.gif

Will someone with PPT2000 give it a try? Please compare its appearance in Netscape or IE (after it has made one complete turn, thereby being fully downloaded, or saved to a local disk file and then opened in the browser) with its appearance in PPT2000. (Sorry, I have only PPT97 which we've established doesn't support animated GIFs.)

Also, I think all the reports for PPT2000 have been on Macs. What about Windows PPT2000? Does it give a smooth animation?

Thanks for all the help -- Eric

At 6/6/02, you wrote:
In my opinion, the fact that the file (1aoi_2.gif) is 4.3 MB is the problem. That is an extremely large animated .gif file. It runs slow even on a 2 GHz P4 machine (running Windows 2000) with 500 MB of RAM.

Ricky

>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
>


----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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_bs685kJOYc57OuT95DA6uA)" X-MSMail-priority: Normal References: <200206061959.g56Jxoh03995@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re: animated gifs in powerpoint? Date: Thu, 06 Jun 2002 22:50:19 +0200 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_bs685kJOYc57OuT95DA6uA) This is not exactly the question, but what about Accelrys WebLab viewer to diqplay molecular animations in PowerPoint presentations ? Does somebody use it ? Paul Pillot ----- Original Message ----- From: Eric Martz To: rasmol@lists.umass.edu Sent: Friday, June 07, 2002 1:06 AM Subject: Re: animated gifs in powerpoint? Hi, Tim, I personally do all my own slides in HTML -- but then my slides are mostly Chime pages! The question of animated GIFs arose because a colleague wishes to use them in PowerPoint, and because I'd like to document how to do it in the forthcoming revision of Protein Explorer's Help/Index/Glossary. It is a FAQ! -Eric At 6/6/02, you wrote: >hi Eric, > >have you thought about converting your PP slides to HTML instead? that >would solve your animated gif problems, and give you more control over >layout, distribution, portability, etc. > >my apologies; I usually find that sort of suggestion unhelpful myself; and I >would guess that you have good reasons for using PP. OTOH, I tried both PP >and HTML for presentations in grad school and found HTML superior. thought >it might help here. > >regards, > >tim >-- >molvisions - 3D molecular visualization >waltham, ma usa > --Boundary_(ID_bs685kJOYc57OuT95DA6uA)
This is not exactly the question, but what about Accelrys WebLab viewer to diqplay molecular animations in PowerPoint presentations ? Does somebody use it ?
 
Paul Pillot
----- Original Message -----
From: Eric Martz
Sent: Friday, June 07, 2002 1:06 AM
Subject: Re: animated gifs in powerpoint?

Hi, Tim,

I personally do all my own slides in HTML -- but then my slides are mostly Chime pages! The question of animated GIFs arose because a colleague wishes to use them in PowerPoint, and because I'd like to document how to do it in the forthcoming revision of Protein Explorer's Help/Index/Glossary. It is a FAQ!

-Eric

At 6/6/02, you wrote:
>hi Eric,
>
>have you thought about converting your PP slides to HTML instead?  that
>would solve your animated gif problems, and give you more control over
>layout, distribution, portability, etc.
>
>my apologies; I usually find that sort of suggestion unhelpful myself; and I
>would guess that you have good reasons for using PP.  OTOH, I tried both PP
>and HTML for presentations in grad school and found HTML superior.  thought
>it might help here.
>
>regards,
>
>tim
>--
>molvisions - 3D molecular visualization
>waltham, ma  usa
>< --Boundary_(ID_bs685kJOYc57OuT95DA6uA)-- Content-return: allowed boundary="Boundary_(ID_aOdI0EJfUuCCIn4a4ituAQ)" ++++------+------+------+------+------+------+------+------+------+------+ From: David Margulies Subject: RE: animated gifs in powerpoint? Date: Thu, 06 Jun 2002 17:30:45 -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_aOdI0EJfUuCCIn4a4ituAQ) Works fine in mac ppt2001 as long as first loaded from the web to desktop and then inserted as a movie file. If dragged from the web, only the static images stays. D > ---------- > From: Eric Martz > Reply To: rasmol@lists.umass.edu > Sent: Thursday, June 6, 2002 7:22 PM > To: rasmol@lists.umass.edu > Cc: chris@bio.umass.edu > Subject: Re: animated gifs in powerpoint? > > OK, Ricky makes a good point about the 4 mB size of the original animated > GIF I offered. > So, here is an animated GIF that weighs in at a measley 0.1 megabyte (100 > kB). > http://www.umass.edu/microbio/chime/beta/pdb/gifs/an_dna3.gif > > Will someone with PPT2000 give it a try? Please compare its appearance in > Netscape or IE (after it has made one complete turn, thereby being fully > downloaded, or saved to a local disk file and then opened in the browser) > with its appearance in PPT2000. (Sorry, I have only PPT97 which we've > established doesn't support animated GIFs.) > > Also, I think all the reports for PPT2000 have been on Macs. What about > Windows PPT2000? Does it give a smooth animation? > > Thanks for all the help -- Eric > > At 6/6/02, you wrote: > > > In my opinion, the fact that the file (1aoi_2.gif) is 4.3 MB is the > problem. That is an extremely large animated .gif file. It runs slow even > on a 2 GHz P4 machine (running Windows 2000) with 500 MB of RAM. > > Ricky > > >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 > > > > > > --Boundary_(ID_aOdI0EJfUuCCIn4a4ituAQ) RE: animated gifs in powerpoint?

Works fine in mac ppt2001 as long as first loaded from the web to desktop and then inserted as a movie file.  If dragged from the web, only the static images stays.

D

--Boundary_(ID_aOdI0EJfUuCCIn4a4ituAQ)-- X-Accept-Language: en References: <200206061959.g56Jxoh03995@marlin.bio.umass.edu> <000f01c20d9b$c5803180$83af0f50@zig> ++++------+------+------+------+------+------+------+------+------+------+ From: "Joseph J. Grabowski" Subject: Re: animated gifs in powerpoint? Date: Thu, 06 Jun 2002 17:40:53 -0400 To: rasmol@lists.umass.edu Paul Pillot wrote:
This is not exactly the question, but what about Accelrys WebLab viewer to diqplay molecular animations in PowerPoint presentations ? Does somebody use it ?
 

 
I have used the ActiveX plugin of Accelrys' WebLab Viewer lite (freeware?) to animate pdb files in Powerpoint, on a PC, running either W98, or W2000, with both Office 2000 and Office XP.  It works like a charm; I had no troubles over Fall 2001 and Spring 2002 and the learning curve was shallow.

 As with other animations, one does not see the molecule until in Slide Show mode.

  One annoyance is that when I print the PowerPoint slides to handout as classroom notes, the embedded molecular structures do not print - though the background does if you have it set to something besides white.

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
----------------------------------------------------------
The great aim of education is not knowledge but action.
            -- Herbert Spencer
  ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <5.1.0.14.0.20020606123637.026e4c30@murraystate.edu> <200206061731.g56HVUh27591@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "J. Ricky Cox" Subject: Re: animated gifs in powerpoint? Date: Thu, 06 Jun 2002 16:45:23 -0500 To: rasmol@lists.umass.edu Eric-

Netscape 4.75:  Smooth and is turning at a good rate (on Windows 2000 and XP)
IE 6.0:  Turning much slower and a bit choppy (on Windows 2000 and XP)


PPT2002 (on Windows 2000):  Even slower and choppier

PPT 2000 (on Windows 98):  Turns as fast as in Netscape 4.75, but there is a glitch every second or third turn...definitely not as smooth compared to Netscape 4.75

Therefore, my size argument is wrong.....sorry....


At 04:22 PM 6/6/2002 -0700, you wrote:

OK, Ricky makes a good point about the 4 mB size of the original animated GIF I offered.
So, here is an animated GIF that weighs in at a measley 0.1 megabyte (100 kB).
http://www.umass.edu/microbio/chime/beta/pdb/gifs/an_dna3.gif

Will someone with PPT2000 give it a try? Please compare its appearance in Netscape or IE (after it has made one complete turn, thereby being fully downloaded, or saved to a local disk file and then opened in the browser) with its appearance in PPT2000. (Sorry, I have only PPT97 which we've established doesn't support animated GIFs.)

Also, I think all the reports for PPT2000 have been on Macs. What about Windows PPT2000? Does it give a smooth animation?

Thanks for all the help -- Eric

At 6/6/02, you wrote:
In my opinion, the fact that the file (1aoi_2.gif) is 4.3 MB is the problem. That is an extremely large animated .gif file. It runs slow even on a 2 GHz P4 machine (running Windows 2000) with 500 MB of RAM.

Ricky

>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
>


----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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_475a3KrTBtWhOQVPgrM3Fw)" X-MSMail-priority: Normal References: <200206061731.g56HVUh27591@marlin.bio.umass.edu> <200206062015.g56KFLh04605@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re: animated gifs in powerpoint? Date: Fri, 07 Jun 2002 07:43:28 +0200 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_475a3KrTBtWhOQVPgrM3Fw) - Eric, Netscape 4.75 : smooth and fast Netscape 6.2 : smooth and a little bit slower than in Netscape 4.75 IE6.0 : less smooth and slower Works fine in ppt2000, and seems to be faster than in IE6.0 Paul (my configuration : Win me, Pentium IV, 256 Mo Ram) ----- Original Message ----- From: Eric Martz To: rasmol@lists.umass.edu Cc: chris@bio.umass.edu Sent: Friday, June 07, 2002 1:22 AM Subject: Re: animated gifs in powerpoint? OK, Ricky makes a good point about the 4 mB size of the original animated GIF I offered. So, here is an animated GIF that weighs in at a measley 0.1 megabyte (100 kB). http://www.umass.edu/microbio/chime/beta/pdb/gifs/an_dna3.gif Will someone with PPT2000 give it a try? Please compare its appearance in Netscape or IE (after it has made one complete turn, thereby being fully downloaded, or saved to a local disk file and then opened in the browser) with its appearance in PPT2000. (Sorry, I have only PPT97 which we've established doesn't support animated GIFs.) Also, I think all the reports for PPT2000 have been on Macs. What about Windows PPT2000? Does it give a smooth animation? Thanks for all the help -- Eric At 6/6/02, you wrote: In my opinion, the fact that the file (1aoi_2.gif) is 4.3 MB is the problem. That is an extremely large animated .gif file. It runs slow even on a 2 GHz P4 machine (running Windows 2000) with 500 MB of RAM. Ricky >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 > --Boundary_(ID_475a3KrTBtWhOQVPgrM3Fw)
- Eric,
 
Netscape 4.75 : smooth and fast
Netscape 6.2 : smooth and a little bit slower than in Netscape 4.75
IE6.0 : less smooth and slower
 
Works fine in ppt2000, and seems to be faster than in IE6.0
 
Paul
 
(my configuration : Win me, Pentium IV, 256 Mo Ram)
----- Original Message -----
From: Eric Martz
Sent: Friday, June 07, 2002 1:22 AM
Subject: Re: animated gifs in powerpoint?

OK, Ricky makes a good point about the 4 mB size of the original animated GIF I offered.
So, here is an animated GIF that weighs in at a measley 0.1 megabyte (100 kB).
http://www.umass.edu/microbio/chime/beta/pdb/gifs/an_dna3.gif

Will someone with PPT2000 give it a try? Please compare its appearance in Netscape or IE (after it has made one complete turn, thereby being fully downloaded, or saved to a local disk file and then opened in the browser) with its appearance in PPT2000. (Sorry, I have only PPT97 which we've established doesn't support animated GIFs.)

Also, I think all the reports for PPT2000 have been on Macs. What about Windows PPT2000? Does it give a smooth animation?

Thanks for all the help -- Eric

At 6/6/02, you wrote:
In my opinion, the fact that the file (1aoi_2.gif) is 4.3 MB is the problem. That is an extremely large animated .gif file. It runs slow even on a 2 GHz P4 machine (running Windows 2000) with 500 MB of RAM.

Ricky

>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:
>
> --Boundary_(ID_475a3KrTBtWhOQVPgrM3Fw)-- References: <200206061731.g56HVUh27591@marlin.bio.umass.edu> <200206062015.g56KFLh04605@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Joel Kowit Subject: Re: animated gifs in powerpoint? Date: Fri, 07 Jun 2002 21:21:29 -0400 To: rasmol@lists.umass.edu Hi: I tried both the 0.1 MB image (an_dna3.gif) and the 4.3 MB image on PPT2000. The smaller image looked the same on PPT2000 and netscape 4.08. When I tried the larger image on PPT, it rotated in an irregular fashion, and slowly, for about a minute, getting stuck about once every turn. Then it seemed like someone had greased the wheels and the image started to rotate more smoothly. Within two minutes, it looked just as nice on PPT2000 as on Netscape. If I deleted the image and reinserted it, it ran smoothly immediately. But if I closed PPT and reopened it, I had to wait the same two minutes for the motion to become smooth. Weird. Joel OK, Ricky makes a good point about the 4 mB size of the original animated GIF I offered. So, here is an animated GIF that weighs in at a measley 0.1 megabyte (100 kB). http://www.umass.edu/microbio/chime/beta/pdb/gifs/an_dna3.gif Will someone with PPT2000 give it a try? Please compare its appearance in Netscape or IE (after it has made one complete turn, thereby being fully downloaded, or saved to a local disk file and then opened in the browser) with its appearance in PPT2000. (Sorry, I have only PPT97 which we've established doesn't support animated GIFs.) Also, I think all the reports for PPT2000 have been on Macs. What about Windows PPT2000? Does it give a smooth animation? Thanks for all the help -- Eric At 6/6/02, you wrote: In my opinion, the fact that the file (1aoi_2.gif) is 4.3 MB is the problem. That is an extremely large animated .gif file. It runs slow even on a 2 GHz P4 machine (running Windows 2000) with 500 MB of RAM. Ricky >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 > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: inquirycomplement system Date: Sat, 08 Jun 2002 13:13:13 -0400 (EDT) To: rasmol I am trying to prepare a presentation about the complement system, I would like to know if there is any rasmol or chime script that presents it, or where can I find some relative structures? thanks a lot in advance. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: inquirycomplement system Date: Sat, 08 Jun 2002 13:47:58 -0400 To: rasmol@lists.umass.edu it was 1:13 PM EDT on (Saturday) 8 June 2002 when agc said: > I am trying to prepare a presentation about the complement system, I > would like to know if there is any rasmol or chime script that presents > it, or where can I find some relative structures? thanks a lot in advance. > > hi agc, can you give some more info? IIRC complement is a pretty sizable cascade. do you have the names of proteins that you want? what specific interactions interest you? do you want RasMol or Chime animations, or still images, or something else? length? target audience? one place to start is . a search for "complement" returned 208 structures; unfortunately, a cursory scan shows that many are not related to the complement system itself. again, more info would help narrow the search. another place to look is the World Index of Molecular Visualization Resources at . 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: German/Germany, de-DE, en References: ++++------+------+------+------+------+------+------+------+------+------+ From: jr Subject: Re: inquirycomplement system Date: Mon, 10 Jun 2002 09:56:28 +0200 To: rasmol@lists.umass.edu agc wrote: > I am trying to prepare a presentation about the complement system, I > would like to know if there is any rasmol or chime script that presents > it, or where can I find some relative structures? thanks a lot in advance. > you may have a look at http://www.imb-jena.de/~jr/tmp/complement.html Or explore the database for complement structures by your own, starting with PDB/SWISS-PROT Cross References searching the SWISS-PROT descriptions. Regards, Jan ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.5762.3 Thread-Topic: inquirycomplement system Thread-Index: AcIPFLmn+HIbmxvkSFmO9QHYW5C09QBzpSuO content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: "Campbell, Malcolm" Subject: RE: inquirycomplement system Date: Mon, 10 Jun 2002 21:00:17 -0400 To: rasmol@lists.umass.edu Tim, did you know about Chimera from UCSF? http://www.cgl.ucsf.edu/chimera/ Just checking. 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) 209 Ridge Road (Shipping) Davidson, NC 28035 USA macampbell@davidson.edu http://www.bio.davidson.edu/campbell 704-894-2692 (voice) 704-894-2512 (fax) > ---------- > From: Timothy Driscoll > Reply To: rasmol@lists.umass.edu > Sent: Saturday, June 8, 2002 1:47 PM > To: rasmol@lists.umass.edu > Subject: Re: inquirycomplement system > > it was 1:13 PM EDT on (Saturday) 8 June 2002 when agc said: > > > I am trying to prepare a presentation about the complement system, I > > would like to know if there is any rasmol or chime script that presents > > it, or where can I find some relative structures? thanks a lot in advance. > > > > > > hi agc, > > can you give some more info? IIRC complement is a pretty sizable cascade. > do you have the names of proteins that you want? what specific interactions > interest you? do you want RasMol or Chime animations, or still images, or > something else? length? target audience? > > one place to start is . a search for "complement" > returned 208 structures; unfortunately, a cursory scan shows that many are > not related to the complement system itself. again, more info would help > narrow the search. > > another place to look is the World Index of Molecular Visualization > Resources at . > > > 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-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id g5IA1qh08451 ++++------+------+------+------+------+------+------+------+------+------+ From: Jean Richelle Subject: help needed for french translation Date: Tue, 18 Jun 2002 11:59:46 +0200 To: RasMol List Dear all, Is there somebody that could tell me how "dot surface" is correctly translated in French ? Best regards, 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-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Fred Fack Subject: Re: help needed for french translation Date: Tue, 18 Jun 2002 12:28:02 +0200 To: rasmol@lists.umass.edu Dear Jean, I do not know whether there is a special expression but "surface pointillée" should translate the "dot surface". If there were a generally used expression I would be interested in knowing it. Fred ----- Original Message ----- Sent: Tuesday, June 18, 2002 11:59 AM From: "Jean Richelle" Subject: help needed for french translation To: "RasMol List" Dear all, Is there somebody that could tell me how "dot surface" is correctly translated in French ? Best regards, 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-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re: help needed for french translation Date: Tue, 18 Jun 2002 22:52:03 +0200 To: rasmol@lists.umass.edu Surface en points ? ----- Original Message ----- Sent: Tuesday, June 18, 2002 11:59 AM From: "Jean Richelle" Subject: help needed for french translation To: "RasMol List" Dear all, Is there somebody that could tell me how "dot surface" is correctly translated in French ? Best regards, 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: Francois Sampieri Subject: Re: help needed for french translation Date: Wed, 19 Jun 2002 12:17:01 +0200 To: rasmol@lists.umass.edu Dear Jean, Molecular surfaces are usually rendered as 'solid' like an actual hard opaque object, or as 'dot surfaces' (surfaces de points) where bonds can be seen through. Regards, Francois Sampieri >Dear all, > >Is there somebody that could tell me how "dot surface" is correctly >translated in French ? > >Best regards, > >Jean >_____________________________________________________________________________ ____________________________________________ UMR 6560 CNRS-Universite de la Mediterranee Laboratoire de Biochimie - IFR Jean Roche Faculte de Medecine Nord, Bd Pierre Dramard 13916 Marseille Cedex 20 E-mail: sampieri.f@jean-roche.univ-mrs.fr Fax: (33) 4 91 65 75 95 Tel: (33) 4 91 69 88 44 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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 needed for french translation Thread-Index: AcIXeumdhqukomwGRrG7IYc2XJuejgAA9jVD content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: X-OriginalArrivalTime: 19 Jun 2002 10:52:48.0054 (UTC) FILETIME=[732EFD60:01C2177F] X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id g5JAsPh12975 ++++------+------+------+------+------+------+------+------+------+------+ From: NEUHAUS Jean-Marc Subject: =?iso-8859-1?Q?RE=A0=3A_help_needed_for_french_translation?= Date: Wed, 19 Jun 2002 12:52:36 +0200 To: rasmol@lists.umass.edu, rasmol@lists.umass.edu Dear all, I would favor "surface pointillée", as pointiller means "Dessiner, graver, peindre en utilisant des points" (Petit Robert). Regards, Jean-Marc Neuhaus Laboratoire de biochimie, Institut de Botanique Université de Neuchâtel rue Emile-Argand 9 CH-2007 Neuchâtel, Suisse tel. ++41 32 718 2207 ; fax: ++41 32 718 2201 jean-marc.neuhaus@unine.ch -------- Message d'origine-------- De: Francois Sampieri [mailto:sampieri.f@jean-roche.univ-mrs.fr] À: rasmol@lists.umass.edu Objet: Re: help needed for french translation ++++------+------+------+------+------+------+------+------+------+------+ Date: mer. 19.06.2002 12:17 Cc: Dear Jean, Molecular surfaces are usually rendered as 'solid' like an actual hard opaque object, or as 'dot surfaces' (surfaces de points) where bonds can be seen through. Regards, Francois Sampieri >Dear all, > >Is there somebody that could tell me how "dot surface" is correctly >translated in French ? > >Best regards, > >Jean >_____________________________________________________________________________ ____________________________________________ UMR 6560 CNRS-Universite de la Mediterranee Laboratoire de Biochimie - IFR Jean Roche Faculte de Medecine Nord, Bd Pierre Dramard 13916 Marseille Cedex 20 E-mail: sampieri.f@jean-roche.univ-mrs.fr Fax: (33) 4 91 65 75 95 Tel: (33) 4 91 69 88 44 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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 g5JCwvh15228 ++++------+------+------+------+------+------+------+------+------+------+ From: Andrew Coulson Subject: =?iso-8859-1?Q?RE=A0:_help_needed_for_french_translation?= Date: Wed, 19 Jun 2002 13:58:18 +0100 To: rasmol@lists.umass.edu At 12:52 PM 19/6/02 +0200, you wrote: >Dear all, >I would favor "surface pointillée", as pointiller means "Dessiner, graver, >peindre en utilisant des points" (Petit Robert). Surely this indicates the use of 'points' (as opposed to 'lines', 'strokes' or 'tones')in rendering the surface rather the representation of a surface by a subset of its points --- as implied by 'surface en points'? Andrew Coulson >Regards, >Jean-Marc Neuhaus > >Laboratoire de biochimie, Institut de Botanique >Université de Neuchâtel >rue Emile-Argand 9 >CH-2007 Neuchâtel, Suisse >tel. ++41 32 718 2207 ; fax: ++41 32 718 2201 >jean-marc.neuhaus@unine.ch > >-------- Message d'origine-------- >De: Francois Sampieri [mailto:sampieri.f@jean-roche.univ-mrs.fr] >Date: mer. 19.06.2002 12:17 >À: rasmol@lists.umass.edu >Cc: >Objet: Re: help needed for french translation > >Dear Jean, > >Molecular surfaces are usually rendered as 'solid' like an actual hard >opaque object, or as 'dot surfaces' (surfaces de points) where bonds can >be seen through. > >Regards, > >Francois Sampieri > > >Dear all, > > > >Is there somebody that could tell me how "dot surface" is correctly > >translated in French ? > > > >Best regards, > > > >Jean > >_________________________________________________________________________ > ____ > >____________________________________________ >UMR 6560 CNRS-Universite de la Mediterranee >Laboratoire de Biochimie - IFR Jean Roche >Faculte de Medecine Nord, Bd Pierre Dramard >13916 Marseille Cedex 20 >E-mail: sampieri.f@jean-roche.univ-mrs.fr >Fax: (33) 4 91 65 75 95 >Tel: (33) 4 91 69 88 44 > > > > > > > Andrew Coulson Andrew.Coulson@ed.ac.uk ICMB, Swann Building Office: +44 (0) 131 650 5363 University of Edinburgh Home: +44 (0) 131 665 3779 King's Buildings, Mayfield Road Mobile: 07885 677022 Edinburgh EH9 3JR Fax: +44 (0) 131 650 8650 United Kingdom Fax: +44 (0) 131 650 7055 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <01C20334.C27DC400@host213-120-42-198.webport.bt.net> ++++------+------+------+------+------+------+------+------+------+------+ From: "Michael H. Patrick" Subject: RE: Mutant Proteins Date: Thu, 20 Jun 2002 08:33:51 -0500 To: rasmol@lists.umass.edu Could you direct me to that pdb file.........I could find several files with mutations at residue 12 but none at 13 Michael 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 >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] >Sent: Friday, May 24, 2002 12:15 AM >To: Buzz Hoagland >Cc: rasmol@lists.umass.edu >Subject: Re: Mutant Proteins > >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: Eric Martz Subject: Post-Poc Opening, France, MolVis & Docking Date: Thu, 20 Jun 2002 12:35:16 -0400 To: rasmol@lists.umass.edu Cc: Sylvain.Petitjean@loria.fr [forwarded to the list by E.M. for a nonsubscriber] LORIA/INRIA and LCTN laboratories Nancy, France Post-Poctoral Position Available We have an opening for a post-doctoral fellow for up to 2 years, commencing september/october 2002 or later, to work on: Enhancing Molecular Docking Through High-Performance Computing and Advanced Visualization Molecular docking is the natural process by which molecules recognize and interact with one another. From a computational standpoint, it also refers to the prediction of the structures of ligand-receptor complexes from the conformations of unbound ligand and unbound receptor. Molecular docking is at the center of such practical applications as protein engineering and drug design. It has already helped to design new ligands for anti-AIDS and anti-cancer agents and for the treatment of diabetes. Structure-based molecular docking programs are based on the assumption that ligands which form favorable interactions with the receptor must have high binding affinity. They rely on the number-crunching capabilities of computers to generate and evaluate large numbers of possible bindings. Computers however do not have the experience of human beings and molecular docking methods severely limit the biochemists' ability to analyze the bindings computed and exploit their intuition and expertise to generate sound and reliable solutions. Also, most approaches to molecular docking do not take advantage of the visualization capabilities offered by modern workstations. Major challenges in this field are (1) predicting how molecules will dock with one another and (2) identifying the factors that determine the specificity of interaction. To make significant advances, it is necessary to develop novel methods to facilitate the docking techniques by enhancing our ability to understand and analyze docking interactions and to develop hypotheses about which molecules are most likely to interact favorably. These factors can be incorporated into molecular docking by including advanced visualization and haptic (sense of touch) feedback in the process. The main goal of this project is to develop an immersive, interactive and easy-to-use modelling environment to enhance molecular docking. The candidate will have at its disposal the state-of-the-art SGI high-performance computing technologies available at LORIA, notably the Reality Center immersive visualization facility and the Onyx 3800 shared-memory system platform. In particular, the postdoctoral candidate is expected: - To integrate existing molecular docking programs with the LORIA collaborative computing environment. - To implement a haptic interface to facilitate interaction with molecular models, through a high-fidelity, 3D force-feedback device. - To combine visualization and haptic feedback to allow interactive docking simulations in the Reality Center. - To develop a multimodal user interface to facilitate the work of molecular scientists. The successful candidate will have a solid background in SGI graphics software and architecture. He is also expected to have a working knowledge of programming and scripting languages such as Java, Perl and TCL/TK. Candidates having experience in parallel computing and/or grid computing will be given priority. Salary will be approximately 21400 euros per annum. There are no restrictions on the nationality of the applicant. For more information on this position as well as indication of interest, please contact either Bernard Maigret (Bernard.Maigret@lctn.uhp-nancy.fr) http://www.lctn.uhp-nancy.fr or Sylvain Petitjean (Sylvain.Petitjean@loria.fr) http://www.loria.fr ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- bev@cs.umass.edu, gregratner@hotmail.com ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: free hit meters/website visitor analysis Date: Thu, 20 Jun 2002 14:15:48 -0400 To: rasmol@lists.umass.edu Cc: net@bio.umass.edu, sbrewer@bio.umass.edu, vining@chem.umass.edu, Frieda Reichsman (http://www.moleculesinmotion.com/) recently made me
aware of the existence of free services to
monitor the traffic at websites. You just sign up and copy a small block of
html/javascript into your web page. This block of code causes a button to be
displayed on your page; in some cases this button includes a hit count.
Clicking on the button displays an analysis of visitors to your site. All
hit meter services include: hits vs. unique visitors, browsers (IE vs.
Netscape and versions), operating systems, screen resolution, color depth,
whether java and javascript were enabled in the client's browser. Most
include other parameters as well. (None tell you if the client's browser
had Chime installed :-( but that is very tricky to do in IE.)

Below are my observations for some of the free hit meters that I found. If
you know of a provider not listed below that you like, please let us know.
In general, it is possible to set up multiple accounts to monitor more than
one site or page, although most hit meter services don't explicitly say
this; none explicitly request that you not have multiple free accounts. Just
go ahead and register for more than one account. Most of the providers offer
a paid service with additional benefits, but for my noncommercial sites, I
have no need for those benefits.

Terminology is not used consistently or carefully, e.g. "visitors" may mean
page hits, not unique visitors, and "visits" may mean unique visitors,
depending on the provider -- so pay attention and you can figure out what
they mean because they all report both page hits and unique visitors.

I recommend inserting the meter button code at the very bottom of your page,
and not inside a table. In the event that the meter service is unavailable,
it is possible that there would be a long delay before anything below the
meter button would display on your page. Placing the button at the bottom of
the page ensures that everything above the button will be readable in this
unlikely event.


All providers include "demo pages" to show what their analyses look like.
However, very few actually show you what their button looks like before you
register. Therefore I have indicated below example sites where I have
actually installed the button so you can see it in a real situation. If you
notice any problems when visiting my pages with these newly installed
buttons, please let me know!


A site that lists many hit meter providers, with some indication about what
they provide, is
http://globalconnector.netfirms.com/webmaster/sitestatistic.html

Below I have listed AT THE TOP the providers I liked best. Bear in mind that I
have only 24 hours experience with them!

sitemeter.com (my favorite)
Button can show unique visitor count; stats public (but optionally private).
  Several button styles available, one shows count and date count started.
  Example: http://proteinexplorer.org
  Stats show % but not counts for each category.
  Results colored so it is easy to tell % IE for all versions.
  Stats include client browser language, dhtml, style sheets, PNG graphics.

realtracker.com
Button does NOT show a count; stats public.
Button alternates between count and ad for RealTracker; this animation sometimes causes the mouse pointer to flash annoyingly anywhere on the page in IE (but not in Netscape).
Example: http://www-unix.oit.umass.edu/~emartz/martzpots/index2.htm
(You will learn something about my parents if you go there.)
No tech support; analysis sometimes displays in non-English language.
Click the "System" link for OS, browsers, etc.
free-hit-counters.com
Button does NOT show a count; stats public.
Analysis does not display in Netscape; only in IE. I emailed them about this and they responded promptly, promising to fix it 'soon'.
Example: http://molvisindex.org
Results are sorted by frequency making it hard to tell e.g. % IE all versions.

I HAVE NOT TRIED USING THOSE BELOW

hit-o-meter.com
I tried it extensively from a local test file and ran into several bugs and problems. I emailed the author who responded promptly and fixed some but not all of my concerns. Product seems immature and has serious bugs. Bizzarely, Adobe Acrobat is invoked before the button displays -- I wonder what happens if Adobe is not installed.
Free accounts limited to 5.
thecounter.com
Slick-looking, mature-looking site, but no free live ln-line reports; only weekly email reports are free. Therefore stats are not public.
webtrendsalive.com
Glossy-looking site but I couldn't get their demo to display and site was very slow to respond.
hitometer.netscape.com
No longer taking new accounts.
webstat.com
Free version has no count on button and no public access to stats.
-Eric


/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
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: Jennifer Muzyka Subject: Re: free hit meters/website visitor analysis Date: Thu, 20 Jun 2002 16:18:48 -0400 To: rasmol@lists.umass.edu Another good hit meter, which I have used for two or three years, is HitBox (www.hitbox.com). -Jennifer At 02:15 PM 6/20/02 -0400, you wrote: >Frieda Reichsman (http://www.moleculesinmotion.com/) recently made me >aware of the existence of free services to >monitor the traffic at websites. You just sign up and copy a small block of >html/javascript into your web page. This block of code causes a button to be >displayed on your page; in some cases this button includes a hit count. >Clicking on the button displays an analysis of visitors to your site. All >hit meter services include: hits vs. unique visitors, browsers (IE vs. >Netscape and versions), operating systems, screen resolution, color depth, >whether java and javascript were enabled in the client's browser. Most >include other parameters as well. (None tell you if the client's browser >had Chime installed :-( but that is very tricky to do in IE.) > >Below are my observations for some of the free hit meters that I found. If >you know of a provider not listed below that you like, please let us know. >In general, it is possible to set up multiple accounts to monitor more than >one site or page, although most hit meter services don't explicitly say >this; none explicitly request that you not have multiple free accounts. Just >go ahead and register for more than one account. Most of the providers offer >a paid service with additional benefits, but for my noncommercial sites, I >have no need for those benefits. > >Terminology is not used consistently or carefully, e.g. "visitors" may mean >page hits, not unique visitors, and "visits" may mean unique visitors, >depending on the provider -- so pay attention and you can figure out what >they mean because they all report both page hits and unique visitors. > >I recommend inserting the meter button code at the very bottom of your page, >and not inside a table. In the event that the meter service is unavailable, >it is possible that there would be a long delay before anything below the >meter button would display on your page. Placing the button at the bottom of >the page ensures that everything above the button will be readable in this >unlikely event. > > >All providers include "demo pages" to show what their analyses look like. >However, very few actually show you what their button looks like before you >register. Therefore I have indicated below example sites where I have >actually installed the button so you can see it in a real situation. If you >notice any problems when visiting my pages with these newly installed >buttons, please let me know! > > >A site that lists many hit meter providers, with some indication about what >they provide, is >http://globalconnector.netfirms.com/webmaster/sitestatistic.html > >Below I have listed AT THE TOP the providers I liked best. Bear in mind >that I >have only 24 hours experience with them! > >sitemeter.com (my favorite) >Button can show unique visitor count; stats public (but optionally private). > Several button styles available, one shows count and date count started. > Example: http://proteinexplorer.org > Stats show % but not counts for each category. > Results colored so it is easy to tell % IE for all versions. > Stats include client browser language, dhtml, style sheets, PNG graphics. > >realtracker.com >Button does NOT show a count; stats public. >Button alternates between count and ad for RealTracker; this animation >sometimes causes the mouse pointer to flash annoyingly anywhere on the >page in IE (but not in Netscape). >Example: http://www-unix.oit.umass.edu/~emartz/martzpots/index2.htm >(You will learn something about my parents if you go there.) >No tech support; analysis sometimes displays in non-English language. >Click the "System" link for OS, browsers, etc. > >free-hit-counters.com >Button does NOT show a count; stats public. >Analysis does not display in Netscape; only in IE. I emailed them about >this and they responded promptly, promising to fix it 'soon'. >Example: http://molvisindex.org >Results are sorted by frequency making it hard to tell e.g. % IE all >versions. >I HAVE NOT TRIED USING THOSE BELOW > >hit-o-meter.com >I tried it extensively from a local test file and ran into several bugs >and problems. I emailed the author who responded promptly and fixed some >but not all of my concerns. Product seems immature and has serious bugs. >Bizzarely, Adobe Acrobat is invoked before the button displays -- I wonder >what happens if Adobe is not installed. >Free accounts limited to 5. > >thecounter.com >Slick-looking, mature-looking site, but no free live ln-line reports; only >weekly email reports are free. Therefore stats are not public. > >webtrendsalive.com >Glossy-looking site but I couldn't get their demo to display and site was >very slow to respond. > >hitometer.netscape.com >No longer taking new accounts. > >webstat.com >Free version has no count on button and no public access to stats. > >-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: <200206201820.g5KIK3h04593@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: free hit meters/website visitor analysis Date: Thu, 20 Jun 2002 16:42:27 -0400 To: rasmol@lists.umass.edu At 6/20/02, Jennifer Muzyka wrote: >Another good hit meter, which I have used for two or three years, is HitBox >(www.hitbox.com). >-Jennifer Thanks, Jennifer. I took a look. I couldn't tell whether their 'button' shows a count. Whether the stats are public is optional. However, they want to put relatively large, animated, distracting ads on your site, whereas the hit meters I listed earlier have small, low key buttons (not animated) that only advertise the hit meter site. Based on the ads the require for the free service, I would still rank the other services higher on my personal list. -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: DNA Chime tutorial now works in IE Date: Tue, 25 Jun 2002 22:38:30 -0400 To: rasmol@lists.umass.edu I have today released version 2.8 of my Chime-based tutorial on DNA Structure (version one goes way back to 1996). This new version works in Internet Explorer as well as Netscape, and has a new animation showing codons as well as a new page documenting codons in DNA, mRNA, and tRNA etc. The "More Resources on DNA" page has been expanded and updated. This tutorial is free and downloadable for off-line use. Get it from my Chime Resources page, http://www.umass.edu/microbio/chime -- where you will see quite a few new decorations, and explicit indication of which resources are IE-compatible. The Chime Resources page is being visited by 100-140 people/weekday even in the summer, and the DNA Structure Tutorial main page by over 200 people/weekday. At the latter site, 80% of visitors are using Internet Explorer. At last now they can use the tutorial! /* - - - - - - - - - - - - - - - - - - - - - - - - - - - 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: don't use realtracker Date: Wed, 03 Jul 2002 13:28:22 -0400 To: rasmol@lists.umass.edu Recently, I mentioned here some free hit counters that can be placed on websites to monitor traffic. One of them, realtracker.com, turns out to pop open windows when you exit, displaying ads including an ad for a Britney porn site. Therefore we have stopped using realtracker, and I recommend anybody that installed a realtracker hit meter should replace it immediately with another hit meter from a different site. I have used sitemeter.com on most of my sites and they have been very satisfactory so far. Another one, free-hit-meters.com, claims to have removed their exit-popunder ad function in response to a complaint I made, but I have also stopped using their service so I can't verify that. -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-Accept-Language: es References: <200206260242.g5Q2gxh13376@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Gabriel Pons Subject: Re: protein Explorer in spanish Date: Tue, 09 Jul 2002 12:41:40 +0200 To: rasmol@lists.umass.edu Queridos rasmolones, chimoleones y visualizadores moleculares: Hemos finalizado con exito la traducción al español del programa protein Explorer desarrollado por nuestro "gurú" Eric. Podeis acceder al programa en: http://www2.uah.es/biomodel/pe/inicio.htm También Eric ha colocado enlaces en la pagina general de PE. La traducción de la versión 1.86 no es completa aunque sí esta lo fundamental. Esperamos completarla en los próximos meses y actualizarla a las últimas versiones en ingles. Gabriel Pons ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: protein Explorer in spanish Date: Tue, 09 Jul 2002 11:30:39 -0400 To: rasmol@lists.umass.edu Forwarded for Patrick Barry by Eric Martz to circumvent technical difficulties: ----- Tantas gracias! Me gusta mucho el sitio! ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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 g6AJmWh28029 ++++------+------+------+------+------+------+------+------+------+------+ From: Leticia Britos Subject: Re: protein Explorer in spanish Date: Wed, 10 Jul 2002 16:46:51 -0300 To: rasmol@lists.umass.edu Hi, I teach biochemistry and molecular biology to high school biology teachers in Uruguay (South America). I use RasMol a lot and find it extremely useful. Teachers love it. I have no problem with the language but most of my students have to struggle with the commands in english. I know they are quite easy and, on the other hand, it´s a good thing they have to make an effort and practice their english (which is taught here in Uruguay all through elementary and secondary school). However, it takes a lot more to introduce the program in english. So I thought Protein Explorer in spanish would be a solution. But at the institute I work the network of computers only have internet explorer and it is not easy to install new programs, without getting stuck in the red tape. That´s why I find Rasmol so useful, for its simplicity in the installation (I even send the program to my students by e-mail, along with some pdb files) and in its use too. My question is: is there a possibility of a spanish version of RasMol? Although I do not master programing skills, I offer to help in any way needed. Best regards, Leticia At 11:30 a.m. 09/07/2002 -0400, you wrote: >Forwarded for Patrick Barry by Eric Martz to circumvent >technical difficulties: >----- > >Tantas gracias! Me gusta mucho el sitio! > > M. Sc. Leticia Britos Sección Bioquímica- Lab. 305 Facultad de Ciencias Universidad de la República Iguá 4225 C.P. 11400 Montevideo URUGUAY ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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 g6AM4Xh03625 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: protein Explorer in spanish Date: Wed, 10 Jul 2002 18:03:24 -0400 (EDT) To: rasmol@lists.umass.edu Try RasMol 2.7.2.1 and execute the command "Spanish". ===================================================== 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 Wed, 10 Jul 2002, Leticia Britos wrote: > Hi, > I teach biochemistry and molecular biology to high school biology teachers > in Uruguay (South America). I use RasMol a lot and find it extremely > useful. Teachers love it. I have no problem with the language but most of > my students have to struggle with the commands in english. I know they are > quite easy and, on the other hand, it´s a good thing they have to make an > effort and practice their english (which is taught here in Uruguay all > through elementary and secondary school). However, it takes a lot more to > introduce the program in english. So I thought Protein Explorer in spanish > would be a solution. But at the institute I work the network of computers > only have internet explorer and it is not easy to install new programs, > without getting stuck in the red tape. That´s why I find Rasmol so useful, > for its simplicity in the installation (I even send the program to my > students by e-mail, along with some pdb files) and in its use too. > My question is: is there a possibility of a spanish version of RasMol? > Although I do not master programing skills, I offer to help in any way needed. > > Best regards, > > Leticia > > > > > > At 11:30 a.m. 09/07/2002 -0400, you wrote: > >Forwarded for Patrick Barry by Eric Martz to circumvent > >technical difficulties: > >----- > > > >Tantas gracias! Me gusta mucho el sitio! > > > > > > M. Sc. Leticia Britos > Sección Bioquímica- Lab. 305 > Facultad de Ciencias > Universidad de la República > Iguá 4225 > C.P. 11400 Montevideo > URUGUAY > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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:1.0rc2) Gecko/20020510 X-Accept-Language: es-AR, es, en References: <5.1.0.14.1.20020710163026.026d7fd8@fcien.edu.uy> ++++------+------+------+------+------+------+------+------+------+------+ From: Fernando Subject: Re: protein Explorer in spanish Date: Wed, 10 Jul 2002 19:41:40 -0300 To: rasmol@lists.umass.edu Dear Leticia, Since two years ago there is a Spanish version for RasMol. Moreover, it was the first (other than english) for "multilingual version". The "spanish menus" appears when you type "spanish " in the program prompt and there is available for Unix, Win and Mac. You can download from: http://www.openrasmol.org http://www.microbiologia.org.ar/software/ http://www.microbiologia.com.ar/software/ ftp://microbiologia.org.ar/pub/software/molecular Regards Leticia Britos wrote: > Hi, > I teach biochemistry and molecular biology to high school biology > teachers in Uruguay (South America). I use RasMol a lot and find it > extremely useful. Teachers love it. I have no problem with the language > but most of my students have to struggle with the commands in english. I > know they are quite easy and, on the other hand, it´s a good thing they > have to make an effort and practice their english (which is taught here > in Uruguay all through elementary and secondary school). However, it > takes a lot more to introduce the program in english. So I thought > Protein Explorer in spanish would be a solution. But at the institute I > work the network of computers only have internet explorer and it is not > easy to install new programs, without getting stuck in the red tape. > That´s why I find Rasmol so useful, for its simplicity in the > installation (I even send the program to my students by e-mail, along > with some pdb files) and in its use too. > My question is: is there a possibility of a spanish version of RasMol? > Although I do not master programing skills, I offer to help in any way > needed. > > Best regards, > > Leticia > > > > > > At 11:30 a.m. 09/07/2002 -0400, you wrote: > >> Forwarded for Patrick Barry by Eric Martz to circumvent >> technical difficulties: >> ----- >> >> Tantas gracias! Me gusta mucho el sitio! >> >> > > M. Sc. Leticia Britos > Sección Bioquímica- Lab. 305 > Facultad de Ciencias > Universidad de la República > Iguá 4225 > C.P. 11400 Montevideo > URUGUAY > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <5.1.0.14.1.20020710163026.026d7fd8@fcien.edu.uy> ++++------+------+------+------+------+------+------+------+------+------+ From: Gabriel Pons Subject: Re: protein Explorer in spanish Date: Thu, 11 Jul 2002 09:31:34 +0200 To: rasmol@lists.umass.edu Dear leticia: I understand that rasmol is simple, apparently, because the sintaxis is not as simple and you have to remeber all commands and type them perfectly. Besides, commands are not translated to the spanish versions. With PE, you have options to use in spanish words most of the commands, so you don´t need to use the command slot, except for expertise mode. At the present time there is a PE version that works with internet explorer. We plan to adapt the spanish PE translations to these new versions as soon as possible. Gabriel Pons Leticia Britos ha escrito: > Hi, > I teach biochemistry and molecular biology to high school biology teachers > in Uruguay (South America). I use RasMol a lot and find it extremely > useful. Teachers love it. I have no problem with the language but most of > my students have to struggle with the commands in english. I know they are > quite easy and, on the other hand, it´s a good thing they have to make an > effort and practice their english (which is taught here in Uruguay all > through elementary and secondary school). However, it takes a lot more to > introduce the program in english. So I thought Protein Explorer in spanish > would be a solution. But at the institute I work the network of computers > only have internet explorer and it is not easy to install new programs, > without getting stuck in the red tape. That´s why I find Rasmol so useful, > for its simplicity in the installation (I even send the program to my > students by e-mail, along with some pdb files) and in its use too. > My question is: is there a possibility of a spanish version of RasMol? > Although I do not master programing skills, I offer to help in any way needed. > > Best regards, > > Leticia > > At 11:30 a.m. 09/07/2002 -0400, you wrote: > >Forwarded for Patrick Barry by Eric Martz to circumvent > >technical difficulties: > >----- > > > >Tantas gracias! Me gusta mucho el sitio! > > > > > > M. Sc. Leticia Britos > Sección Bioquímica- Lab. 305 > Facultad de Ciencias > Universidad de la República > Iguá 4225 > C.P. 11400 Montevideo > URUGUAY > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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:1.0rc2) Gecko/20020510 X-Accept-Language: es-AR, es, en References: <5.1.0.14.1.20020710163026.026d7fd8@fcien.edu.uy> <3D2D3456.5B3CF69E@bellvitge.bvg.ub.es> ++++------+------+------+------+------+------+------+------+------+------+ From: Fernando Subject: Re: protein Explorer in spanish Date: Thu, 11 Jul 2002 05:09:40 -0300 To: rasmol@lists.umass.edu Hi, The traslate is only for the "window menus" and the "system message" in the prompt entry. Traslate the commands requiere mayor code rewrite to make a "spanish" script compatible with a "english" script, for example. Regards, Gabriel Pons wrote: > Dear leticia: > > I understand that rasmol is simple, apparently, because the sintaxis is not as > simple and you have to remeber all commands and type them perfectly. Besides, > commands are not translated to the spanish versions. With PE, you have options to > use in spanish words most of the commands, so you don´t need to use the command > slot, except for expertise mode. At the present time there is a PE version that > works with internet explorer. We plan to adapt the spanish PE translations to > these new versions as soon as possible. > > Gabriel Pons > > Leticia Britos ha escrito: > > >>Hi, >>I teach biochemistry and molecular biology to high school biology teachers >>in Uruguay (South America). I use RasMol a lot and find it extremely >>useful. Teachers love it. I have no problem with the language but most of >>my students have to struggle with the commands in english. I know they are >>quite easy and, on the other hand, it´s a good thing they have to make an >>effort and practice their english (which is taught here in Uruguay all >>through elementary and secondary school). However, it takes a lot more to >>introduce the program in english. So I thought Protein Explorer in spanish >>would be a solution. But at the institute I work the network of computers >>only have internet explorer and it is not easy to install new programs, >>without getting stuck in the red tape. That´s why I find Rasmol so useful, >>for its simplicity in the installation (I even send the program to my >>students by e-mail, along with some pdb files) and in its use too. >>My question is: is there a possibility of a spanish version of RasMol? >>Although I do not master programing skills, I offer to help in any way needed. >> >>Best regards, >> >>Leticia >> >>At 11:30 a.m. 09/07/2002 -0400, you wrote: >> >>>Forwarded for Patrick Barry by Eric Martz to circumvent >>>technical difficulties: >>>----- >>> >>>Tantas gracias! Me gusta mucho el sitio! >>> >>> >> >>M. Sc. Leticia Britos >>Sección Bioquímica- Lab. 305 >>Facultad de Ciencias >>Universidad de la República >>Iguá 4225 >>C.P. 11400 Montevideo >>URUGUAY >> > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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 g6BBCHh16057 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: protein Explorer in spanish Date: Thu, 11 Jul 2002 07:10:24 -0400 (EDT) To: rasmol@lists.umass.edu Just for the record: RasMol does have a menu bar and it does a great deal. Since the multilingual version of RasMol (e.g. RasMol 2.7.2.1) were introduced, the menu bar has had alternate presentations in different languages, messages have been offered in the language selected, and many of the command-line commands are accepted in forms from multiple languages. I applaud any moves by Chime, PE and other graphics programs in the same direction. I also remind the authors of those revisions, that, if they should happen to use any substantial portion of the multilingual code and/or translations from the RasMol 2.7 series as the basis to derive their own changes, then the programs that they produce are covered by the GPL-like RasMol license conditions, and become open source. I encourage such moves, since I think science and education are best served when their tools are fully and openly understood, and fully available to others for further development of our field. -- 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, 11 Jul 2002, Gabriel Pons wrote: > Dear leticia: > > I understand that rasmol is simple, apparently, because the sintaxis > is not as simple and you have to remeber all commands and type them > perfectly. Besides, commands are not translated to the spanish > versions. With PE, you have options to use in spanish words most of > the commands, so you don´t need to use the command slot, except for > expertise mode. At the present time there is a PE version that works > with internet explorer. We plan to adapt the spanish PE translations > to these new versions as soon as possible. > > Gabriel Pons > > Leticia Britos ha escrito: > > > Hi, > > I teach biochemistry and molecular biology to high school biology teachers > > in Uruguay (South America). I use RasMol a lot and find it extremely > > useful. Teachers love it. I have no problem with the language but most of > > my students have to struggle with the commands in english. I know they are > > quite easy and, on the other hand, it´s a good thing they have to make an > > effort and practice their english (which is taught here in Uruguay all > > through elementary and secondary school). However, it takes a lot more to > > introduce the program in english. So I thought Protein Explorer in spanish > > would be a solution. But at the institute I work the network of computers > > only have internet explorer and it is not easy to install new programs, > > without getting stuck in the red tape. That´s why I find Rasmol so useful, > > for its simplicity in the installation (I even send the program to my > > students by e-mail, along with some pdb files) and in its use too. > > My question is: is there a possibility of a spanish version of RasMol? > > Although I do not master programing skills, I offer to help in any way needed. > > > > Best regards, > > > > Leticia > > > > At 11:30 a.m. 09/07/2002 -0400, you wrote: > > >Forwarded for Patrick Barry by Eric Martz to circumvent > > >technical difficulties: > > >----- > > > > > >Tantas gracias! Me gusta mucho el sitio! > > > > > > > > > > M. Sc. Leticia Britos > > Sección Bioquímica- Lab. 305 > > Facultad de Ciencias > > Universidad de la República > > Iguá 4225 > > C.P. 11400 Montevideo > > URUGUAY > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: 11 Jul 2002 14:41:35.0507 (UTC) FILETIME=[0E789630:01C228E9] ++++------+------+------+------+------+------+------+------+------+------+ From: Brian White Subject: Animation/Simulation of protein folding Date: Thu, 11 Jul 2002 10:44:52 -0400 To: rasmol@lists.umass.edu Hi all - Is there a .pdb file of a series of images of a protein folding out there somewhere? This could be a simulation - I just want to show my students the idea of it exploring conformations & gradually wrapping up. 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-- X-Accept-Language: es References: <3D2D99E0.DE65EDA8@umb.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Gabriel Pons Subject: Re: Animation/Simulation of protein folding Date: Thu, 11 Jul 2002 16:53:41 +0200 To: rasmol@lists.umass.edu Hi: That is a very interesting point. I have tried something very rudimentary, taking myoglobin and preparing several models progressively folding and unfolding. I used weblab to rotate some angles and progressively unfold the protein. Then you can put them in inverse order and see them starting with the most unfolded until the complete folded protein. But I understand that more intermediate models are need. If you are interested I will send the pdb file to you. Gabriel Pons Brian White ha escrito: > Hi all - > Is there a .pdb file of a series of images of a protein folding out > there somewhere? This could be a simulation - I just want to show my > students the idea of it exploring conformations & gradually wrapping up. > > 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-- References: <3D2D99E0.DE65EDA8@umb.edu> X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id g6BFfxh26358 ++++------+------+------+------+------+------+------+------+------+------+ From: Jesus Sanz Subject: Re: Animation/Simulation of protein folding Date: Thu, 11 Jul 2002 17:39:54 +0200 To: rasmol@lists.umass.edu At 16:53 11/07/02, Gabriel Pons wrote: > I have tried something very rudimentary, >taking myoglobin and preparing several models progressively folding and >unfolding. I used weblab to rotate some angles and progressively unfold the >protein. Then you can put them in inverse order and see them starting with >the most unfolded until the complete folded protein. But I understand that >more intermediate models are need. If you are interested I will send the pdb >file to you. > In response to Brian White >Brian White ha escrito: > > > Hi all - > > Is there a .pdb file of a series of images of a protein folding out > > there somewhere? This could be a simulation - I just want to show my > > students the idea of it exploring conformations & gradually wrapping up. > > > > Hi there! I have done the same that Gabriel suggests, i.e., model the unfolded form from a PDB structure simply varying several Ramachandran angles. To obtain the intermediate states, I used Protein Morpher (http://www.umass.edu/microbio/chime/morpher/index.htm). The first impression is very good, but the worst thing is that if you select the linear interpolation mode (the easiest), you get strange artifacts (i.e., atoms passing through each other, etc..) due to the extreme conformational change. Therefore, it is better to use any of the more complex methods described in the page above. Jesus ----------------------------------- Prof. Jesus M. Sanz Centro de Biologia Molecular y Celular -- Universidad Miguel Hernandez Edificio Torregaitán. Avda. Ferrocarril, s/n. ELCHE, 03202-Alicante, SPAIN Tel:(34) 966 658 460/474 Fax:(34) 966 658 758 http://cbmc.umh.es/jmsanz/Jesussanz.htm E-mail: jmsanz@umh.es "Conciencia: voz interior que nos avisa que alguien puede estar mirando" (H.L. Mencken) ------------------------------------- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <3D2D99E0.DE65EDA8@umb.edu> <5.1.0.14.0.20020711172549.009f50d0@mussol.umh.es> ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re: Animation/Simulation of protein folding Date: Thu, 11 Jul 2002 20:20:43 +0200 To: rasmol@lists.umass.edu There are also movies of protein folding at this address : http://folding.stanford.edu/results.html 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: "Herbert J. Bernstein" Subject: IRIX 6.2 RasMol 2.7.2.1 Binaries for SGI computers Date: Wed, 17 Jul 2002 11:04:41 -0400 (EDT) To: rasmol@lists.umass.edu, pdb-l@rcsb.org We are pleased to announce the availability of IRIX 6.2 binaries of RasMol 2.7.2.1. These binaries have also been tested under IRIX 6.5 and are available from the Accessible Retired Computers in Biology (ARCiB) web site, http://arcib.dowling.edu, at Dowling College. Our thanks to Dr. John Westbrook of Rutgers and the PDB and NDB projects for the donation of an SGI Challenge computer to the ARCiB project, and to Dr. Ron Black of Dowling College for the donation of several SGI O2's. The Challenge was used to compile the new SGI binaries and the O2's used to test operation under IRIX 6.5. Our thanks to the NSF for funding of the ARCiB project. -- Herbert 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 ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Jim Perkins Subject: silly question Date: Thu, 18 Jul 2002 15:52:49 -0500 To: rasmol@lists.umass.edu This is going to sound like a very silly question but I'm curious what is the generally accepted pronunciation of "Chime"? Since the name is presumably derived from the word Chemical or Chemistry, I would guess it's pronounced with a hard "K" sound. However, it's spelled exactly the same as the sound a doorbell makes (with a soft "ch" sound as in "choose"). I'm giving a talk next week about how I use Chime in my illustration work and it occured to me that I wasn't sure how it is normally pronounced. Thanks! Jim ___________________________________________________________ James A. Perkins, MS, MFA Assistant Professor of Medical Illustration College of Imaging Arts and Sciences Rochester Institute of Technology Bldg. 7A, Room 3415 73 Lomb Memorial Drive Rochester, NY 14623 585-475-2443 fax: 585-475-6447 japfaa@rit.edu ___________________________________________________________ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Microsoft-Entourage/9.0.1.3108 ++++------+------+------+------+------+------+------+------+------+------+ From: "S. R. Judd" Subject: Re: silly question Date: Fri, 19 Jul 2002 10:47:53 -0500 To: rasmol@lists.umass.edu I don't know the official pronunciation. But somehow, I never before felt cognitive dissonance when I pronounced "Chemical Mime" like the English word "chime". -- S. Renee Judd Assistant Professor, Natural Science Department College of Arts and Sciences National-Louis University rjudd@nl.edu ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Phillip Barak Subject: Re: silly question Date: Fri, 19 Jul 2002 11:12:06 -0500 To: rasmol@lists.umass.edu As for official pronunciation, I was told by one of the Chime development people some years back that they pronounce it with the "ch" as in "chug" rather as in chi or chemical. (And for those interested, my related research has indicated that the "original" pronunciation of the "GIF" file type for graphics is with soft g, like "jib", instead of hard g like graphics.) 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/ co-curator, The Virtual Museum of Minerals & Molecules, www.soils.wisc.edu/virtual_museum/ ======================================================================= At 10:47 AM 7/19/2002 -0500, you wrote: >I don't know the official pronunciation. But somehow, I never before felt >cognitive dissonance when I pronounced "Chemical Mime" like the English word >"chime". > > >-- >S. Renee Judd >Assistant Professor, Natural Science Department >College of Arts and Sciences >National-Louis University >rjudd@nl.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-Originating-IP: [12.91.250.227] X-OriginalArrivalTime: 19 Jul 2002 21:08:23.0736 (UTC) FILETIME=[6AF54B80:01C22F68] ++++------+------+------+------+------+------+------+------+------+------+ From: "Pat O'Hern" Subject: Re: silly question Date: Fri, 19 Jul 2002 21:08:23 +0000 To: rasmol@lists.umass.edu

Jim-

Not only is Chime with a soft ch correct (as others have said), but chime pronounced with a hard ch is the word used in biology to describe the liquidy contents of the stomach during the process of digestion. Depending on the audience, I can hear the giggles now. Stick with the soft ch.

Pat




Patricia A. O'Hern
Computer-based Training
and Web Design
318 N. Decatur Lane
Decatur, GA 30033
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----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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_7u+wQJMkg8sgpWZXgLkpLA)" ++++------+------+------+------+------+------+------+------+------+------+ From: Ismith1945@aol.com Subject: Re: silly question Date: Sat, 20 Jul 2002 15:00:05 -0400 (EDT) To: rasmol@lists.umass.edu --Boundary_(ID_7u+wQJMkg8sgpWZXgLkpLA) Pat Isn't it spelt chyme? Ian. --Boundary_(ID_7u+wQJMkg8sgpWZXgLkpLA) Pat

Isn't it spelt chyme?

Ian. --Boundary_(ID_7u+wQJMkg8sgpWZXgLkpLA)-- X-Originating-IP: [12.91.235.201] X-OriginalArrivalTime: 20 Jul 2002 21:15:55.0359 (UTC) FILETIME=[A28F3EF0:01C23032] ++++------+------+------+------+------+------+------+------+------+------+ From: "Pat O'Hern" Subject: Re: silly question Date: Sat, 20 Jul 2002 21:15:55 +0000 To: rasmol@lists.umass.edu Ian- Yes, but we're talking pronunciation here. Pat >>Isn't it spelt chyme? >>Ian. Patricia A. O'Hern 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 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 _________________________________________________________________ Send and receive Hotmail on your mobile device: http://mobile.msn.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-MIMEOLE: Produced By Microsoft Exchange V6.0.5762.3 Thread-Topic: silly question Thread-Index: AcIwMs+sDt0FTCTUSZS0dHYJn9bwZwAAHi/w content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: X-OriginalArrivalTime: 20 Jul 2002 21:21:41.0750 (UTC) FILETIME=[71065160:01C23033] ++++------+------+------+------+------+------+------+------+------+------+ From: "Morgan, William T." Subject: RE: silly question Date: Sat, 20 Jul 2002 16:21:41 -0500 To: rasmol@lists.umass.edu FOLKS - Let's get out acts together! If you wish to chit chat about "stuff" - go ahead - but for the love of Mike do NOT do it on the whole bloody list! Thanks, Bill Morgan ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Date: Sun, 21 Jul 2002 09:19:50 -0400 To: "LIST: rasmol" greetings, do you have OS X? you'll definitely want to check out only version 0.1 and obviously a WIP, but it looks like a decent start to something! plus it reaffirms my feeling that the Aqua interface can be a damn beautiful thing. in my opinion, of course ;-) -tim -- molvisions - 3D molecular visualization wake forest, nc 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: lotus chung Subject: Installation questions Date: Mon, 29 Jul 2002 09:34:42 -0700 (PDT) To: rasmol@lists.umass.edu Hello, Has anyone seen this problem before? I want to install RasMol in X window. When I ran the "make" command, the system gave me the following output: gcc -O2 -march=i386 -mcpu=i686 -I/usr/X11R6/include -Dlinux -D__i386__ -D_POSIX_C_SOURCE=199309L -D_POSIX_SOURCE -D_XOPEN_SOURCE -D_BSD_SOURCE -D_SVID_SOURCE -DFUNCPROTO=15 -DNARROWPROTO -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DEIGHTBIT -c -o rasmol.o rasmol.c rasmol.c:46:24: sys/termio.h: No such file or directory make: *** [rasmol.o] Error 1 Basically, it can't find the sys/termio.h file. Do you know how to go about solving this problem? I have redhat linux 7.3. Thanks so much! Lotus __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.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-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: pmesh/tmesh and gaussian cube surfaces in Chime Date: Wed, 31 Jul 2002 13:22:51 -0400 To: Dovga@oumail.openu.ac.il Cc: djohnston@otterbein.edu, rasmol@lists.umass.edu, chime-team@mdli.com >From: Dov Garmise >To: "'emartz@microbio.umass.edu'" >Subject: Feedback from Chime Resources >Date: Sun, 28 Jul 2002 17:05:14 +0200 > >Hi Eric, >My name is Dov Garmise. I am a multimedia developer from Open University >Israel. >I have a question. I don't know if you generally answer questions but I hope >you could help me or at least point me to the right direction. > >I want to create a tutorial with Chime showing symmetry in molecules. I want >to make something similar to what was done in >http://www.otterbein.edu/home/fac/dnhjhns/symmetry/intro.html. In that site >the "load pmesh" feature of Chime was used to load a tmesh file, which >showed a surface in the molecule, thus showing the symmetry of the molecule. > >What I want to know is how these surfaces are created. Which software >exports tmesh files and how are these files defined to fit the specific >molecule? > >Let me just say that I am pretty new to molecular visualization. I know how >to create molecules with ChemOffice, but have never worked with surfaces. > >Any help will be appreciated. >Thanks, >Dov Garmise > Dear Dov: I've been curious about the tmesh format readable by Chime for years. I have some examples that MDL originally had on their website, but the format or software used to generate them is not documented. Nevertheless, they do load and display surfaces. Evidently Dean Johnston figured it out and I hope he'll enlighten us. Chime's has a little used 'load surface gaussian filename surfacename' option for "Gaussian Cube" files. I got a friend who has access to Gaussian to export a surface cube file which is 6 megabytes. Sure enough, I was able to display it in Chime. I don't know anything about Gaussian or these file formats. I can send you the files he sent me if you wish (the file ending in .cub is the one I displayed in Chime). I can also send you the original MDL demo files that display pmesh/tmesh if you wish. Beyond that I have no help to offer. If you wish to pursue this I suggest that you ask questions on the Molecular Visualization Freeware (RasMol) email list (URL below) and keep it informed of any progress. I'm copying this to the list in case anyone has something to contribute. Messages sent to the list are archived and provide a searchable database. Another method people have used is to create a PDB file containing pseudo "atoms" that, when displayed at tiny spacefill diameter, represent a surface as dots. I don't have a URL to this site handy but maybe someone on the list knows? The only site indexed under "molecular orbitals" at http://molvisindex.org is in the Organic Chem category, and is http://www.chem.uic.edu/web1/OCOL-II/WIN/HOME.HTM notably http://www.chem.uic.edu/web1/OCOL-II/WIN/STRUCT.HTM but the author Paul Young hasn't exploited Chime much to show orbitals as far as I could notice. -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 Molecular Visualization Freeware EMail Discussion List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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-FC-Icon-ID: 2032 X-FC-MachineGenerated: true ++++------+------+------+------+------+------+------+------+------+------+ From: "Kathleen M. Gorski" Subject: Re: pmesh/tmesh and gaussian cube surfaces in Chime Date: Wed, 31 Jul 2002 13:32:23 -0400 To: rasmol@lists.umass.edu I will be away and not checking email until August 9th. thanks, kathy g ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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/10.1.0.2006 ++++------+------+------+------+------+------+------+------+------+------+ From: "James W. Caras" Subject: Chime, browsers, and Netscape 7 Date: Fri, 02 Aug 2002 13:55:51 -0500 To: rasmol@lists.umass.edu Hi all- FYI, at the BCCE last week all of the symposia on molecular visualization I attended shared a common theme: most everyone commented on the dismal state of browser support for Chime in their talks, and considerable discussion focused on this after the presentations. However, I was very excited and relieved to witness the very new Netscape 7 (pre-release 1 I believe) running Chime with no problems on a PC laptop. I had heard tales of others getting it working on Netscape 6, but did not believe them until I saw it with my own eyes. I cannot replicate this on the Mac (OS X), but I will struggle with it a bit more... 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 Home/Work (512) 636-8342 Mobile ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. /|||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: lotus chung Subject: Ball & Stick question. Date: Fri, 02 Aug 2002 16:22:31 -0700 (PDT) To: rasmol@lists.umass.edu Hi, I am trying to display ball and stick in the structure of a molecule via command line. I can not find the command that allows user to do that. Does anyone know how to do it? Thanks very much! Best, Lotus __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.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-- X-Accept-Language: fr,en-US References: <20020802232231.32792.qmail@web13701.mail.yahoo.com> ++++------+------+------+------+------+------+------+------+------+------+ From: Jean-Philippe Demers Subject: Re: Ball & Stick question. Date: Fri, 02 Aug 2002 19:38:35 -0400 To: rasmol@lists.umass.edu Hi Lotus, There is no single command that corresponds to the Chime menu command "Ball & Stick". Instead, you can use "wireframe 0.15; spacefill 0.45" Jean-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-- ++++------+------+------+------+------+------+------+------+------+------+ From: lotus chung Subject: Re: Ball & Stick question. Date: Fri, 02 Aug 2002 17:28:32 -0700 (PDT) To: rasmol@lists.umass.edu Hi, Jean, Thanks so much! Best, Lotus --- Jean-Philippe Demers wrote: > Hi Lotus, > > There is no single command that corresponds to the > Chime menu command "Ball > & Stick". > Instead, you can use "wireframe 0.15; spacefill > 0.45" > > Jean-Philippe > > > __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.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-- X-Accept-Language: en References: <20020802232231.32792.qmail@web13701.mail.yahoo.com> ++++------+------+------+------+------+------+------+------+------+------+ From: "Gordon W. Ayers" Subject: Re: Ball & Stick question. Date: Sat, 03 Aug 2002 18:50:54 -0500 To: rasmol@lists.umass.edu I have not tried this myself but the rasmol 2.7.1 manual states that the command SPACEFILL will do the job Gord lotus chung wrote: > Hi, > > I am trying to display ball and stick in the structure > of a molecule via command line. I can not find the > command that allows user to do that. Does anyone know > how to do it? Thanks very much! > > Best, > Lotus > > __________________________________________________ > Do You Yahoo!? > Yahoo! Health - Feel better, live better > http://health.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-- ++++------+------+------+------+------+------+------+------+------+------+ From: lotus chung Subject: A question on calling RasMol from a perl script Date: Sun, 04 Aug 2002 09:13:00 -0700 (PDT) To: rasmol@lists.umass.edu Hi, I wrote a perl script to call RasMol. The perl script will open the console and the graphic window of RasMol. Then I want to use the same perl script to tell RasMol to run the "script " as if it is typed in the console window. In other words, what is the syntax of telling perl script to input rasmol commands into the rasmol console window automatically? Thanks so much! Best, Lotus __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.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-- ++++------+------+------+------+------+------+------+------+------+------+ From: lotus chung Subject: Re: Ball & Stick question. Date: Sun, 04 Aug 2002 09:14:53 -0700 (PDT) To: rasmol@lists.umass.edu Hi, Gordon, Thanks for the suggestion. This problem is sorted out. Thank you. Best, Lotus --- "Gordon W. Ayers" wrote: > I have not tried this myself but the rasmol 2.7.1 > manual states that the > command > > SPACEFILL will do the job > > Gord > > > lotus chung wrote: > > > Hi, > > > > I am trying to display ball and stick in the > structure > > of a molecule via command line. I can not find > the > > command that allows user to do that. Does anyone > know > > how to do it? Thanks very much! > > > > Best, > > Lotus > > > > __________________________________________________ > > Do You Yahoo!? > > Yahoo! Health - Feel better, live better > > http://health.yahoo.com > > > > > __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.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-- ++++------+------+------+------+------+------+------+------+------+------+ From: lotus chung Subject: A question on calling RasMol from a perl script (contiuned) Date: Sun, 04 Aug 2002 12:11:03 -0700 (PDT) To: rasmol@lists.umass.edu Hi, all, I forgot to mention in my earlier posting that I am running my perl script on a client in Mac OS 10. Thanks. Best, Loleta __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.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-- ++++------+------+------+------+------+------+------+------+------+------+ From: lotus chung Subject: A question on calling RasMol from a perl script (contiuned) Date: Sun, 04 Aug 2002 12:11:26 -0700 (PDT) To: rasmol@lists.umass.edu Hi, all, I forgot to mention in my earlier posting that I am running my perl script on a client in Mac OS 10. Thanks. Best, Lotus __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.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-- 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: <20020804161300.44888.qmail@web13708.mail.yahoo.com> ++++------+------+------+------+------+------+------+------+------+------+ From: mike Subject: Re: A question on calling RasMol from a perl script Date: Sun, 04 Aug 2002 13:17:58 -0700 To: rasmol@lists.umass.edu Hi, I've written a handful of TCL scripts to control rasmol under Linux. Let me know if you think they might be helpful as examples. I can send them to you. Page 9 of the 2.7.2 manual gives details for AppleEvents. Mike lotus chung wrote: > Hi, > > I wrote a perl script to call RasMol. The perl script > will open the console and the graphic window of > RasMol. Then I want to use the same perl script to > tell RasMol to run the "script " as > if it is typed in the console window. In other words, > what is the syntax of telling perl script to input > rasmol commands into the rasmol console window > automatically? Thanks so much! > > Best, > Lotus > > __________________________________________________ > Do You Yahoo!? > Yahoo! Health - Feel better, live better > http://health.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-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Douglas Kojetin Subject: RE: A question on calling RasMol from a perl script Date: Mon, 05 Aug 2002 00:05:00 -0400 To: rasmol@lists.umass.edu Hi- I'd like to see an example if possible. Many thanks, Doug -----Original Message----- On Behalf Of mike Sent: Sunday, August 04, 2002 4:18 PM From: owner-rasmol@lists.umass.edu [mailto:owner-rasmol@lists.umass.edu] Subject: Re: A question on calling RasMol from a perl script To: rasmol@lists.umass.edu Hi, I've written a handful of TCL scripts to control rasmol under Linux. Let me know if you think they might be helpful as examples. I can send them to you. Page 9 of the 2.7.2 manual gives details for AppleEvents. Mike lotus chung wrote: > Hi, > > I wrote a perl script to call RasMol. The perl script > will open the console and the graphic window of > RasMol. Then I want to use the same perl script to > tell RasMol to run the "script " as > if it is typed in the console window. In other words, > what is the syntax of telling perl script to input > rasmol commands into the rasmol console window > automatically? Thanks so much! > > Best, > Lotus > > __________________________________________________ > Do You Yahoo!? > Yahoo! Health - Feel better, live better > http://health.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-- ++++------+------+------+------+------+------+------+------+------+------+ From: lotus chung Subject: Re: A question on calling RasMol from a perl script Date: Mon, 05 Aug 2002 09:36:43 -0700 (PDT) To: rasmol@lists.umass.edu Hi, Mike, Can I see some as examples? Thanks so much. Thanks, Lotus --- mike wrote: > Hi, > > I've written a handful of TCL scripts to control > rasmol > under Linux. Let me know if you think they might be > helpful > as examples. I can send them to you. > > Page 9 of the 2.7.2 manual gives details for > AppleEvents. > > Mike > > lotus chung wrote: > > > Hi, > > > > I wrote a perl script to call RasMol. The perl > script > > will open the console and the graphic window of > > RasMol. Then I want to use the same perl script > to > > tell RasMol to run the "script " > as > > if it is typed in the console window. In other > words, > > what is the syntax of telling perl script to input > > rasmol commands into the rasmol console window > > automatically? Thanks so much! > > > > Best, > > Lotus > > > > __________________________________________________ > > Do You Yahoo!? > > Yahoo! Health - Feel better, live better > > http://health.yahoo.com > > > > > > > > > > > > __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.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-- ++++------+------+------+------+------+------+------+------+------+------+ From: lotus chung Subject: RasMol for OS10? Date: Mon, 05 Aug 2002 10:05:04 -0700 (PDT) To: rasmol@lists.umass.edu Hi, Is there a version of RasMol for OS10? Also, when I try to run RasMol in x window under red hat linux 7.3, the canvas window of RasMol can't be displayed. Does anyone know why? Thanks. Best, Lotus __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.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-- 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 ++++------+------+------+------+------+------+------+------+------+------+ From: mike Subject: control rasmol from a script Date: Mon, 05 Aug 2002 11:35:51 -0700 To: rasmol@lists.umass.edu, lotusch2000@yahoo.com, djkojeti@unity.ncsu.edu This is a multi-part message in MIME format. --Boundary_(ID_z8Js30ALh47vdzA7+xHSSA) lotus chung wrote: > Hi, Mike, > > Can I see some as examples? Thanks so much. > > Thanks, > Lotus Douglas Kojetin wrote: > Hi- > > I'd like to see an example if possible. > > Many thanks, > Doug The 8 scripts are from last spring. They are the *only* Tcl scripts i've ever written ... so it can't be all that difficult! Cheers, Mike ================================================================= The key feature is that rasmol will let other software programs tell it what to do, as described in the first few pages of the Rasmol manual. It is simple in Linux ... maybe win/mac too. The 7 examples start off trivial and lead up to automatic scene captures for making movies. The first script rotates whatever molecule is loaded into Rasmol. 1) startup rasmol 2) load a molecule 3) in a shell, run the command: ISB_rasrot_1.tcl - does a 360 degree rotation about the y-axis. It should work right away under Linux. If in doubt, check to see if you have "wish" installed. wish(1) is the Tcl interpreter that will read the script and send the commands to rasmol. ISB_rasrot_2.tcl rotates the molecule about both the x and y axes. ==== Additional features are in the next few scripts. To run script 3, edit the file by changing the pdb file name to one that you have handy. I've been keeping all my pdbs in a folder called "PDB", so I specify the pdb file as "PDB/1HHV.pdb". If you have questions about the rasmol commands that i've put in script 3, you'll find them described Rasmol manual. I've added in just a little bit in each successive script so that you can follow along even if you are not familiar with the Tcl scripting language -- which I wasn't familiar with either before I started this. It is a simple language, with great www resources, like this site: http://tcl.activestate.com/man/tcl8.3/ This 4th script lets you set parameters at the same time that you issue the command: and the 5th, predefines default values for the parameters so that it is not essential to pass them on the command line: The 6th contains additional parameters. and the 7th script show the style that i use to save each rotation image to file, so that i can glom the images together to make a movie (using another little script called crop.tcl). Cheers, Mike --Boundary_(ID_z8Js30ALh47vdzA7+xHSSA) Content-disposition: inline; filename=ISB_rasrot_1.tcl #!/usr/bin/wish #TCL script for rotating rasmol for {set N 0} { $N <= 360 } {incr N 1} { send rasmol rotate y 1 after 30 ;# pause for 30milleseconds between rotations } exit --Boundary_(ID_z8Js30ALh47vdzA7+xHSSA) Content-disposition: inline; filename=ISB_rasrot_2.tcl #!/usr/bin/wish for {set N 0} { $N <= 360 } {incr N 1} { send rasmol rotate x 1 send rasmol rotate y 1 send rasmol rotate z 0 after 30 ;# pause for 30milleseconds between rotations } exit --Boundary_(ID_z8Js30ALh47vdzA7+xHSSA) Content-disposition: inline; filename=ISB_rasrot_3.tcl #!/usr/bin/wish set rotation_incr 1 set pdb_file "1HVV.pdb" set delay 30 send rasmol zap send rasmol load $pdb_file send rasmol reset for {set ii 0} { $ii <= 360 } {incr ii $rotation_incr} { send rasmol rotate x [expr $rotation_incr * 0 ] send rasmol rotate y [expr $rotation_incr * 0 ] send rasmol rotate z [expr $rotation_incr * 1 ] after $delay } exit --Boundary_(ID_z8Js30ALh47vdzA7+xHSSA) Content-disposition: inline; filename=ISB_rasrot_4.tcl #!/usr/bin/wish ######################################## # # PARSE THROUGH THE COMMAND-LINE ARGUMENT LIST # # lindex stands for list index. # # the variable argv is the list of parameters # # given on the command line, for example: # # ISB_rasrot_4.tcl 1 PDB/1HVV.pdb 30 # set rotation_incr [lindex $argv 0] set pdb_file [lindex $argv 1] set delay [lindex $argv 2] send rasmol zap send rasmol load $pdb_file send rasmol reset send rasmol ribbons for {set ii 0} { $ii <= 360 } {incr ii $rotation_incr} { after $delay send rasmol rotate x [expr $rotation_incr * 0 ] send rasmol rotate y [expr $rotation_incr * 1 ] send rasmol rotate z [expr $rotation_incr * 0 ] } exit --Boundary_(ID_z8Js30ALh47vdzA7+xHSSA) Content-disposition: inline; filename=ISB_rasrot_5.tcl #!/usr/bin/wish ####################################### # # SET DEFAULT VALUES so that user can # execute this script WITHOUT command line arguments # set rotation_incr 1 ; # set pdb_file "PDB/1HVV.pdb" ; # PDB/1HVV.pdb set delay 30 ; # 1000 = 1 second, controls rotation speed by pausing between rotations ######################################## # # PARSE THROUGH THE COMMAND-LINE ARGUMENT LIST # if {$argc>=3} { set rotation_incr [lindex $argv 0] set pdb_file [lindex $argv 1] set delay [lindex $argv 2] } send rasmol zap send rasmol load $pdb_file send rasmol reset send rasmol ribbons send rasmol color brown send rasmol background white for {set ii 0} { $ii <= 360 } {incr ii $rotation_incr} { after $delay send rasmol rotate x [expr $rotation_incr * 0 ] send rasmol rotate y [expr $rotation_incr * 1 ] send rasmol rotate z [expr $rotation_incr * 0 ] } exit --Boundary_(ID_z8Js30ALh47vdzA7+xHSSA) Content-disposition: inline; filename=ISB_rasrot_6.tcl #!/usr/bin/wish ####################################### # # SET DEFAULT VALUES so that user can # execute this script with command line arguments # set rotation_incr 1 ; # set pdb_file "PDB/1HVV.pdb" ; # PDB/1HVV.pdb set delay 30 ; # 1000 = 1 second, controls rotation speed by pausing between rotations set init_x 0 ; # intial x rotation in degrees set init_y 0 ; # intial y rotation in degrees set init_z 0 ; # intial z rotation in degress ######################################## # # PARSE THROUGH THE COMMAND-LINE ARGUMENT LIST # set ii -1 if {$argc>=1} { incr ii 1; set rotation_incr [lindex $argv $ii] } if {$argc>=2} { incr ii 1; set pdb_file [lindex $argv $ii] } if {$argc>=3} { incr ii 1; set delay [lindex $argv $ii] } if {$argc>=4} { incr ii 1; set init_x [lindex $argv $ii] } if {$argc>=5} { incr ii 1; set init_y [lindex $argv $ii] } if {$argc>=6} { incr ii 1; set init_z [lindex $argv $ii] } if {$task == "record"} { set of_dir $of_prefix exec mkdir -p $of_dir exec rm -f $of_dir/${of_prefix}*$of_suffix } send rasmol zap send rasmol load $pdb_file send rasmol reset send rasmol ribbons send rasmol color brown send rasmol background white send rasmol rotate x $init_x send rasmol rotate y $init_y send rasmol rotate z $init_z for {set ii 0} { $ii <= 360 } {incr ii $rotation_incr} { after $delay send rasmol rotate x [expr $rotation_incr * 0 ] send rasmol rotate y [expr $rotation_incr * 1 ] send rasmol rotate z [expr $rotation_incr * 0 ] } exit --Boundary_(ID_z8Js30ALh47vdzA7+xHSSA) Content-disposition: inline; filename=ISB_rasrot_7.tcl #!/usr/bin/wish ####################################### # # DETERMINE THE ID OF THE RASMOL WINDOW # The approach used here is fragile. # It would be better to find some way to # do this within Tcl # #set tstr [exec xwininfo -int -root -tree | grep rasmol | head -n 1] #set tstr [string trim $tstr] #set tlist [split $tstr] #set win_id [lindex $tlist 0] #puts "$win_id \n" set rasmol_win_id [lindex [split [string trim [exec xwininfo -int -root -tree | grep rasmol | head -n 1]]] 0] ####################################### ####################################### # # SET DEFAULT VALUES so that user can # execute this script with command line arguments # set task "" ; # makegifs set of_prefix "xx_" ; # image files will be name prefixXXX.suffix set rotation_incr 1 ; # set pdb_file "PDB/1HVV.pdb" ; # PDB/1HVV.pdb set delay 30 ; # 1000 = 1 second, controls rotation speed by pausing between rotations set init_x 0 ; # intial x rotation in degrees set init_y 0 ; # intial y rotation in degrees set init_z 0 ; # intial z rotation in degress set of_suffix "gif" ; # image files will be name prefixXXX.suffix ######################################## # # PARSE THROUGH THE COMMAND-LINE ARGUMENT LIST # set ii -1 if {$argc>=3} { incr ii 1; set task [lindex $argv $ii] incr ii 1; set of_prefix [lindex $argv $ii] incr ii 1; set rotation_incr [lindex $argv $ii] } if {$argc>=4} { incr ii 1; set pdb_file [lindex $argv $ii] } if {$argc>=5} { incr ii 1; set delay [lindex $argv $ii] } if {$argc>=6} { incr ii 1; set init_x [lindex $argv $ii] } if {$argc>=7} { incr ii 1; set init_y [lindex $argv $ii] } if {$argc>=8} { incr ii 1; set init_z [lindex $argv $ii] } if {$task == "record"} { set of_dir $of_prefix exec mkdir -p $of_dir exec rm -f $of_dir/${of_prefix}*$of_suffix } send rasmol zap send rasmol load $pdb_file send rasmol reset send rasmol ribbons send rasmol color brown send rasmol background white send rasmol rotate x $init_x send rasmol rotate y $init_y send rasmol rotate z $init_z for {set ii 0} { $ii <= 360 } {incr ii $rotation_incr} { if {$task == "record"} { set of_file ${of_prefix}[format %04d $ii].$of_suffix puts "[format %04d $ii] $of_dir/$of_file" exec import -window $rasmol_win_id $of_dir/$of_file exec gzip -f $of_dir/$of_file } after $delay send rasmol rotate x [expr $rotation_incr * 0 ] send rasmol rotate y [expr $rotation_incr * 1 ] send rasmol rotate z [expr $rotation_incr * 0 ] } puts " " ################################################# # # the geometry reported by xwininfo(1) is helpful # # when croping with convert(1). see notes in anim.sh # if {$task == "record"} { exec xwininfo -all -id $rasmol_win_id > $of_dir/$of_prefix.xwininfo puts "\n[exec grep geometry $of_dir/$of_prefix.xwininfo] (useful for croping with convert(1))" puts "\n some commands for select-n-paste in X:" puts "\n ./crop.wsh $rotation_incr $of_dir/z$of_prefix gif" puts "" } exit --Boundary_(ID_z8Js30ALh47vdzA7+xHSSA) Content-disposition: inline; filename=crop.tcl #!/usr/bin/wish ########################################################## # # -geometry 276x304+0+-2 # convert -crop 224x224+14+38 xx_0000.gif.gz - | convert -crop 0x0 - - | display - # # x crop size = geom_x - 14 -38 # y crop size = geom_y - 38 - 42 # # convert -crop 224x224+14+38 ########################################################## # # set default values # # of = outfile # if = infile # set if_incr 1 set of_prefix "ww_" set of_suffix "gif" set if_prefix "xx_" set if_suffix "gif.gz" set if_width 443 set if_height 441 ########################################################## # # parse through command line arguments # set ii -1 if {$argc>=1} { incr ii 1; set if_incr [lindex $argv $ii] } if {$argc>=2} { incr ii 1; set of_prefix [lindex $argv $ii] } if {$argc>=3} { incr ii 1; set of_suffix [lindex $argv $ii] } if {$argc>=4} { incr ii 1; set if_prefix [lindex $argv $ii] } if {$argc>=5} { incr ii 1; set if_suffix [lindex $argv $ii] } if {$argc>=6} { incr ii 1; set if_width [lindex $argv $ii] } if {$argc>=7} { incr ii 1; set if_height [lindex $argv $ii] } #puts "\n deleting files " #puts "\n rm -f ${of_prefix}*$of_suffix \n" #exec rm -f ${of_prefix}*.gif #exec ls -l ${of_prefix}*.gif set an_width [expr $if_width - 14 - 38] set an_height [expr $if_height - 38 - 40] for {set ii 0; set jj 0} { $ii <= 340 } {incr ii $if_incr; incr jj 1} { set if_file $if_prefix[format %04d $ii].$if_suffix set of_file $of_prefix[format %04d $jj].$of_suffix puts "$if_file $of_file" exec convert -crop ${an_width}x${an_height}+14+38 $if_file $of_file } ######################################################### # puts "\n some commands for select-n-paste in X " puts "\n convert -loop 100 -delay 100 -adjoin ${of_prefix}*.gif $of_prefix.gif " puts "\n animate $of_prefix.gif " puts "" exit --Boundary_(ID_z8Js30ALh47vdzA7+xHSSA)-- Content-return: allowed Importance: Normal X-MSMail-priority: Normal References: <20020805170504.18500.qmail@web13709.mail.yahoo.com> ++++------+------+------+------+------+------+------+------+------+------+ From: "Vikberg, Gunnar" Subject: Re: RasMol for OS10? Date: Mon, 05 Aug 2002 21:17:22 -0500 (CDT) To: rasmol@lists.umass.edu Lotus, > Is there a version of RasMol for OS10? Also, when I > try to run RasMol in x window under red hat linux 7.3, > the canvas window of RasMol can't be displayed. Does > anyone know why? Thanks. If you are compiling your own version of RasMol under RedHat Linux 7.3, check the "Makefile" in the source directory. In it, you should find a line close to the top (maybethe first one after the comments) that says: DEFS = -DEIGHTBIT Change this line so that it reads: DEFS = -DTHIRTYTWOBIT or DEFS = -DSIXTEENBIT If you are using a 24 bit display, then the THIRTYTWOBIT option should work fine for you. The reason the display is not coming up along with the command line is that it is notable to find the proper color depth for the type of settings you are using in X. I hope this helps. Best of luck, Gunnar Vikberg ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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/9.0.1.3108 ++++------+------+------+------+------+------+------+------+------+------+ From: Tom Manderfield Subject: Re: RasMol for OS10? Date: Tue, 06 Aug 2002 09:40:42 -0400 To: rasmol@lists.umass.edu Lotus, I haven't tried to compile the Unix version of RasMol on Mac OS X, so I am not sure of the answer to your question directly. The rest of the information that follows contains instructions for scripting Rasmol externally without a MacOSX version of RasMol. The version of Rasmol for the Classic Environment of Mac OS (versions up to 9.2) may be scripted by entering Rasmol commands via the keyboard to the consol. To do this with an external script, such as AppleScript, requires bringing RasMol to the frontmost application and driving the keyboard via third party Scripting Addition (OSAX). The results work quite well. Your scripting language would need to interface with the Scripting Addition via AppleEvents, such as does AppleScript, Dylan, MacPerl, JavaScript OSA, MacPython 2.0, Mac Tcl/Tk with an Tcl OSA component, and others which supports Apple's Open Scripting Architecture (OSA). Tom On 08/05/2002 01:05 PM, "lotus chung" wrote: > Hi, > > Is there a version of RasMol for OS10? Also, when I > try to run RasMol in x window under red hat linux 7.3, > the canvas window of RasMol can't be displayed. Does > anyone know why? Thanks. > > Best, > Lotus > > __________________________________________________ > Do You Yahoo!? > Yahoo! Health - Feel better, live better > http://health.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-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: RasMol for OS10? Date: Tue, 06 Aug 2002 11:38:59 -0400 To: rasmol@lists.umass.edu it was 10:05 AM EDT on (Monday) 5 August 2002 when lotus chung said: > Hi, > > Is there a version of RasMol for OS10? > > Best, > Lotus > hi Lotus, I have not found a Carbonized version of RasMol anywhere. there are several X-Windows packages floating around, but I have not pursued this route so I can't comment beyond giving you a few links: if you or anyone else do find/make a Carbonized RasMol, please let me know! -tim -- molvisions - 3D molecular visualization wake forest, nc 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: <200207311728.g6VHSrd23413@marlin.bio.umass.edu> X-MIME-Autoconverted: from Quoted-printable to 8bit by marlin.bio.umass.edu id g77BOkd18147 ++++------+------+------+------+------+------+------+------+------+------+ From: nyitray@cerberus.elte.hu Subject: Re: Chime, browsers, and Netscape 7 Date: Wed, 07 Aug 2002 13:24:11 +0200 To: rasmol@lists.umass.edu On 2 Aug 02, at 13:55, James W. Caras wrote: > However, I was very excited and relieved to witness the very new Netscape 7 > (pre-release 1 I believe) running Chime with no problems on a PC laptop. Hi, I tried to install chime2.6(SP3) on the new Netscape 7 (running on Win2000 PC) but failed (the installer didn't recognize the browser folder). Any advise or trick how to do this? *********************************** Laszlo Nyitray, PhD Associate Professor Dept.Biochemistry, Eotvos University Budapest, Pázmány P. sétány 1/C H-1117 Hungary tel:361-381-2171 fax:361-381-2172 e-mail:nyitray@cerberus.elte.hu xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Barry Rowe Subject: OSX Date: Fri, 09 Aug 2002 12:56:28 -0700 (PDT) To: rasmol@lists.umass.edu I'm new to the list...... My question is about using rasmol or chime on mac OSX. What is available to visualize molecules on OSX? We use chime in OS9 and on the PC, but I can't find any reference to anyone using OSX and chime. Thanks, barry ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: OSX Date: Fri, 09 Aug 2002 16:40:54 -0400 To: rasmol@lists.umass.edu it was 12:56 PM EDT on (Friday) 9 August 2002 when Barry Rowe said: > I'm new to the list...... My question is about using rasmol or chime on > mac OSX. What is available to visualize molecules on OSX? We use chime > in OS9 and on the PC, but I can't find any reference to anyone using OSX > and chime. > > Thanks, > > barry > hi Barry, welcome. the short answer: not much is readily available for OS X yet, at least not natively, but most everything runs in Classic mode just fine. the long answer: iMol 0.1 is the only OS X native mol vis app that I've seen so far. it's neat, but as yet, it lacks the power of RasMol and Chime. don't try manipulating large structures in iMol. of course, it is still a very early release. RasMol 2.7 can be run in Classic mode in OS X without trouble, but AFAIK there is no native Carbon version yet. Chime 2.6 is limited to Classic as well, and Netscape pre-6 to boot on the Mac side. Chime works fine in Communicator 4.7x in Classic, as do all Chime-based Web sites that I've tested. an alpha release of Swiss PDB Viewer 3.7 is available for OS X. it works fine OMM (OS X 10.1.5) as long as I set the display to "thousands of colors" (thanks to a tip from Nicolas Guex). some features are not yet available, but stability was okay during my limited testing. WebLab is now DSViewer, and I can not find a Mac version. Cn3D 4 is a Classic app as far as I can tell. their Web site says it will run under OS X okay. I haven't tried it. Mage is still limited to OS 9. I could open and run in it Classic, but I did not try much more. MolView 1.5 opens and runs fine in Classic mode. I have not tested it extensively. you can run X Windows programs in OS X, too (RasMol, MolMol, RIBBONS, VMD). I know nothing about this, though, so I can't offer any help. maybe someone else on the list has experience in X Windows. for more info, you might try some of these links: hope that helps! tim -- molvisions - 3D molecular visualization wake forest, nc 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: "Herbert J. Bernstein" Subject: Re: OSX Date: Sat, 10 Aug 2002 03:42:20 -0400 (EDT) To: rasmol@lists.umass.edu You can use the classic mac versions of RasMol right now, and truly native ports of the latest release should be available in the Fall. You will find some early ports if you do a google search. -- HJB ===================================================== 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 Fri, 9 Aug 2002, Barry Rowe wrote: > I'm new to the list...... My question is about using rasmol or chime on mac OSX. What is available to visualize molecules on OSX? We use chime in OS9 and on the PC, but I can't find any reference to anyone using OSX and chime. > Thanks, > > barry > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: farquasi Subject: Re: OSX Date: Sat, 10 Aug 2002 21:43:24 -0500 To: rasmol@lists.umass.edu Tim, Thanks for your help. I will explore what you sent me and get back to you about it working so you know it works. Thanks. barry On Friday, August 9, 2002, at 03:40 PM, timothy driscoll wrote: > it was 12:56 PM EDT on (Friday) 9 August 2002 when Barry Rowe said: > >> I'm new to the list...... My question is about using rasmol or chime >> on >> mac OSX. What is available to visualize molecules on OSX? We use >> chime >> in OS9 and on the PC, but I can't find any reference to anyone using >> OSX >> and chime. >> >> Thanks, >> >> barry >> > > hi Barry, > > welcome. the short answer: not much is readily available for OS X yet, > at > least not natively, but most everything runs in Classic mode just fine. > > the long answer: > > iMol 0.1 is the only OS X native mol vis app that I've seen so far. > it's > neat, but as yet, it lacks the power of RasMol and Chime. don't try > manipulating large structures in iMol. of course, it is still a very > early > release. > > RasMol 2.7 can be run in Classic mode in OS X without trouble, but AFAIK > there is no native Carbon version yet. > > Chime 2.6 is limited to Classic as well, and Netscape pre-6 to boot on > the > Mac side. Chime works fine in Communicator 4.7x in Classic, as do all > Chime-based Web sites that I've tested. > > an alpha release of Swiss PDB Viewer 3.7 is available for OS X. it > works > fine OMM (OS X 10.1.5) as long as I set the display to "thousands of > colors" > (thanks to a tip from Nicolas Guex). some features are not yet > available, > but stability was okay during my limited testing. > > WebLab is now DSViewer, and I can not find a Mac version. > > Cn3D 4 is a Classic app as far as I can tell. their Web site says it > will > run under OS X okay. I haven't tried it. > > Mage is still limited to OS 9. I could open and run in it Classic, > but I > did not try much more. > > MolView 1.5 opens and runs fine in Classic mode. I have not tested it > extensively. > > > you can run X Windows programs in OS X, too (RasMol, MolMol, RIBBONS, > VMD). > I know nothing about this, though, so I can't offer any help. maybe > someone > else on the list has experience in X Windows. > > > for more info, you might try some of these links: > > > > > > > hope that helps! > > tim > -- > molvisions - 3D molecular visualization > wake forest, nc usa > > > > Barry Rowe O- farquasi@mac.com Chemistry / Physics Teacher http://roweba.com Champaign Centennial High School NCSA ChemViz Team Lord Earnest Rutherford said: "All of Science is either Physics or stamp collecting." ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Surface residues, interchain contacts Date: Tue, 13 Aug 2002 15:07:04 -0700 To: lpsobol@wiccmail.weizmann.ac.il, lpedel@weizmann.ac.il Cc: rasmol@lists.umass.edu Dear Meir and Vladimir: A question has come up about aggregate properties of the atoms in contact between chains vs. surface atoms in general. I'm sharing these questions with the Molecular Visualization Freeware/RasMol list hoping some subscribers there can help. 1. From CSU, it is possible to get summary properties for an entire chain, for example, total number of atoms contacting another chain, and percentages of those contacting atoms that are carbon/sulfur vs. oxygen/nitrogen, or sidechain vs backbone? If not, do you know of software that gives such summaries? 2. Do you know (from CSU or any other software) a way to generate a list of residues or atoms on the 'surface' of a molecule or chain? Ideally I'd like to cast this list into a script of select commands for RasMol/Chime. I note that this can be done in WHAT IF (http://www.cmbi.kun.nl/gv/servers/WIWWWI/) with Protein Analysis, Accessible Molecular Surface. This list could be captured and used in a spreadsheet or other software, e.g. to make a list of 'surface' residues, or a command script to select surface residues. I'm wondering if there is any other server that provides more in the way of summary statistics than does WHAT IF (which provides only average accessible area per amino acid type for the entire molecule). It is possible to get a list of residues or atoms putatively noncovalently bonded to any selected moiety in Protein Explorer. In QuickViews, select the desired moiety, the DISPLAY Contacts. When the display is completed, entering these two commands in the command-entry slot will show the list (which can be copied from the message box): select balled show residue ['residue' must be singular, not 'residues'] or show atoms or show chain ['chain' must be singular, not 'chains'] Best regards, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il 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: <200207311728.g6VHSrd23413@marlin.bio.umass.edu> <20020807112409.B2D3044638@mx1.elte.hu> ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re Re: Chime, browsers, and Netscape 7 Date: Fri, 23 Aug 2002 09:56:05 +0200 To: rasmol@lists.umass.edu Chime can't be installed automatically on Netscape 6.2 or 7 (nor on Mozilla). If you want to get Chime work with these browsers, you have to copy the plugin files from another Chime compatible browser plugin directory (for example, from the plug-in directory of Netscape Communicator or Internet Explorer) Good luck Paul Pillot ----- Original Message ----- Sent: Wednesday, August 07, 2002 1:24 PM From: Subject: Re: Chime, browsers, and Netscape 7 To: On 2 Aug 02, at 13:55, James W. Caras wrote: > However, I was very excited and relieved to witness the very new Netscape 7 > (pre-release 1 I believe) running Chime with no problems on a PC laptop. Hi, I tried to install chime2.6(SP3) on the new Netscape 7 (running on Win2000 PC) but failed (the installer didn't recognize the browser folder). Any advise or trick how to do this? *********************************** Laszlo Nyitray, PhD Associate Professor Dept.Biochemistry, Eotvos University Budapest, Pázmány P. sétány 1/C H-1117 Hungary tel:361-381-2171 fax:361-381-2172 e-mail:nyitray@cerberus.elte.hu xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft Exchange V6.0.5762.3 Thread-Topic: Re Re: Chime, browsers, and Netscape 7 Thread-Index: AcJKex2M+Rx0YMBZSeOGRNyElkUHdgApqxx6 content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: "Campbell, Malcolm" Subject: Re: Chime, browsers, and Netscape 7 Date: Fri, 23 Aug 2002 23:59:16 -0400 To: rasmol@lists.umass.edu With much effort, I figured out where to download Netscape 7.0_PR1 for Mac OSX, in English. ftp://ftp.netscape.com/pub/netscape7/english/7.0_PR1/mac/macosx/sea/ click on the .bin file. I installed this and tried to get chime to work. I put an old copy of plugin in the library>internet plugins folder. I went to preferences and tried to set this as a new helper application. I was unsuccessful. I was able to follow the earlier advice and get Netscape 7 for OS 8/9 to run chime on a Mac running only OS 9.2, once I placed a copy of Chime plugin into the plugin folder. This worked with no additional tinkering. Can anyone else figure out ways to get chime to work on Mac OSX? Thanks, Malcolm ------------------------------------------------------ A. Malcolm Campbell, Ph.D. Associate Professor of Biology Director of the Genome Consortium for Active Teaching coEditor-in-Chief of Cell Biology Education: Journal of Life Sciences Education Biology Department P. O. Box 7118 (US Mail) 209 Ridge Road (Shipping) Davidson, NC 28035 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-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: RasMac in Classic: TruBlueEnvironme process? Date: Wed, 28 Aug 2002 14:18:55 -0400 To: "LIST: rasmol" hi folks, I am running RasMac 2.6 in the Classic environment of OS X (9.2.2 and 10.1.5, G4, 256MB RAM, 2x500 MHz proc). Classic spawns a process called TruBlueEnvironme when it is running. normally this process accounts for about 10% of my CPU use, even with Classic apps like Netscape running. in contrast, if I launch RasMac, TruBlueEnvironme ramps up to 95-105% and OS X starts giving me "low memory" errors (even if RasMol is empty). anyone know what's going on here? does a similar thing happen in "regular" OS 9? (I don't know how to monitor processes in OS 9.) thanks, tim -- molvisions - molecular graphics & visualization http://www.molvisions.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: ++++------+------+------+------+------+------+------+------+------+------+ From: Eric C Niederhoffer Subject: Re: RasMac in Classic: TruBlueEnvironme process? Date: Wed, 28 Aug 2002 14:03:29 -0500 To: rasmol@lists.umass.edu Tim: I'm not sure what you mean by "regular" OS 9. I checked RasMac 2.7.2.1 in OS 9.0.4 on my PowerPC G3 (beige), 266 MHz, 160 MB. The system used 25 MB before and 26 MB after launching RasMac. The only active processes were the OS, Eudora Pro 4.2, and RasMac. Eric >hi folks, > >I am running RasMac 2.6 in the Classic environment of OS X (9.2.2 and >10.1.5, G4, 256MB RAM, 2x500 MHz proc). Classic spawns a process called >TruBlueEnvironme when it is running. normally this process accounts for >about 10% of my CPU use, even with Classic apps like Netscape running. in >contrast, if I launch RasMac, TruBlueEnvironme ramps up to 95-105% and OS X >starts giving me "low memory" errors (even if RasMol is empty). anyone know >what's going on here? does a similar thing happen in "regular" OS 9? (I >don't know how to monitor processes in OS 9.) > >thanks, > >tim >-- >molvisions - molecular graphics & visualization >http://www.molvisions.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: timothy driscoll Subject: Re: RasMac in Classic: TruBlueEnvironme process? Date: Wed, 28 Aug 2002 15:36:03 -0400 To: rasmol@lists.umass.edu it was 2:03 PM EDT on (Wednesday) 28 August 2002 when Eric C Niederhoffer said: > Tim: > > I'm not sure what you mean by "regular" OS 9. > hi Eric, you know - regular ;-) what I mean is OS 9 that is not running as Classic under/over OS X. aka stand-alone OS 9. > I checked RasMac 2.7.2.1 in OS 9.0.4 on my PowerPC G3 (beige), 266 MHz, > 160 MB. The system used 25 MB before and 26 MB after launching RasMac. > The only active processes were the OS, Eudora Pro 4.2, and RasMac. > that's RAM, and by default RasMol takes 1MB for itself - that's the 25-26MB difference that you're seeing. sorry if I wasn't clear - I'm not running out of RAM, apparently I'm running out of processor cycles (?). there have been several messages related to running RasMol in OS X, which is where this whole thing started for me. here's what I know, or think I know: TruBlueEnvironme is the name of the OS X process that "runs" Classic (as best as I can tell) - it appears when I launch Classic, and it generally uses about 10-20% of the total CPU %. if I launch other Classic apps this % increases, and is naturally higher while Classic apps are working, but it never goes extraordinarily high. but if I launch RasMol and leave it open (no file has to be loaded), I can watch the TruBlueEnvironme process ramp up to over 95% of CPU %. for some reason, then, Classic is hoarding all of my CPU cycles when RasMol is open, even if RasMol isn't doing anything. OS X includes a utility called ProcessViewer that lets you see how your system assets are allocated as different things happen on your computer. Windows has a similar utility, tho I'm not sure what it's called. does anyone know how to monitor system allocation in OS9? I'm curious now if this is a Classic-related issue, or more generally applicable to OS 9. -tim -- molvisions - molecular graphics & visualization http://www.molvisions.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: <4AE8AED63DA0244FA26B3EE309675DD40247AE2C@lola.davidson.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Joel Kowit Subject: Re: Chime, browsers, and Netscape 7 Date: Thu, 29 Aug 2002 17:22:04 -0400 To: rasmol@lists.umass.edu I'm beginning to use Microsoft Frontpage to create web pages & would appreciate any suggestions on how to insert &/or create a Chime Tutorial with Frontpage. Gif animation files, hyperlinks, jpeg files, etc can be inserted using drag & drop, but I'm not sure how to proceed with Chime. Thanks. Joel Kowit Dept. Biology Emmanuel. College Boston, MA 02115 617-735-9949 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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, browsers, and Netscape 7 Date: Thu, 29 Aug 2002 17:52:02 -0400 To: "LIST: rasmol" at 5:22 PM EDT on (Thursday) 29 August 2002 Joel Kowit said: > I'm beginning to use Microsoft Frontpage to create web pages & would > appreciate any suggestions on how to insert &/or create a Chime Tutorial > with Frontpage. Gif animation files, hyperlinks, jpeg files, etc can be > inserted using drag & drop, but I'm not sure how to proceed with Chime. > Thanks. > > Joel Kowit hi Joel, there is no automated method for inserting a Chime object into a Web page using an HTML editor. the HTML can be inserted manually by adding the appropriate EMBED tag; for example: there are many options that one might include in the EMBED tag; check out the Chime page at MDL for one list. note, however, that this is not "valid" html, since EMBED is not supported, and will fail validation. such is life ;-) there is no "scripting" software to create a Chime tutorial from scratch; hoowever, it can be done manually in many ways. perhaps the easiest method is to create a view in RasMol, save it as an spt file, and load that into Chime. you can find exhaustive details on how to do this sort of thing at . or more specifically, . hth, tim -- molvisions - molecular graphics & visualization http://www.molvisions.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: Protein Explorer 1.98 Beta is Available Date: Fri, 30 Aug 2002 22:26:02 -0400 To: rasmol@lists.umass.edu I have released Protein Explorer 1.98 Beta, which supercedes all previous alpha and beta versions. Please access it via its permanent URL http://proteinexplorer.org -- old bookmarks to other URL's may no longer work. It is safest to clear your browser's cache beforehand. This upgrade was largely devoted to performance polishing, bug fixes and fleshing out documentation and some functions. There are no major enhancements. I do not intend to add any new features for the full release of version 2.0 (no longer to be beta!), which I expect to do in a month or so. Those of you who plan to use PE in classes starting next week will, I expect, find this version quite familiar. It should work smoothly with your existing lesson plans. Note however that the "One-Hour Tour" has been revised to take advantage of some new convenience features, so it is slightly different. (It is no longer called the "QuickTour" since it was pointed out to me that one hour does not meet everyone's expectation of "quick".) Lesson Plans now include the wonderful on-line set of projects designed by Feig and Jabri at Indiana U, and published in Biochem. & Mol. Biol. Education's most recent issue. http://molvis.sdsc.edu/protexpl/teaching.htm This version is downloadable, but the installation instructions have changed. The new procedure is, I hope, easier and much less prone to annoying complications. Please do report to me any repeatable behavior that you suspect to be a bug, or anything unclear or inconsistent -- and if you do, PLEASE GIVE COMPLETE DETAILS. I have tested this release more thoroughly than any previous release, on diverse Windows systems and one Macintosh OS 8.6. Nevertheless, there are bound to be bugs in function, as well as some gaps in clarity or anachronisms that I've overlooked in the documentation. This version works more completely in Internet Explorer, and with far fewer bugs, than did the previous alpha version 1.922. And of course it continues to work best of all in Netscape 4.79. MINOR ENHANCEMENTS include: --A new convenience button that renders the entire molecule as a cartoon with secondary structure coloring. --A new chain-coloring scheme in FirstViews that is more reliable at distinguishing chains. --QuickViews' SELECT menu has a new option "Saved" that permits saving a laboriously selected atom set to restore easily later (but only within the same session). The atom set selected by clicking is automatically saved. --QuickViews' SELECT menu has a new option "Neighbors" with an adjustable distance. --QuickViews' DISPLAY Contacts has a new checkbox "Hide contacting water". This avoids coloring the surface in an unnecessarily complex way if your main interest is in non-water contacts. --QuickViews' DISPLAY *Hide* has been redesigned to make more sense, and now includes "hide everything". --After creating a surface with QuickViews' DISPLAY Surface, you can now color the surface with any plain color on the COLOR menu. --To make them more obvious, two prior capabilities have been added to the QuickViews DISPLAY menu, namely "Sequences" and "Evolution" (ConSurf). Similarly, the Polarity5 color scheme has been redundantly listed on the COLOR menu as "+/- Charge". --Considerable effort was devoted to preventing situations where, in the past, you could click an innocuous-looking button, such as the Hide/Show Water button, and (with a very large molecule) the system then unexpectedly froze, sometimes for a minute or more, before completing the operation. (Thanks to Diana Ditmore for help with this.) --Throughout, documentation at all levels has been improved, clarified, expanded, and updated -- with the exception of the "Tutorial", which is very long, little used (in my impression), and rather out of date regarding new features. --A particularly cool feature for advanced users is that PE's animation of multiple-model ensembles (designed for morphs) now generates a RasMol-compatible script that makes construction of an animated GIF relatively easy. There is an animated GIF link to this on the FrontDoor (or go directly to http://molvis.sdsc.edu/protexpl/animgif.htm). This feature uses a capability of Chime that allows some commands to be executed only in Chime (prefixed with ##) and others to be executed only in RasMol (suffixed with #!). This capability, while present since 1996, never got incorporated into MDL's script documentation (but is now documented within PE). Although I requested that Tim Maffett implement these while he was developing Chime 1.0 at MDL, I never found a good use for them until now, 6 year later. -Eric P.S. Although it remains my fondest desire, development of the script recorder and full support for Presentations within Protein Explorer is still in the future, only because finishing up PE version "2" took me all summer. Also, optimal utilization of the "show pdbheader" command remains a future goal. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il 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 C Niederhoffer Subject: Protein Explorer 1.98 beta Date: Tue, 03 Sep 2002 15:01:24 -0500 To: RasMol email list Chimers: I recently downloaded and installed Protein Explorer 1.98 beta on my Mac PowerPC G3 266 MHz, 160 MB, OS 9.0.4. I started it up per the instructions and tried to run one of the demonstration files indicated on the front page. There is a pop-up Chime speed meter with a broken icon and a message on the main page that says to wait for the Chime speed test to complete, but after 5 minutes I lost interest and closed the window. I cannot go any further with the new PE because the same Chime timing boxes appear. Any suggestions? The problem occurs with either Chime 2.0a or 2.6, which work fine on my computer as I can run off my own and other sites. Eric 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-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric C Niederhoffer Subject: PE 1.98 beta update Date: Tue, 03 Sep 2002 15:29:50 -0500 To: RasMol email list Chimers: As a follow-up to my observation concerning PE 1.98 beta running on my Mac G3, I have successfully run PE 1.98 beta from the Mass web site and the Chime speed meter zipped through its initial testing without a hitch. I am still waiting for my local copy of PE 1.98 beta to complete its Chime timing task! Eric 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-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: PE 1.98 beta update Date: Tue, 03 Sep 2002 20:18:50 -0700 To: rasmol@lists.umass.edu At 9/3/02, Eric C Niederhoffer wrote: >Chimers: > >As a follow-up to my observation concerning PE 1.98 beta running on >my Mac G3, I have successfully run PE 1.98 beta from the Mass web >site and the Chime speed meter zipped through its initial testing >without a hitch. > >I am still waiting for my local copy of PE 1.98 beta to complete its >Chime timing task! > >Eric >eniederhoffer@siumed.edu Dear Eric: My apologies, and thank you very much for reporting this problem -- too often people seem to just give up and I don't hear for weeks about some rather blatant issues. First let me assure you that I tested PE 1.98 for hours on my Mac G4, as well as several Windows machines before releasing it. Not that I caught everything (stay tuned) but the speed meter worked every time. On a 100 MHz 80486, the test takes over one minute; on my 400 MHz G4 it takes 13 seconds, and on any newer Windows computer, a similarly short time. And as you have now seen, it is done only once. It is not repeated in subsequent sessions, even after a reboot. The benefits of having PE know Chime's speed are considerable, so I felt the speed-meter was worth quite a bit of effort (which it has now more than consumed :-) That said, just now I re-tested it on my Mac G4 and observed the hangup of the speed meter that you reported. The speed-meter window opened, and as planned, was immediately forced behind the main window, but when I looked in the speed-meter window, a broken plugin was there -- Chime had failed to load even though it was installed and the browser had passed the test for Chime being installed! This happened to me twice. I then quit Netscape and tried again, and the next few times it worked. 1. For version 1.981 due out soon, I'll add a type="chemical/x-pdb" to the invocation of Chime to see if that makes this more reliable. I notice that I left that out. You can do that yourself with BBEdit if you wish -- it is in the file Protein Explorer 1.98:shared:speed_ch.htm 2. I suggest that with your problematic downloaded copy, you quit Netscape (not just close all windows) and try again several times. Once it "fires" properly, it won't bother you again. 3. If you wish (probably you don't), after successful completion of the speed test and after PE has completed loading, you can enter the command alias "speed". This gives the option of clearing the cookies that save the results, so in the next session, speed will be re-tested. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il 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: Protein Comparator 1.98 broken on Macs Date: Tue, 03 Sep 2002 20:23:50 -0700 To: rasmol@lists.umass.edu Today I discovered, and confirmed on a second computer, that on Macs (but not on Windows) the Protein Comparator feature of PE 1.98 is broken. Molecules load and display but all subsequent function is blocked because of a javascript error. Because of the onset of classes here, it may be a few days before I can release PE 1.981 with this fixed. I hope this doesn't inconvenience anyone too seriously -- in any case, you are on alert about this bug for now. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Giulio Vistoli Subject: Announcing VEGA1.4.2 Date: Wed, 04 Sep 2002 13:16:00 +0200 To: pdb-l@rcsb.org, rasmol@lists.umass.edu, chemweb@ic.ac.uk Dear collegues, we are glad to announce the new release of VEGA1.4.2 ( http://users.unimi.it/ddl ) our well known program to convert, manage and visualize of 3D structures for several platforms (Win32, Linux, Irix, AmigaOs). New features of VEGA1.4.2: - PowerNet plugin: TCP/IP protocol, PDB direct connection, script managment interface. - REBOL scripting language. Some scripts are included in the package. - AMD Athlon/Duron and Pentium 4 optimizations. - Edit atom dialog box. - GAMESS output loader. - Updated Gasteiger-Marsili charge attribution. - Bug fixes and new extended commands. REBOL is a messaging language that provides a broad range of practical solutions to the daily challenges of Internet computing. REBOL offers a new approach to the exchange and interpretation of network-based information over a wide variety of computing platforms. REBOL scripts are as easy to write as HTML or shell scripts: a script can be a single line or an entire application. The PowerNet plugin includes a useful interface to manage the REBOL scripts. Trough these scripts it's possible to control the VEGA function in order to automate the most common and repetitive operations. Giulio Vistoli & Alessandro Pedretti --------------- Giulio Vistoli Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano Italia Tel. +39-02-50317522 Fax +39-02-50317565 giulio.vistoli@unimi.it http://users.unimi.it/ddl ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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 V5.00.2314.1300 X-MSMail-priority: Normal References: <006101c25404$733746c0$424f959f@Villa> ++++------+------+------+------+------+------+------+------+------+------+ From: Sophia Siedlberg Subject: Re: Announcing VEGA1.4.2 (About REBOL) Date: Wed, 04 Sep 2002 13:48:40 -0700 To: rasmol@lists.umass.edu Dear Giulio Vistoli > REBOL is a messaging language that provides a broad range of practical > solutions to the daily challenges of Internet computing. REBOL offers a new > approach to the exchange and interpretation of network-based information > over a wide variety of computing platforms. > REBOL scripts are as easy to write as HTML or shell scripts: a script can be > a single line or an entire application. > The PowerNet plugin includes a useful interface to manage the REBOL scripts. > Trough these scripts it's possible to control the VEGA function in order to > automate the most common and repetitive operations. Having read this part of your announcement I am interested in knowing more about the scope of REBOL. As a low level programmer (C++, Pascal etc) I am now interested in developing on a platform independant scripting language, in which I could theoretically have class libraries, a GUI, etc. HTML, JAVA and XML, dont quite have the specialised functions I would like. As a bio-informatacist, I would like to be completeley platform independant. What does REBOL offer in this sense? And what platforms can this be adapted to? I am very interested to know more. I am unable to visit web pages at present so a forewarded reply or more information about the possible advantages of REBOL would be helpful. All the best Sophia Siedlberg Orlania Biosystems. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Michael Sternberg Subject: Re: Announcing VEGA1.4.2 Date: Wed, 04 Sep 2002 18:08:11 +0200 (MET DST) To: rasmol@lists.umass.edu Giulio Vistoli wrote: > we are glad to announce the new release of VEGA1.4.2 > ( http://users.unimi.it/ddl ) our well known program to convert, manage and > visualize of 3D structures for several platforms (Win32, Linux, Irix, > AmigaOs). Thanks. This is quite a versatile program for analysing and converting molecular structure files. Kudos to the authors for releasing it open source. Forgive me what comes next -- from the announcement and the screenshots at the home page it is clear that the program is meant to be a graphical one. Having used Rasmol for a number of years, but being curious, I downloaded, installed and ran Vega under Linux (all flawlessly, and well documented). I expected something in the same vein as Rasmol. Yet I was befuddled as to why it just dumped a PDB version of an input file to stdout. Well, one has to actively switch on OpenGL as an output format. I wasn't quite prepared for what I saw next: > env VEGADIR=$cwd LD_LIBRARY_PATH=$cwd\:$LD_LIBRARY_PATH ./vega \ Molecules/Pdb/1crn.pdb.gz -f opengl ERROR 202: OpenGL output is available for Windows only. Ugh! Isn't OpenGL meant to be highly portable? Ciao, -- Michael Sternberg, Ph.D. | Argonne National Laboratory email: sternberg.at.anl.gov | 9700 S Cass Ave, Argonne, IL 60439-4831 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <200209040007.g8407x921630@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric C Niederhoffer Subject: Re: PE 1.98 beta update Date: Wed, 04 Sep 2002 13:45:21 -0500 To: rasmol@lists.umass.edu Cc: emartz@microbio.umass.edu Eric: I tried suggestion 2 three more times and it failed to resolve the Chime speed meter problem. Only one "X" appeared in the progress box after 10 minutes. I tried suggestion 1 by adding the type="chemical/x-pdb" to the EMBED tag that calls Chime. I relaunched the browser three times with no success in completing the Chime speed meter test. I do get a black box now instead of the broken icon in the Chime speed meter window. Suggestion 3 depends on success in 1 and 2. I hope these observations help pin-point the holdup. Eric >1. For version 1.981 due out soon, I'll add a type="chemical/x-pdb" to the >invocation of Chime to see if that makes this more reliable. I notice that >I left that out. You can do that yourself with BBEdit if you wish -- it is >in the file Protein Explorer 1.98:shared:speed_ch.htm > >2. I suggest that with your problematic downloaded copy, you quit Netscape >(not just close all windows) and try again several times. Once it "fires" >properly, it won't bother you again. > >3. If you wish (probably you don't), after successful completion of the >speed test and after PE has completed loading, you can enter the command >alias "speed". This gives the option of clearing the cookies that save the >results, so in the next session, speed will be re-tested. > >-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-- References: <200209040007.g8407x921630@marlin.bio.umass.edu> <200209040007.g8407x921630@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: PE 1.98 beta update Date: Wed, 04 Sep 2002 16:13:46 -0700 To: Eric C Niederhoffer , rasmol@lists.umass.edu Dear Eric:

I have confirmed that on a G3 running OS9.2.1 I was not able to workaround the speed-meter stall, and with a downloaded copy of PE it happens 100% of the time on the G3. On my G4 running OS8.6, and also on a G4 running OSX/Classic, the stall happens rarely. On Windows, it never happens. Even on the G3, as you noticed, it works when you run PE from the server rather than a downloaded copy. Go figure! (I will be ...) In 1.981 when I can get to it, I'll provide a bypass escape button for G3's.

Since you are willing to edit the program files, Eric (and anyone else) here is a quick fix:

In the file Protein Explorer 1.98:shared:cmd2way2.htm

edit the function init_fis() changing the 'else' to look like this. The changes are in red. Be sure to put // before next_doc() to comment it out. This sets the relative speed to 0.25 (that's what I got on a G3) and bypasses the testing. The only thing this speed value is used for is to warn you (and suggest better alternatives) when you request an operation that will take a long time (>~12 seconds; in some cases a minute or two, during which your computer is 'frozen').


function init_fis()
{
  if (top.isIE)
  {
  top.fi_height = document.body.clientHeight;
  top.fi_width = document.body.clientWidth;
  setTimeout("next_doc()", 200);
  }
  else // in Netscape this whole charade is unnecessary
    // (until the speed tests were added)
  {
    top.set_chime_speed(0.25, 4., 0., 0., 0.);
    document.location.href = top.fi_next_doc;
    // next_doc();
  }
}

-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
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-- RasMol email list boundary="Boundary_(ID_/0sUqPaeKVg0Mq9G/6z3Cg)" References: <200209040007.g8407x921630@marlin.bio.umass.edu> <200209040007.g8407x921630@marlin.bio.umass.edu> <200209042002.g84K2r901561@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric C Niederhoffer Subject: Re: PE 1.98 beta update Date: Wed, 04 Sep 2002 15:32:27 -0500 To: Eric Martz , --Boundary_(ID_/0sUqPaeKVg0Mq9G/6z3Cg) Eric: Success! The quick fix did the job. Eric >Since you are willing to edit the program files, Eric (and anyone >else) here is a quick fix: > >In the file Protein Explorer 1.98:shared:cmd2way2.htm > >edit the function init_fis() changing the 'else' to look like this. >The changes are in red. Be sure to put // before next_doc() to >comment it out. This sets the relative speed to 0.25 (that's what I >got on a G3) and bypasses the testing. The only thing this speed >value is used for is to warn you (and suggest better alternatives) >when you request an operation that will take a long time (>~12 >seconds; in some cases a minute or two, during which your computer >is 'frozen'). > > >function init_fis() >{ > if (top.isIE) > { > top.fi_height = document.body.clientHeight; > top.fi_width = document.body.clientWidth; > setTimeout("next_doc()", 200); > } > else // in Netscape this whole charade is unnecessary > // (until the speed tests were added) > { > top.set_chime_speed(0.25, 4., 0., 0., 0.); > document.location.href = top.fi_next_doc; > // next_doc(); > } >} > >-Eric --Boundary_(ID_/0sUqPaeKVg0Mq9G/6z3Cg) Eric: Success! The quick fix did the job. Eric Since you are willing to edit the program files, Eric (and anyone else) here is a quick fix: In the file Protein Explorer 1.98:shared:cmd2way2.htm edit the function init_fis() changing the 'else' to look like this. The changes are in red. Be sure to put // before next_doc() to comment it out. This sets the relative speed to 0.25 (that's what I got on a G3) and bypasses the testing. The only thing this speed value is used for is to warn you (and suggest better alternatives) when you request an operation that will take a long time (>~12 seconds; in some cases a minute or two, during which your computer is 'frozen'). function init_fis() { if (top.isIE) { top.fi_height = document.body.clientHeight; top.fi_width = document.body.clientWidth; setTimeout("next_doc()", 200); } else // in Netscape this whole charade is unnecessary // (until the speed tests were added) { FFFF,0000,0000top.set_chime_speed(0.25, 4., 0., 0., 0.); document.location.href = top.fi_next_doc; // next_doc(); } } -Eric --Boundary_(ID_/0sUqPaeKVg0Mq9G/6z3Cg)-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-MSMail-priority: Normal References: <006101c25404$733746c0$424f959f@Villa> <3D762EDA.CD3B47E3@anchim.chm.anl.gov> ++++------+------+------+------+------+------+------+------+------+------+ From: Giulio Vistoli Subject: Re: Announcing VEGA1.4.2 Date: Thu, 05 Sep 2002 10:56:47 +0200 To: sternberg@anl.gov, rasmol@lists.umass.edu Dear Collegues, the OpenGL is a high portable graphic language, but it's very hard to build a GUI (Graphic user Interface) able to run on some different operating systems without spend a lot of time to develop it. Thus, the real problem isn't the OpenGL, but the GUI: the VEGA OpenGL version was developed using Borland C/C++ Builder 4.0 and the Visual Component Language (VCL) included in this RAD (Rapid Application Environment) tool. When the OpenGL project started, the CLX layer was not released by Borland. CLX is an environment similar to VCL, but it exists bot for MS Windows and Linux operating system. The migration from VCL to CLX requires a lot of time (the OpenGL source code size is about 11 Mb !!!) and the plugin system must be reengineered for Linux. VEGA is the first molecular modelling software with polymorphic code that detects the CPU installed in your system, selects the appropriate code and uses it for the maximum performances. This approach requires additional time to develop specific code for each CPU type (see non-x86 systems). The Linux OpenGL implementation isn't provided directly by SGI but by MESA libraries and there is another compatibility problem. Rasmol is a very useful software, but doesn't have got OpenGL output, it doesn't use any 3D hardware acceleration, it have got a minimalist graphic interface and thus the Rasmol porting is much less difficult. I'm sorry, but I don't have so much time because my first work isn't the VEGA development and please remember that VEGA is a freeware software .... Best regards Alessandro Pedretti -- Dr. Alessandro Pedretti Ist. di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano (Italy) Tel. +39 02 503 17522 Fax +39 02 503 17565 E-Mail: alessandro.pedretti@unimi.it WWW: http://users.unimi.it/~ddl ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <200209040007.g8407x921630@marlin.bio.umass.edu> <200209040007.g8407x921630@marlin.bio.umass.edu> <200209042002.g84K2r901561@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: Chime support Date: Thu, 05 Sep 2002 08:26:44 -0400 To: rasmol@lists.umass.edu Could we please have an update on which browser versions support Chime, and to what extent support will continue? I would like to update the recommendations on our site. Thanks very much, Joan Slonczewski ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Chime support Date: Thu, 05 Sep 2002 13:06:02 -0700 To: rasmol@lists.umass.edu [Forwarded by Eric Martz to circumvent technical difficulties] From: Robert Dickey >On the Chime site there is a Compatibility Checklist link for Chime 2.6SP3. >Chime 2.6SP4 will be out in September, and will include support for Windows >XP. > >Regards, >Bob Dickey (MDL Chime Team Leader) > >-----Original Message----- >From: Joan Slonczewski [mailto:slonczewski@kenyon.edu] >Sent: Thursday, September 05, 2002 5:27 AM >To: rasmol@lists.umass.edu >Subject: Chime support > > >Could we please have an update on which browser versions support Chime, >and to what extent support will continue? I would like to update the >recommendations on our site. >Thanks very much, >Joan Slonczewski ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: farquasi Subject: Re: Chime support Date: Thu, 05 Sep 2002 18:59:20 -0500 To: rasmol@lists.umass.edu I joined this list for just this information. I tried to get information by sending an email to the support center at MDL, but got no answer. Here is my question: How can we make chime work with Mac OS X? barry On Thursday, September 5, 2002, at 03:06 PM, Eric Martz wrote: > From: Robert Dickey > [Forwarded by Eric Martz to circumvent technical difficulties] > > >> On the Chime site there is a Compatibility Checklist link for Chime >> 2.6SP3. >> Chime 2.6SP4 will be out in September, and will include support for >> Windows >> XP. >> >> Regards, >> Bob Dickey (MDL Chime Team Leader) >> >> -----Original Message----- >> From: Joan Slonczewski [mailto:slonczewski@kenyon.edu] >> Sent: Thursday, September 05, 2002 5:27 AM >> To: rasmol@lists.umass.edu >> Subject: Chime support >> >> >> Could we please have an update on which browser versions support >> Chime, >> and to what extent support will continue? I would like to update the >> recommendations on our site. >> Thanks very much, >> Joan Slonczewski > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > > Barry Rowe O- farquasi@mac.com Chemistry / Physics Teacher http://roweba.com Champaign Centennial High School NCSA ChemViz Team Lord Earnest Rutherford said: "All of Science is either Physics or stamp collecting." ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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 support Date: Thu, 05 Sep 2002 20:49:27 -0400 To: rasmol@lists.umass.edu at 6:59 PM EDT on (Thursday) 5 September 2002 farquasi said: > > How can we make chime work with Mac OS X? > you can not, short of running it in Classic. -tim -- molvisions - molecular graphics & visualization http://www.molvisions.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: farquasi Subject: Re: Chime support Date: Thu, 05 Sep 2002 21:03:15 -0500 To: rasmol@lists.umass.edu As I thought. Are there any known plans to make it work with OS X? barry On Thursday, September 5, 2002, at 07:49 PM, timothy driscoll wrote: > at 6:59 PM EDT on (Thursday) 5 September 2002 farquasi said: >> >> How can we make chime work with Mac OS X? >> > > you can not, short of running it in Classic. > > -tim > -- > molvisions - molecular graphics & visualization > http://www.molvisions.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-- > > Barry Rowe O- farquasi@mac.com Chemistry / Physics Teacher http://roweba.com Champaign Centennial High School NCSA ChemViz Team Lord Earnest Rutherford said: "All of Science is either Physics or stamp collecting." ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: =?iso-8859-1?Q?Jes=FAs_Manuel_Peregrina_Garc=EDa?= Subject: PROTEIN, BETA-TURN Date: Fri, 06 Sep 2002 09:37:46 +0200 To: rasmol@lists.umass.edu Hi Chimers: With the intention of illustrating the students the importance of the secondary structure, I am looking for a protein (PDB) in which the modification of one or several beta-turns is the responsible for a change in its tertiary structure and therefore change its biological activity, preferably cause some illness type. I would like to have both, the initial and the modified structures in PDB format. Can somebody help me? Thank you in advance. PERE -- ======================================================== Dr. Jesús Manuel Peregrina Complejo Científico Tecnológico Departamento de Química. Universidad de La Rioja Grupo de Síntesis Química de la Rioja, U.A.-C.S.I.C. C/ Madre de Dios, 51. E-26006 Logroño (La Rioja). Spain Tfn. +34-941-299654 Fax +34-941-299621 mailto:jesusmanuel.peregrina@dq.unirioja.es http://www.unirioja.es/dptos/dq/qo/qo.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-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Does anyone still have to use Netscape 4.08? Date: Sat, 07 Sep 2002 14:39:38 -0400 To: rasmol@lists.umass.edu There is a problem supporting Netscape 4.08 in Protein Explorer that is complicated to fix. Does anyone still need Netscape 4.08 to work with Protein Explorer? A couple of years ago, some computer labs elected to keep 4.08 and not to move into the later 4.X series, because of some security and installation issues. If your teaching lab still has only Netscape 4.08, please let me know. If I don't hear from anyone, the next version of Protein Explorer will require Netscape 4.7 or later. Thanks, -Eric P.S. Netscape has released 4.8 (following 4.79) and it works fine with Protein Explorer. They've made it harder to find: under Tools at the left, click on Browser Central, and there, click on Product Archive. There is no reason I'm aware of to bother to upgrade from any 4.7x version, though. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il 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: Protein Explorer 1.981 works better on Macs Date: Sun, 08 Sep 2002 14:14:24 -0400 To: rasmol@lists.umass.edu Cc: sandler@microbio.umass.edu, Joel.Sussman@weizmann.ac.il, mangel@bnl.gov I have released Protein Explorer 1.981 at http://proteinexplorer.org and it is downloadable. Before trying the new version on-line, clear the cache in your browser! Netscape: Edit, Preferences, Advanced, Cache, clear both memory and disk. IE: Tools, Internet Options, under Temporary Internet Files, Delete files. Windows users who have already downloaded 1.98 need not upgrade to this version unless you plan to change the colors of surfaces in QuickViews (improved and debugged), or want the new DNA mismatch repair enzyme in the Atlas (look under protein-nucleic acid complexes, challenging, 3rd item, and see if you can find the DNA base mismatch in 1E3M! For a good laugh, DISPLAY HBonds and look at the mismatched pair!). Macintosh users who downloaded 1.98 should replace it with 1.981. Protein Comparator now works on the Mac, and for Mac PPC users who could not get downloaded PE to start at all due to stalling of the black frame at the lower left (Chime speed testing), this has been redesigned. Thanks to those of you who reported the problems that were fixed, I am not aware of any remaining serious bugs in this version. But keep talking to me if you think you found one! -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il 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: Microsoft-Entourage/10.1.0.2006 X-OriginalArrivalTime: 09 Sep 2002 16:47:23.0473 (UTC) FILETIME=[9231CC10:01C25820] ++++------+------+------+------+------+------+------+------+------+------+ From: Warren Gallagher Subject: Re: Does anyone still have to use Netscape 4.08? Date: Mon, 09 Sep 2002 11:47:26 -0500 To: rasmol@lists.umass.edu 9. September, 2002 On 9/7/02 1:39 PM, "Eric Martz" wrote: > There is a problem supporting Netscape 4.08 in Protein Explorer that is > complicated to fix. Does anyone still need Netscape 4.08 to work with > Protein Explorer? > > A couple of years ago, some computer labs elected to keep 4.08 and not to > move into the later 4.X series, because of some security and installation > issues. If your teaching lab still has only Netscape 4.08, please let me know. !~~~~~~~~~~~~~~~~~~~~ All of the teaching labs on our campus (University of Wisconsin-Eau Claire) are still using 4.08. Computing and Network Services have so far resisted our many requests over the years to upgrade to 4.7x. Maybe the planned incompatibility with Protein Explorer will provide a rational that they can accept for doing the upgrade. !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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-OriginalArrivalTime: 09 Sep 2002 17:56:25.0280 (UTC) FILETIME=[36E76400:01C2582A] References: <200209071847.g87IlE913308@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Jennifer Muzyka Subject: Re: Does anyone still have to use Netscape 4.08? Date: Mon, 09 Sep 2002 13:56:24 -0400 To: rasmol@lists.umass.edu Here's a warning about upgrading to Netscape 4.7x. When we did so last fall here at Centre College, we ran into problems. The newer version loads more slowly, and the impatient users sometimes tried starting a second copy of the program before the first one loaded fully. The result was what the IT folks described as "thrashing" and it brought our network to its knees. By fall break or the end of the term, IT switched us all to IE instead. -Jennifer At 11:47 AM 9/9/2002 -0500, you wrote: >9. September, 2002 > >On 9/7/02 1:39 PM, "Eric Martz" wrote: > > There is a problem supporting Netscape 4.08 in Protein Explorer that is > > complicated to fix. Does anyone still need Netscape 4.08 to work with > > Protein Explorer? > > > > A couple of years ago, some computer labs elected to keep 4.08 and not to > > move into the later 4.X series, because of some security and installation > > issues. If your teaching lab still has only Netscape 4.08, please let > me know. >!~~~~~~~~~~~~~~~~~~~~ > > All of the teaching labs on our campus (University of Wisconsin-Eau >Claire) are still using 4.08. Computing and Network Services have so far >resisted our many requests over the years to upgrade to 4.7x. Maybe the >planned incompatibility with Protein Explorer will provide a rational that >they can accept for doing the upgrade. > > > >!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >Warren Gallagher >Associate Professor >Chemistry Department >University of Wisconsin-Eau Claire >Eau Claire, WI 54702 >TEL: (715) 836-5388 >FAX: (715) 836-4979 > > 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 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- -IMBIF fixed. ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime 2.6 SP4 out; PE doesn't work with it yet; 'show version' and Date: Thu, 12 Sep 2002 12:53:03 -0700 To: rasmol@lists.umass.edu Dear Chimeleons: Bob Dickey, head of the MDL Chime team, has alerted me that MDL today released Chime 2.6SP4. The good news is that if you send this Chime the command "show version" it reports the current Chime version. This was done at my request (Thanks, Bob!) to make it possible for Windows Internet Explorer to detect the version of Chime automatically. This command is not yet documented in MDL's on-line script manual. There are some other fixes and enhancements that you can read about in the release notes. The bad news is that Protein Explorer does not recognize this version. That is because the word "Chemscape" has been discontinued by MDL and PE is looking for "Chemscape Chime", whereas the new version reports itself as "MDL[R in circle] Chime". Bob did warn me about this in advance but I forgot to deal with it in PE 1.98. Since the changes in SP4 are, for most purposes, minor, I recommend that anyone who uses Protein Explorer should ***NOT*** upgrade at this time. As soon as I can release PE 1.982 it will work with SP4, and the annoying interface that presently asks you to tell PE the version of your Chime manually, when you are using IE, will go away. Although not detailed in the SP4 release notes, the "-IMBIF" problem I described at length earlier on this list is supposed to be fixed automatically when you uninstall your old Chime and install 2.6SP4. This problem precludes IE from processing commands sent to Chime via javascript (with the IMBIF mechanism), and occurs when earlier versions of Chime were installed ONLY into Netscape while IE 5.0 was present on the system. The troubleshooting help for PE 1.981 includes the procedure for editing the Windows registry to fix this (http://molvis.sdsc.edu/protexpl/troubles.htm), but this should be automatically fixed with SP4. Again, I'd like to thank Bob and the rest of the Chime Team at MDL for addressing, in MDL's SP4 release, the -IMBIF and version reporting issues that I deemed urgent. These fixes will make the lives of all Chimeleons easier! -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il 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: Microsoft-Entourage/10.1.0.2006 ++++------+------+------+------+------+------+------+------+------+------+ From: "James W. Caras" Subject: Re: Chime, browsers, and Netscape 7 Date: Thu, 12 Sep 2002 23:06:37 -0500 To: rasmol@lists.umass.edu I also have seen both PCs and Macs on OS9 running Chime on Netscape 7. I have had people report that structure tutorials making use of LiveConnect function with this setup. As for Mac OSX, I have had no luck, but cannot imagine that the fix would be that hard. We just need to squeak a bit louder. Jamie On 8/23/02 10:59 PM, "Campbell, Malcolm" wrote: > With much effort, I figured out where to download Netscape 7.0_PR1 for Mac > OSX, in English. > > ftp://ftp.netscape.com/pub/netscape7/english/7.0_PR1/mac/macosx/sea/ > > click on the .bin file. > > I installed this and tried to get chime to work. I put an old copy of plugin > in the library>internet plugins folder. I went to preferences and tried to set > this as a new helper application. I was unsuccessful. > > I was able to follow the earlier advice and get Netscape 7 for OS 8/9 to run > chime on a Mac running only OS 9.2, once I placed a copy of Chime plugin into > the plugin folder. This worked with no additional tinkering. > > Can anyone else figure out ways to get chime to work on Mac OSX? > > Thanks, > Malcolm > > ------------------------------------------------------ > A. Malcolm Campbell, Ph.D. Associate Professor of Biology > Director of the Genome Consortium for Active Teaching > > coEditor-in-Chief of Cell Biology Education: Journal of Life Sciences > Education > > > Biology Department > P. O. Box 7118 (US Mail) > 209 Ridge Road (Shipping) > Davidson, NC 28035 USA > > macampbell@davidson.edu > http://www.bio.davidson.edu/campbell > 704-894-2692 (voice) > 704-894-2512 (fax) > > > > ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. /|||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-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: Mac OSx Date: Fri, 13 Sep 2002 06:49:00 +0200 To: rasmol@lists.umass.edu I recall reading that OSx is UNIX based. Is this right, or am I mistaken? I thought there was an existing UNIX port for rasmol, etc. If the general code structure of OSx is, in fact, UNIX based, re-porting from UNIX to OSx should be relatively simple, right? Simple does not necessarily translate to quick, sad to say. Has anyone investigated the possibility of writing a Javabean to ease cross-platform woes? Of course, as Mr. Caras points out - the squeeky wheel gets the grease. Need we keep reinventing the wheel with every incarnation of software? I had thought the whole purpose of Java et. al. was to firm up the possibility of cross-platform processes. I will ask a friend who specializes in web-based Java to take a look at this problem. Lewis Edgel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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-Antivirus: scanned by sophie at shiva.jussieu.fr ++++------+------+------+------+------+------+------+------+------+------+ From: christian.simon@ppce.jussieu.fr (Christian Simon) Subject: Re: Mac OSx Date: Fri, 13 Sep 2002 08:44:13 +0200 (FRA Ete) To: rasmol@lists.umass.edu Dear Lewis, There is already a "port" for MacOSX. Have a look on the Fink web site: http://fink.sourceforge.net/ The Fink application on MacOSX allows you to install, quite rapidly and simply, HUNDREDS of packages from *nix world, including X, KDE, Gnome, scientific apps, games, compilers, dev. tools ... Fink allows you to: 1- download the binary packages from Fink site (when available) or 2- download the sources (from rasmol site for example, or from of other free applications sites), patch them automatically, compile them (automatically), install them (still automatically). This sound magical, isn't it ? ... and rasmol works. This is only a quick overview. For real technical explanations, look at Fink site and mailing list. -- Christian ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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-NIMR0-MailScanner: Found to be clean ++++------+------+------+------+------+------+------+------+------+------+ From: Alex Brown Subject: Re: Mac OSx Date: Fri, 13 Sep 2002 13:00:39 +0100 To: rasmol@lists.umass.edu Hi. Following the advice given by Christian Simon, I downloaded a RasMol package from the GNU-Darwin web site (rasmol-2.7.2_1.tqz). I installed it using 'tar -zxf rasmol-2.7.2_1.tqz. This gave four executables - rasmol, rasmol-8, rasmol-16 and rasmol-32, but only rasmol-16 works properly on my Mac (PowerBook G4, OS X 10.1.5, under Darwin with XFree86). I had to fiddle about to set up execution and manual paths, but basiclly, it works. However, I am unable to get the help file and 'about' files to function - when RasMol starts, it cannot find the help file. Whereabouts should the help file be placed ? Thanks, Alex Brown. On Friday, September 13, 2002, at 07:44 am, Christian Simon wrote: > Dear Lewis, > > There is already a "port" for MacOSX. Have a look on the Fink web site: > > http://fink.sourceforge.net/ > > The Fink application on MacOSX allows you to install, quite rapidly and > simply, > HUNDREDS of packages from *nix world, including X, KDE, Gnome, > scientific apps, games, compilers, dev. tools ... > > Fink allows you to: > 1- download the binary packages from Fink site (when available) > > or > > 2- download the sources (from rasmol site for example, or from of other > free > applications sites), patch them automatically, compile them > (automatically), > install them (still automatically). This sound magical, isn't it ? > ... and rasmol works. > > This is only a quick overview. For real technical explanations, > look at Fink site and mailing list. > -- > Christian > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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_3gMZB2c6kKZr4SsfFZ6WtQ)" X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Bug in MolUSc and MOI with Chime 2.6 SP4 Date: Fri, 13 Sep 2002 17:29:00 +0200 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_3gMZB2c6kKZr4SsfFZ6WtQ) Dear Chimeleons, I tried yesterday the new chime 2.6 sp4 for windows, with both IE and NS7.0 I noticed that my Chime based molecular visualisation program (namely MolUSc : http://www.ac-orleans-tours.fr/svt/travaux/visionneuse/index.htm) didn't work within IE (but it's still working nice with NS7.0 when Chime is installed on it). I use a version of the IMBIF (http://molvis.sdsc.edu/pe_ie/protexpl/ie.htm) method to command chime from javascripts. In mine, the button is not written in an It can be accessed via javascript with a command like this : if (getElementById) { html=''; html+=''; html+= ""; with (frames['invisible'].document) { open(); write(html); close(); } } note : frames['invisible'].document is needed for mozilla to write in the IFRAME. The IFRAME document can't be accessed as in IE with document.invisible.document. frames['invisible'].document works for both browsers. Paul --Boundary_(ID_ywmgdP+L/VIbDp2rDyxIPw)
To all chimeleons,
In answer to my previous message about the new Chime (2.6 SP4) version.
 
I found a solution for the imbif method to work again.
As I wrote former, the immediate button must be written in a sufficiently large IFRAME, in order to work.
After several tests, the IFRAME width must be at least of 5 pixels. But the IFRAME could be 0 pixels in height.
With this size (0*5), the IFRAME become invisible in Internet Explorer.
But, in mozilla (and therefore in Netscape 6.2, and 7.0), the IFRAME is still visible as a thick stroke. To make it invisible with mozilla, frameborder has to be set to 0.
The entire tag should be written like this :
<IFRAME src='empty.htm' name='invisible' height='0' width='5' frameborder=0 scrolling='no'></IFRAME>
 
It can be accessed via javascript with a command like this :
if (getElementById)
    {
          html='<html><body>';
          html+='<embed type="application/x-spt" hidden=true width=10 height=10 button=push target=molecule script="' + cmds +                     '" immediate=1></embed>';
          html+= "</body></html>";
 
          with (frames['invisible'].document)
          {
               open();
               write(html);
               close();
          }
     }
 
note : frames['invisible'].document is needed for mozilla to write in the IFRAME. The IFRAME document can't be accessed as in IE with document.invisible.document. frames['invisible'].document works for both browsers.
 
Paul
--Boundary_(ID_ywmgdP+L/VIbDp2rDyxIPw)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer 1.982 works with Chime 2.6 SP4 Date: Mon, 16 Sep 2002 00:12:53 -0700 To: rasmol@lists.umass.edu I have released Protein Explorer 1.982. It appears to work in Windows IE with Chime 2.6 SP4 and also 2.6 SP3, in Windows Netscape with Chime 2.6 SP4 all the way back to Chime 2.0.3, and in Mac Netscape from Chime 2.6 SP3 (there is no SP4 for the Mac) back to Chime 2.0a. There is no reason to upgrade to Chime 2.6 SP4 from your present version if it is working satisfactorily, but for those who have downloaded it, the new Chime 2.6 SP4 no longer causes Protein Explorer to fail. Macintosh PPC users: There is no Chime 2.6 SP4 for Macs, only for Windows. If you have downloaded PE 1.981, there is no significant reason to upgrade it to 1.982 for your Mac PPC. TECHNICAL ISSUES FOR CHIME SITE DEVELOPERS (NOT IMPORTANT FOR Protein Explorer USERS): The new "show version" script command works and reports "MDL(R) Chime 2.6 SP4". (2.6 SP3 and all previous versions have this script command, but it reports inappropriately "Chemscape Chime 1.0".) navigator.plugins[i].name now reports "MDL(R) Chime 2.6 SP4" vs. "Chemscape Chime 2.6 SP3" in the previous version. The IMBIF mechanism ("Immediate-Mode Button in Invisible Frame", see http://molvis.sdsc.edu/protexpl/ie.htm, also demonstrated and downloadable at http://www.umass.edu/microbio/chime/chimehow/chimake.htm) for sending command script strings to Chime in IE uses a small or invisible frame or IFRAME. Unexpectedly, as Paul Pillot reported to this list on Sept. 13, an IFRAME of 0 x 0 pixels in height and width, which worked in IE with Chime 2.6 SP3, no longer works. It must now have (according to Paul) a minimum of 5 x 5 pixels. It can still be made invisible by setting frameborder=0 and making the background identical to the surrounding background (as I have done in PE). Luckily, the true frames that I had used e.g. in my DNA tutorial, despite having a height of 0%, still work. For example In order to maintain IE compatibility with both SP4 and SP3, I had to do a major overhaul of PE's Chime testing startup sequence. The new method is summarized at http://molvis.sdsc.edu/protexpl/browtest.htm#chimetesting As far as I am aware, none of my Chime Resources (except for Protein Explorer) at http://www.umass.edu/microbio/chime were broken by the Chime 2.6 SP4 release -- all the rest still work. Let me know of any problems or anything I missed. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il 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 V5.50.4807.1700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: FW: Chime compatibility Date: Mon, 16 Sep 2002 16:59:43 +0200 To: rasmol@lists.umass.edu Here is the response concerning use of a java applet to insure Chime compatibility regardless of browser differences. Response comes from Ankur Gupta of Elan Software. (They manufacture Java authoring tools.) I have still not heard back from my friend concerning the actual process of manufacturing the middlewear device as mentioned. He usually has to hit a slow spot sufficiently long for him to get bored enough to look for something to keep him busy. I assume there are some programmers who read this user's letter - comments please? Lewis Edgel -----Original Message----- Sent: den 13 september 2002 16:48 From: Ankur Gupta [mailto:agupta@elansoft.com] Subject: RE: Chime compatibility To: Lewis Edgel Hello Lewis, Thank you for contacting us. This is an interesting situation :). Please note that the following comments are based on the input I have from you. The following are my comments. The java applet can be used as a middleware layer between your plug-in and the browser into which the plug-in will be loaded. The work of the applet is to read the browser properties and make the required changes and then load the plug-in. But with the applet the issue is to gain access to the end user's system resources: It should be a signed applet. In case of a signed applet, a window pops up asking the end user to click if it is OK to download the applet. This may not be an issue in your case. With the applet, it is some work because it has to go into the system programming to the make required changes. The other possible way is to make changes in the plug-in itself where it will do the required work for different browser types. I do not know the nature of the plug-in though. I hope this explanation was fine. Please let me know if you need anything more. Best regards, Ankur Gupta >-----Original Message----- >From: Lewis Edgel [mailto:lewis.edgel@telia.com] >Sent: Friday, September 13, 2002 3:43 PM >To: support@elansoft.com >Subject: Chime compatibility > > >http://www.mdlchime.com/chime/ > >With each change in browser, Chime requires tinkering. My hope is that some >reusable code could be manufactured to make this plugin virtually immortal >regardless of the number of times that browser manufacturers choose to >change their programs. I am not a programmer and am making this request for >information after just a brief discussion with a programmer who suggested >manufacturing a JavaBean applet as a viable solution to the problem. Seems >the fellow thinks my purchase of something you manufacture would enable him >to produce this as a charity. He had a coworker come into his office and >terminated the call before I got more information. God only knows when he >will call me back as he knows I want him to make a fix for free. >(This won't >be the first time I have bought him software in exchange for his help:) In >the mean time, perhaps you could look at this page and give me some insight >in layman's terms just what he is talking about. > >Lewis Edgel >Centralv. 3B 2tr >19476 Upplands Väsby >Sweden > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: FW: Chime compatibility Date: Mon, 16 Sep 2002 13:10:28 -0500 (CDT) To: rasmol@lists.umass.edu Hi I doubt that this is the most productive solution. From my somewhat limited experience this involves considerable work that is rather pointless. Any changes in the browser or an plugin means that the applet code needs to be rewritten. In fact the browser issues alone make the chime changes trival! Just browsing the protein explorer code shows how complex the task is and the great work done that makes it work. I would think that any effort on this would be more effective by making protein explorer or other scripts that use chime independent of the browser. Perhaps that would mean using rasmol or writting protein explorer in java (to avoid java script) or similar. The downside is lost browser incompatibility. Of course I have no clue on what really should be done or time in this matter. But I do know that providing an intermediate is not really a solution. From my work with the Student Interface to the Biology Workbench, a single simple change in the Biology Workbench can render a tool useless or create formatting problems. Regards Bruce Southey Student Interface for the Biology Workbench: http://peptide.ncsa.uiuc.edu/cgi-bin/sib.py ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Chime 2.0.3 works in Protein Explorer 1.982 Date: Mon, 16 Sep 2002 21:49:55 -0400 To: rasmol@lists.umass.edu Cc: Eric Martz Oops, yet another bug. Protein Explorer 1.982 was supposed to work with Chime 2.0.3 (Windows) but didn't. This old version of Chime is still installed in some of our teaching labs. I've patched PE 1.982 so it now works with Chime 2.0.3. I'll do a better fix later, but for now the on-line versions work from proteinexplorer.org -- just in the nick of time for my Tuesday classes. I did not patch the downloadable version since I assume downloaders can upgrade to Chime 2.6 SP3/4 easily enough. -- Eric Martz, Professor, Department of Microbiology University of Massachusetts, Amherst MA USA http://www.umass.edu/molvis/martz Protein Explorer http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite: http://pdblite.org ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: F-actin structure? Date: Tue, 17 Sep 2002 15:25:37 -0400 To: "LIST: rasmol" hello, does anyone know if any structure of an actin filament (F-actin) has been solved? if so, anyone know where I can get it? I've tried the PDB and molvis index without luck. I'm now scrolling through pubmed refs hoping for some luck. thanks, tim -- molvisions - molecular graphics & visualization http://www.molvisions.com/ september 11 - never forget. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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_ROIqEWh4Sl87KJ5XGaiKEw)" References: ++++------+------+------+------+------+------+------+------+------+------+ From: Eric C Niederhoffer Subject: Re: F-actin structure? Date: Tue, 17 Sep 2002 15:09:37 -0500 To: rasmol@lists.umass.edu --Boundary_(ID_ROIqEWh4Sl87KJ5XGaiKEw) Tim: I think these are of the monomeric form: 1. Otterbein, L. R., Graceffa, P., and Dominguez, R., The crystal=20 structure of uncomplexed actin in the ADP state, Science, 293,=20 708-711 (2001). PDB 1J6Z uncomplexed ADP form, used to generate F-actin as described=20 by Egelman below. 2. van den Ent, F., Amos, L. A., and L=F6we, J., Prokaryotic origin of=20 the actin cytoskeleton, Nature, 413, 39-44 (2001). PDB 1ATN actin PDB 1JCE, 1JCF, 1JCG MreB protein that is similar to actin 3. Egelman, E. H., Actin allostery again?, Nature Struct. Biol., 8,=20 735-736 (2001). PDB 1YAG yeast cytoplasmic actin PDB 2BTF bovine cytoplasmic beta-actin Eric >hello, > >does anyone know if any structure of an actin filament (F-actin) has been >solved? if so, anyone know where I can get it? I've tried the PDB and >molvis index without luck. I'm now scrolling through pubmed refs hoping fo= r >some luck. > >thanks, > >tim >-- >molvisions - molecular graphics & visualization >http://www.molvisions.com/ > >september 11 - never forget. 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 --Boundary_(ID_ROIqEWh4Sl87KJ5XGaiKEw) TimesTim: I think these are of the monomeric form: 1. Otterbein, L. R., Graceffa, P., and Dominguez, R., The crystal structure of uncomplexed actin in the ADP state, Science, 293, 708-711 (2001). PDB 1J6Z uncomplexed ADP form, used to generate F-actin as described by Egelman below. Times2. van den Ent, F., Amos, L. A., and L=F6we, J., Prokaryotic origin of the actin cytoskeleton, Nature, 413, 39-44 (2001). PDB 1ATN actin PDB 1JCE, 1JCF, 1JCG MreB protein that is similar to actin Times3. Egelman, E. H., Actin allostery again?, Nature Struct. Biol., 8, 735-736 (2001). PDB 1YAG yeast cytoplasmic actin PDB 2BTF bovine cytoplasmic beta-actin Eric hello, does anyone know if any structure of an actin filament (F-actin) has been solved? if so, anyone know where I can get it? I've tried the PDB and molvis index without luck. I'm now scrolling through pubmed refs hoping for some luck. thanks, tim --=20 molvisions - molecular graphics & visualization http://www.molvisions.com/ september 11 - never forget. 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 --Boundary_(ID_ROIqEWh4Sl87KJ5XGaiKEw)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: F-actin structure? Date: Tue, 17 Sep 2002 16:22:25 -0700 To: rasmol@lists.umass.edu Cc: goodsell@scripps.edu 1CAG is a nice collagen fiber, see http://molvis.sdsc.edu/atlas/atlas.htm#struc If you find an actin filament, LET ME KNOW!! David Goodsell obviously had PDB files for lots of assemblies including an actin filament for his wonderful poster, so I've copied him in since he doesn't subscribe to this list. -Eric At 9/17/02, you wrote: >hello, > >does anyone know if any structure of an actin filament (F-actin) has been >solved? if so, anyone know where I can get it? I've tried the PDB and >molvis index without luck. I'm now scrolling through pubmed refs hoping for >some luck. > >thanks, > >tim >-- >molvisions - molecular graphics & visualization >http://www.molvisions.com/ /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il 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: F-actin structure? Date: Tue, 17 Sep 2002 16:44:17 -0400 To: rasmol@lists.umass.edu at 4:22 PM EDT on (Tuesday) 17 September 2002 Eric Martz said: > 1CAG is a nice collagen fiber, see > http://molvis.sdsc.edu/atlas/atlas.htm#struc > yes, I've used this before (in the original Lehninger protein structure tutorials). but I'm working on a motor proteins tutorial, and having a devil of a time of it so far, so collagen is no good. > If you find an actin filament, LET ME KNOW!! > the only thing I have so far is a theoretical model from 1997 (!), pdb id 1ALM: HEADER COMPLEX (MUSCLE PROTEINS) 31-MAY-97 1ALM TITLE THE STRUCTURE OF THE ACTO-MYOSIN SUBFRAGMENT-ONE COMPLEX. TITLE 2 RESULTS OF SEARCHES USING DATA FROM ELECTRON MICROSCOPY AND TITLE 3 X-RAY CRYSTALLOGRAPHY. THEORETICAL MODEL, ALPHA CARBONS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOSIN; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: SUBFRAGMENT-1; COMPND 5 BIOLOGICAL_UNIT: HEXAMER OF 2 HEAVY CHAINS, 2 ALKALI LIGHT COMPND 6 CHAINS, AND 2 REGULATORY LIGHT CHAINS; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ACTIN; COMPND 9 CHAIN: V, W, X, Y, Z; COMPND 10 FRAGMENT: F-ACTIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 TISSUE: PECTORALIS MUSCLE; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 7 ORGANISM_COMMON: RABBIT KEYWDS ACTIN, MYOSIN, COMPLEX (MUSCLE PROTEINS), COILED COIL, KEYWDS 2 ACTO-MYOSIN SUBFRAGMENT-1, ACTIN-BINDING EXPDTA THEORETICAL MODEL AUTHOR R.A.MENDELSON,E.P.MORRIS REVDAT 1 17-DEC-97 1ALM 0 JRNL AUTH R.MENDELSON,E.P.MORRIS JRNL TITL THE STRUCTURE OF THE ACTO-MYOSIN SUBFRAGMENT 1 JRNL TITL 2 COMPLEX: RESULTS OF SEARCHES USING DATA FROM JRNL TITL 3 ELECTRON MICROSCOPY AND X-RAY CRYSTALLOGRAPHY JRNL REF PROC.NAT.ACAD.SCI.USA V. 94 8533 1997 not much useful for structural treatment of the powerstroke, unfortunately. nor is it very good for visualizing the actin filament since it contains only 5 monomers. strangely, I can't find any structures of tubulin polymers either (the a-b dimer, but that's it). argh. -tim -- molvisions - molecular graphics & visualization http://www.molvisions.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-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id g8HKkx914953 ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: F-actin structure? Date: Tue, 17 Sep 2002 16:46:16 -0400 To: rasmol@lists.umass.edu at 3:09 PM EDT on (Tuesday) 17 September 2002 Eric C Niederhoffer said: > Tim: > > I think these are of the monomeric form: > > 1. Otterbein, L. R., Graceffa, P., and Dominguez, R., The crystal > structure of uncomplexed actin in the ADP state, Science, 293, > 708-711 (2001). > PDB 1J6Z uncomplexed ADP form, used to generate F-actin as described > by Egelman below. > > 2. van den Ent, F., Amos, L. A., and Löwe, J., Prokaryotic origin of > the actin cytoskeleton, Nature, 413, 39-44 (2001). > PDB 1ATN actin > PDB 1JCE, 1JCF, 1JCG MreB protein that is similar to actin > > 3. Egelman, E. H., Actin allostery again?, Nature Struct. Biol., 8, > 735-736 (2001). > PDB 1YAG yeast cytoplasmic actin > PDB 2BTF bovine cytoplasmic beta-actin > > Eric > hi Eric, thanks for the refs. yes, those structures are all monomeric. I haven't seen Egelman's paper, but I can't find any published structures associated with his name. do you know if he actually created the 3D structure file, or just kludged it for print graphics? thanks, tim -- molvisions - molecular graphics & visualization http://www.molvisions.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-- boundary="Boundary_(ID_1c+XeJ+jyh5h9f2Ey/cejA)" References: ++++------+------+------+------+------+------+------+------+------+------+ From: Eric C Niederhoffer Subject: Re: F-actin structure? Date: Tue, 17 Sep 2002 16:11:40 -0500 To: rasmol@lists.umass.edu --Boundary_(ID_1c+XeJ+jyh5h9f2Ey/cejA) Tim: Egelman cites the following reference for the F-actin model construction: Orlova, A. et al. 2001. J. Mol. Biol. in the press. Eric > > 3. Egelman, E. H., Actin allostery again?, Nature Struct. Biol., 8, > > 735-736 (2001). > > PDB 1YAG yeast cytoplasmic actin > > PDB 2BTF bovine cytoplasmic beta-actin > > > > Eric > > > >hi Eric, > >thanks for the refs. yes, those structures are all monomeric. I haven't >seen Egelman's paper, but I can't find any published structures associated >with his name. do you know if he actually created the 3D structure file, or >just kludged it for print graphics? > >thanks, > >tim --Boundary_(ID_1c+XeJ+jyh5h9f2Ey/cejA) Tim: Egelman cites the following reference for the F-actin model construction: Orlova, A. et al. 2001. J. Mol. Biol. in the press. Eric > 3. Egelman, E. H., Actin allostery again?, Nature Struct. Biol., 8, > 735-736 (2001). > PDB 1YAG yeast cytoplasmic actin > PDB 2BTF bovine cytoplasmic beta-actin > > Eric > hi Eric, thanks for the refs. yes, those structures are all monomeric. I haven't seen Egelman's paper, but I can't find any published structures associated with his name. do you know if he actually created the 3D structure file, or just kludged it for print graphics? thanks, tim --Boundary_(ID_1c+XeJ+jyh5h9f2Ey/cejA)-- RasMol email list ++++------+------+------+------+------+------+------+------+------+------+ From: Eric C Niederhoffer Subject: F-actin Date: Tue, 17 Sep 2002 16:17:21 -0500 To: Timothy Driscoll , Tim: Take a look at this link: http://bilbo.bio.purdue.edu/~amcgough/Gelsolin.html Eric ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: BIOMT transformations Date: Tue, 17 Sep 2002 17:30:53 -0400 To: "LIST: rasmol" hi again, I found a structure of the alpha,beta-tubulin dimer (pdb id 1JFF) with instructions for generating the biologically useful oligomer: REMARK 350 AN OLIGOMER OF TYPE :DIMERIC : CAN BE ASSEMBLED BY REMARK 350 APPLYING THE FOLLOWING TO CHAINS: REMARK 350 A, B, REMARK 350 BIOMT1 1 1.00000 0.00000 0.00000 0.00000 REMARK 350 BIOMT2 1 0.00000 1.00000 0.00000 0.00000 REMARK 350 BIOMT3 1 0.00000 0.00000 1.00000 0.00000 REMARK 350 unfortunately, I have no idea how to interpret this information. I tried submitting this to the EBI PQS server but it was no help here. can anyone tell me how to turn this dimer into the oligomer? maybe SPDV? thanks, tim -- molvisions - molecular graphics & visualization http://www.molvisions.com/ "fly, you fools!" -- molvisions - molecular graphics & visualization http://www.molvisions.com/ "is it secret? is it safe?" -- molvisions - molecular graphics & visualization http://www.molvisions.com/ "you can not pass!" ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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_WgKtxHG2MP9+oR4C9WzSXg)" X-Accept-Language: fr,en-US ++++------+------+------+------+------+------+------+------+------+------+ From: Jean-Philippe Demers Subject: Mechanism of Interaction - v 1.3 Date: Tue, 17 Sep 2002 21:29:14 -0400 To: rasmol@lists.umass.edu --Boundary_(ID_WgKtxHG2MP9+oR4C9WzSXg) Dear Chimeleons, I would like to announce you the recent release of the Mechanism of Interaction (MoI) version 1.3, which is available at http://www3.sympatico.ca/diane.demers/moi/. The version now supports Netscape 7.0, and adjustments were made to be compatible with Chemscape Chime 2.6 SP4, so now we can say that MoI is more "cross browser" than ever... An Automatic Download Manager was also implemented in this new release. I would appreciate your suggestions, especially on the Mac side, because I just have PCs to debug these works. I would also have a comment about the definition of "compatibility with Chime". I would say that some web pages are "static" with Chime, e.g. that commands sent by this page to Chime are already determined by the page author. Other pages could be defined as "dynamic" or "interactive" with Chime, meaning that commands sent by this page are dependent of the end-user actions on the page interface. Well-known examples of interactive pages are the Protein Explorer and the Non-Covalent Bond Finder, by Eric Martz; MolUSc, by Paul Pillot or MoveTo, by Todd Carlson. While some configuration are fully compatible with Chime, other configurations work well to write a Chime plug-in in a page (like Netscape 3.0), but they do not provide a full support enough support to make an "interactive" page work. Recently, I investigated to see whether Netscape 7.0 and Opera were compatible (on a Windows platform) with Chime. I discovered that we were able in both browsers to display a Chime structure and to manipulate this structure with push buttons. I was also able to make a small JavaScript function to write these buttons in an invisible frame (IFRAME). However, it turned that Netscape 7.0 was fully compatible with Chime and that "load" and "script" commands were making Opera simply freeze... "Static" and "interactive" compatibility should be a new parameter to discuss of the quality of Chime support for a specific browser. At the beginning of the summer, James W. Caras had the brilliant idea of collecting all information about browsers, platforms and Chime compatibility. I'm wondering what is the status of this project actually... Cheers, Jean-Philippe Demers --Boundary_(ID_WgKtxHG2MP9+oR4C9WzSXg) Dear Chimeleons,

I would like to announce you the recent release of the Mechanism of Interaction (MoI) version 1.3, which is available at http://www3.sympatico.ca/diane.demers/moi/. The version now supports Netscape 7.0, and adjustments were made to be compatible with Chemscape Chime 2.6 SP4, so now we can say that MoI is more "cross browser" than ever... An Automatic Download Manager was also implemented in this new release. I would appreciate your suggestions, especially on the Mac side, because I just have PCs to debug these works.

I would also have a comment about the definition of "compatibility with Chime". I would say that some web pages are "static" with Chime, e.g. that commands sent by this page to Chime are already determined by the page author. Other pages could be defined as "dynamic" or "interactive" with Chime, meaning that commands sent by this page are dependent of the end-user actions on the page interface. Well-known examples of interactive pages are the Protein Explorer and the Non-Covalent Bond Finder, by Eric Martz; MolUSc, by Paul Pillot or MoveTo, by Todd Carlson.
While some configuration are fully compatible with Chime, other configurations work well to write a Chime plug-in in a page (like Netscape 3.0), but they do not provide a full support enough support to make an "interactive" page work. Recently, I investigated to see whether Netscape 7.0 and Opera were compatible (on a Windows platform) with Chime. I discovered that we were able in both browsers to display a Chime structure and to manipulate this structure with push buttons. I was also able to make a small JavaScript function to write these buttons in an invisible frame (IFRAME). However, it turned that Netscape 7.0 was fully compatible with Chime and that "load" and "script" commands were making Opera simply freeze... "Static" and "interactive" compatibility should be a new parameter to discuss of the quality of Chime support for a specific browser.

At the beginning of the summer, James W. Caras had the brilliant idea of collecting all information about browsers, platforms and Chime compatibility. I'm wondering what is the status of this project actually...

Cheers,

Jean-Philippe Demers --Boundary_(ID_WgKtxHG2MP9+oR4C9WzSXg)-- boundary="Boundary_(ID_h5wwls9NwsY2c2zeiiFhQA)" X-Accept-Language: fr,en-US ++++------+------+------+------+------+------+------+------+------+------+ From: Jean-Philippe Demers Subject: Mechanism of Interaction - v 1.3 Date: Tue, 17 Sep 2002 21:34:29 -0400 To: rasmol@lists.umass.edu --Boundary_(ID_h5wwls9NwsY2c2zeiiFhQA) Dear Chimeleons, I would like to announce you the recent release of the Mechanism of Interaction (MoI) version 1.3, which is available at http://www3.sympatico.ca/diane.demers/moi/. The version now supports Netscape 7.0, and adjustments were made to be compatible with Chemscape Chime 2.6 SP4, so now we can say that MoI is more "cross browser" than ever... An Automatic Download Manager was also implemented in this new release. I would appreciate your suggestions, especially on the Mac side, because I just have PCs to debug these works. I would also have a comment about the definition of "compatibility with Chime". I would say that some web pages are "static" with Chime, e.g. that commands sent by this page to Chime are already determined by the page author. Other pages could be defined as "dynamic" or "interactive" with Chime, meaning that commands sent by this page are dependent of the end-user actions on the page interface. Well-known examples of interactive pages are the Protein Explorer and the Non-Covalent Bond Finder, by Eric Martz; MolUSc, by Paul Pillot or MoveTo, by Todd Carlson. While some configuration are fully compatible with Chime, other configurations work well to write a Chime plug-in in a page (like Netscape 3.0), but they do not provide a full support enough support to make an "interactive" page work. Recently, I investigated to see whether Netscape 7.0 and Opera were compatible (on a Windows platform) with Chime. I discovered that we were able in both browsers to display a Chime structure and to manipulate this structure with push buttons. I was also able to make a small JavaScript function to write these buttons in an invisible frame (IFRAME). However, it turned that Netscape 7.0 was fully compatible with Chime and that "load" and "script" commands were making Opera simply freeze... "Static" and "interactive" compatibility should be a new parameter to discuss of the quality of Chime support for a specific browser. At the beginning of the summer, James W. Caras had the brilliant idea of collecting all information about browsers, platforms and Chime compatibility. I'm wondering what is the status of this project actually... Cheers, Jean-Philippe Demers --Boundary_(ID_h5wwls9NwsY2c2zeiiFhQA) Dear Chimeleons,

I would like to announce you the recent release of the Mechanism of Interaction (MoI) version 1.3, which is available at
http://www3.sympatico.ca/diane.demers/moi/. The version now supports Netscape 7.0, and adjustments were made to be compatible with Chemscape Chime 2.6
SP4, so now we can say that MoI is more "cross browser" than ever... An Automatic Download Manager was also implemented in this new release. I would
appreciate your suggestions, especially on the Mac side, because I just have PCs to debug these works.

I would also have a comment about the definition of "compatibility with Chime". I would say that some web pages are "static" with Chime, e.g. that commands sent
by this page to Chime are already determined by the page author. Other pages could be defined as "dynamic" or "interactive" with Chime, meaning that commands
sent by this page are dependent of the end-user actions on the page interface. Well-known examples of interactive pages are the Protein Explorer and the
Non-Covalent Bond Finder, by Eric Martz; MolUSc, by Paul Pillot or MoveTo, by Todd Carlson.
While some configuration are fully compatible with Chime, other configurations work well to write a Chime plug-in in a page (like Netscape 3.0), but they do not
provide a full support enough support to make an "interactive" page work. Recently, I investigated to see whether Netscape 7.0 and Opera were compatible (on a
Windows platform) with Chime. I discovered that we were able in both browsers to display a Chime structure and to manipulate this structure with push buttons. I
was also able to make a small JavaScript function to write these buttons in an invisible frame (IFRAME). However, it turned that Netscape 7.0 was fully compatible
with Chime and that "load" and "script" commands were making Opera simply freeze... "Static" and "interactive" compatibility should be a new parameter to discuss
of the quality of Chime support for a specific browser.

At the beginning of the summer, James W. Caras had the brilliant idea of collecting all information about browsers, platforms and Chime compatibility. I'm
wondering what is the status of this project actually...

Cheers,

Jean-Philippe Demers --Boundary_(ID_h5wwls9NwsY2c2zeiiFhQA)-- X-Accept-Language: en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Dr Nicholas Keep Subject: Re: F-actin structure? Date: Wed, 18 Sep 2002 10:10:51 +0100 To: rasmol@lists.umass.edu The F actin structure was solved by Ken Holmes and others from fibre diffraction data Holmes, K.C., Popp, D., Gebhard, W. and Kabsch, W. (1990) Atomic model of the actin filament. Nature 347, 44-49. and the more fully refined structure in Lorenz, M., Popp, D and Holmes, K. (1993). (Refinement of the F-actin model against X-ray fibre diffraction data by the use of a directed mutation algorithm. J. Mol. Biol. 234, 826-836). The coordinates from that paper (includes the filament 'straightner' phalloidin are freely available from Michael Lorenz see his web site http://www.mpimf-heidelberg.mpg.de/~michael/ with full instructions of how to ftp them ftp from kuno.mpimf-heidelberg.mpg.de (149.217.48.3) pub/michael thb PDB file has about 20 monomers in (and there is a c program you can download to generate longer filaments if you want). This has a resolution of about 8A -the other technique used for actin filaments helical EM has a resolution of 15-25A. It has also shown that actin filaments are inherently flexible. Although this is the generally accepted model of F-actin, a second model based on the crystal packing in profilin/actin was around in the literature for some time (so it is worth checking the source of any files you might aquire). Somebody mentioned tubulin. The tubulin dimer was solved to 3.5A resolution by electron diffraction by Nogales et al (http://cryoem.berkley.edu). and this was built into EM maps of tubulin Eva Nogales, M Whittaker, RA Milligan, Kenneth H. Downing. High-resolution model of the microtubule. Cell. 96(1):79-88 (1999) I do not know of a download of a PDB file of the microtubule as oppposed to the dimer (which is available from PDB). I would guess Eva Nogales would be the first person to ask. Best wishes Nick -- Dr Nicholas H. Keep School of Crystallography, Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.keep@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G083 Office) 020-7631-6868 (Rosalind Franklin Laboratory) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Dr Nicholas Keep Subject: Re: BIOMT transformations Date: Wed, 18 Sep 2002 10:34:14 +0100 To: rasmol@lists.umass.edu The transformation in the dimer file is the unity matrix ie you already have the biological unit in the crystal structure (the dimer is the biological unit of the non assembled form of tubulin). You can infact generate the protofilament using the crystal pacing but then there are a number of ways that the protofilaments back in microtubules (there is not just one type of microtubule they vary in how many protofilaments there are in the ring and the pitch of the protofilament helices (number of protofilaments ('starts') before the filament goes round on itself). Hope this helps Nick -- Dr Nicholas H. Keep School of Crystallography, Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.keep@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G083 Office) 020-7631-6868 (Rosalind Franklin Laboratory) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Mechanism of Interaction - v 1.3 Date: Wed, 18 Sep 2002 07:47:41 -0400 To: rasmol@lists.umass.edu at 9:34 PM EDT on (Tuesday) 17 September 2002 Jean-Philippe Demers said: > Dear Chimeleons, > > I would like to announce you the recent release of the Mechanism of > Interaction (MoI) version 1.3, which is available at > http://www3.sympatico.ca/diane.demers/moi/. The version now supports > Netscape 7.0, and adjustments were made to be compatible with Chemscape > Chime 2.6 SP4, so now we can say that MoI is more "cross browser" than > ever... An Automatic Download Manager was also implemented in this new > release. I would appreciate your suggestions, especially on the Mac side, > because I just have PCs to debug these works. > hi Jean-Philippe, MOI looks like a nice utility for developers. I've done much of what you have there in various projects, with the very notable exception of IE support, but it's nice to have a single resource that does it all. I have a bunch of Macs here and would be able to give you some feedback, except the link to your downloadable zip file does not work at the moment... also, I suggest removing all references to "Chemscape," since MDL does not include that in the name of the Chime plug-in anymore. > I would also have a comment about the definition of "compatibility with > Chime". I would say that some web pages are "static" with Chime, e.g. > that commands sent > by this page to Chime are already determined by the page author. Other > pages could be defined as "dynamic" or "interactive" with Chime, meaning > that commands > sent by this page are dependent of the end-user actions on the page > interface. > I agree- and an important observation. I hesitate to use the word "static," though, since Chime is always interactive (compared to say a Flash animation, where you have to code in UI controls specifically, Chime always has the mouse-key combos). I describe "static" pages as pages that are "hard-wired" with Chime; the other general type of page is "user-accessible" (not quite so romantic a term ;-). > "Static" and "interactive" compatibility should be a new parameter to > discuss of the quality of Chime support for a specific browser. > your browser observations help underscore the complexity of the issue. not only are there multiple SP versions of Chime which support different capabilities, but many broands and versions of browsers that support different versions of HTML, different versions of javascript, different types of plug-ins, handle cached files differently, etc. yum. but at least it gives us something to do, right? if it were as easy as slicing bread, I'd have to go back to the bench ;-) > At the beginning of the summer, James W. Caras had the brilliant idea of > collecting all information about browsers, platforms and Chime > compatibility. I'm wondering what is the status of this project > actually... > I don't know, but you might send him your observations about Chime in different browsers, so he can add it to his report. -- molvisions - molecular graphics & visualization http://www.molvisions.com/ "fly, you fools!" -- molvisions - molecular graphics & visualization http://www.molvisions.com/ "is it secret? is it safe?" -- molvisions - molecular graphics & visualization http://www.molvisions.com/ "you can not pass!" ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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/10.1.0.2006 ++++------+------+------+------+------+------+------+------+------+------+ From: "James W. Caras" Subject: Re: Mechanism of Interaction - v 1.3 Date: Wed, 18 Sep 2002 08:21:06 -0500 To: rasmol@lists.umass.edu Hi all- I am still compiling information, but I probably should get up what I have. I will try to get it down and send it to this group for comments, for some people might be able to get some configurations to work that I was unable (or unaware). Jamie On 9/17/02 8:34 PM, "Jean-Philippe Demers" wrote: > Dear Chimeleons, > > I would like to announce you the recent release of the Mechanism of > Interaction (MoI) version 1.3, which is available at > http://www3.sympatico.ca/diane.demers/moi/. The version now supports > Netscape 7.0, and adjustments were made to be compatible with Chemscape > Chime 2.6 > SP4, so now we can say that MoI is more "cross browser" than ever... An > Automatic Download Manager was also implemented in this new release. I > would > appreciate your suggestions, especially on the Mac side, because I just > have PCs to debug these works. > > I would also have a comment about the definition of "compatibility with > Chime". I would say that some web pages are "static" with Chime, e.g. > that commands sent > by this page to Chime are already determined by the page author. Other > pages could be defined as "dynamic" or "interactive" with Chime, meaning > that commands > sent by this page are dependent of the end-user actions on the page > interface. Well-known examples of interactive pages are the Protein > Explorer and the > Non-Covalent Bond Finder, by Eric Martz; MolUSc, by Paul Pillot or > MoveTo, by Todd Carlson. > While some configuration are fully compatible with Chime, other > configurations work well to write a Chime plug-in in a page (like > Netscape 3.0), but they do not > provide a full support enough support to make an "interactive" page > work. Recently, I investigated to see whether Netscape 7.0 and Opera > were compatible (on a > Windows platform) with Chime. I discovered that we were able in both > browsers to display a Chime structure and to manipulate this structure > with push buttons. I > was also able to make a small JavaScript function to write these buttons > in an invisible frame (IFRAME). However, it turned that Netscape 7.0 was > fully compatible > with Chime and that "load" and "script" commands were making Opera > simply freeze... "Static" and "interactive" compatibility should be a > new parameter to discuss > of the quality of Chime support for a specific browser. > > At the beginning of the summer, James W. Caras had the brilliant idea of > collecting all information about browsers, platforms and Chime > compatibility. I'm > wondering what is the status of this project actually... > > Cheers, > > Jean-Philippe Demers > ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. /|||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: Eric Martz Subject: Fwd: Re: F-actin structure? Date: Wed, 18 Sep 2002 20:43:12 -0700 To: rasmol@lists.umass.edu >Date: Tue, 17 Sep 2002 14:46:44 -0700 >To: Eric Martz >From: David Goodsell >Subject: Re: F-actin structure? > >Hi Eric-- > >Here is what I did for the pictures of actin in the Molecule of the Month >and the poster. >It is based on Holmes et al. (1990) Nature 347, 44 >That paper gives a matrix for the ADP form--I could not find that in the >PDB, so I used the ATP form in 1atn. The translation vector given in the >paper did not work for me, but the rotation looked good. So I found a >translation by trial and error that created a filament that looked like the >model in the paper. > >Here is the (approximate) matrix to apply to coordinates in 1atn > >-0.71034 -0.58180 0.39614 52. > 0.16333 -0.68369 -0.71126 66. > 0.68465 -0.44053 0.58068 0. > >This will position the monomer next to a helix axis along z. Then, perform >the helix rotation to give the filament--rotation of 166.154 degrees and >translation of 27.538 A. > >This has been good enough for the types of pictures that I draw, but it >will certainly not be accurate enough for atomic-level details of the >interaction. > >Feel free to share this information, but please include all of my disclaimers! > >All the best, > >David ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: [142.150.224.110] X-OriginalArrivalTime: 18 Sep 2002 14:40:09.0572 (UTC) FILETIME=[49C0B240:01C25F21] ++++------+------+------+------+------+------+------+------+------+------+ From: Baagi Mmereki Subject: Unsubscribe Date: Wed, 18 Sep 2002 14:40:09 +0000 To: rasmol@lists.umass.edu

Please unsubscribe baagiwaserowe@hotmail.com




Baagi T. Mmereki

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-- X-Accept-Language: en References: <0H2N005LMTGU1J@supai.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Dr Nicholas Keep Subject: Re: Fwd: Re: F-actin structure? Date: Thu, 19 Sep 2002 09:48:10 +0100 To: rasmol@lists.umass.edu >This has been good enough for the types of pictures that I draw, but it >will certainly not be accurate enough for atomic-level details of the >interaction. The atomic level details of F-actin remain unknown. The methods used to look at the filament are accurate enough to say which amino acids are close (and this is often backed up by chemical crosslinking) but there is no experimental data to say where the side chains are, so measuring distances of possible H bonds or ion pairs is not a valid process. best wishes Nick -- Dr Nicholas H. Keep School of Crystallography, Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.keep@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G083 Office) 020-7631-6868 (Rosalind Franklin Laboratory) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Fwd: Re: b factors ('color temperature' scale) Date: Fri, 20 Sep 2002 14:29:16 -0700 To: rasmol@lists.umass.edu I think this message from Roger Sayle on how RasMol (and Chime) scale temperature colors, and some relevant tricks, will be of interest to many of you. In Chime, I found that "select temp >50" does not work but "select temperature >50" does. -Eric >Date: Thu, 19 Sep 2002 14:21:43 -0600 (MDT) >From: Roger Sayle >To: >cc: Eric Martz >Subject: Re: b factors > > >Hi Daniel & Eric, >> > I'm wondering if you could tell me how rasmol decides to color atoms >> > based on the B factors? For example, does it operate within set >> > ranges/boundaries like sybyl (see below), or does it color based on >> > the distribution of B factors. > >RasMol's temperature colour scheme is relative, and not absolute. The >lowest b-factor present in the input file is blue, and the highest is >red. This is done as many groups store arbitrary data in PDB's bfactor >field. For example, its fairly common to store partial charge in this >field. The "colour charge" option is identical to "colour temperature" >with the exception that the lowest b-factor value is red, and the highest >is blue. > >There is a clever method that can be used to get an abolsute encoding. >Its possible to use pseudo-atoms, with atom name " Q " in the input >PDB file, i.e. element Q. These pseudatoms are then used by RasMol >in the min/max temperature calculation to determine the range, but >are otherwise ignored. Hence, you can add two Q atoms at the start >or end of a PDB file with bfactors 0.0 and 10.0, to always force the >extremes of the colour range (provided all the real atom values are >between 0.0 and 10.0). > >> > Sybyl's coloring scheme >> > o 0.0 = or < Violet < 10.0 >> > o 10.0 = or < Blue < 20.0 >> > o 20.0 = or < Green < 30.0 >> > o 30.0 = or < Yellow < 40.0 >> > o 40.0 = or < Orange < 50.0 >> > o 50.0 = or < Red > >Absolute colour schemes are still possible but using a script, rather >than just the "temperature" menu option. > >select temp >= 0 >colour violet >select temp >= 10 >colour blue >select temp >= 20 >colour green >select temp >= 30 >colour yellow >select temp >= 40 >colour orange >select temp >= 50 >colour red > >Eric's WWW site has some tutorial examples on using "load pdb inline" >to store both PDB file co-ordinates, and RasMol script commands in >a single file. > > >> > The reason I ask is because I'm about to publish a method/program >> > that predicts functional sites and I would like to substitute the B >> > factor values with the probability of the residue being functionaly >> > important. This would allow an end user can view the predictions in >> > rasmol/favorite viewer by simply coloring the molecule by temperature. >> > So a site predicted to be very important would be red and blue would >> > be the other extreme. > >You might also enjoy (the pictures in): > >"PdbAlign, PdbDist and DistAlign: Tools to Aid in Relating Sequence >Variability to Structure", Roger Sayle, Mansoor Saqi, Malcom Weir >and Andrew Lyall. Computer Applications in the Biological Sciences >(CABIOS), 1995, Vol. 11, No. 5, pp. 571-573. > > >I hope this answers your questions. > >Roger >-- >Roger Sayle, >OpenEye Scientific Software, WWW: http://www.eyesopen.com/ >Suite 1107, 3600 Cerrillos Road, >Santa Fe, New Mexico, 87507. > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <0H2T002BEN4HZ4@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: faphd Subject: Re: RASMOL digest 253 Date: Sun, 22 Sep 2002 09:50:57 -0400 To: rasmol@lists.umass.edu Hey, I am trying to remember the website to use the protein explorer. Can you refresh my memory. ----- Original Message ----- Sent: Sunday, September 22, 2002 12:00 AM From: "RASter display of MOLecular structure" Subject: RASMOL digest 253 To: "RASter display of MOLecular structure" > > RASMOL Digest 253 > > Topics covered in this issue include: > > 1) Re: Bug in MolUSc and MOI with Chime 2.6 SP4 > by Paul Pillot > 2) Protein Explorer 1.982 works with Chime 2.6 SP4 > by Eric Martz > 3) FW: Chime compatibility > by Lewis Edgel > 4) Re: FW: Chime compatibility > by southey@ux1.cso.uiuc.edu > 5) Chime 2.0.3 works in Protein Explorer 1.982 > by Eric Martz > 6) F-actin structure? > by timothy driscoll > 7) Re: F-actin structure? > by Eric C Niederhoffer > 8) Re: F-actin structure? > by Eric Martz > 9) Re: F-actin structure? > by timothy driscoll > 10) Re: F-actin structure? > by timothy driscoll > 11) Re: F-actin structure? > by Eric C Niederhoffer > 12) F-actin > by Eric C Niederhoffer > 13) BIOMT transformations > by timothy driscoll > 14) Mechanism of Interaction - v 1.3 > by Jean-Philippe Demers > 15) Mechanism of Interaction - v 1.3 > by Jean-Philippe Demers > 16) Re: F-actin structure? > by Dr Nicholas Keep > 17) Re: BIOMT transformations > by Dr Nicholas Keep > 18) Re: Mechanism of Interaction - v 1.3 > by timothy driscoll > 19) Re: Mechanism of Interaction - v 1.3 > by "James W. Caras" > 20) Unsubscribe > by Baagi Mmereki > 21) Fwd: Re: F-actin structure? > by Eric Martz > 22) Re: Fwd: Re: F-actin structure? > by Dr Nicholas Keep > 23) Fwd: Re: b factors ('color temperature' scale) > by Eric Martz > ------------------------------------------- Introducing NetZero Long Distance Unlimited Long Distance only $29.95/ month! Sign Up Today! www.netzerolongdistance.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: timothy driscoll Subject: Re: RASMOL digest 253 Date: Sun, 22 Sep 2002 14:33:42 -0400 To: rasmol@lists.umass.edu at 9:50 AM EDT on (Sunday) 22 September 2002 faphd said: > Hey, I am trying to remember the website to use the protein explorer. Can > you refresh my memory. > > > enjoy :-) -tim -- molvisions - molecular graphics & visualization http://www.molvisions.com/ "fly, you fools!" -- molvisions - molecular graphics & visualization http://www.molvisions.com/ "is it secret? is it safe?" -- molvisions - molecular graphics & visualization http://www.molvisions.com/ "you can not pass!" ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <0H2T002BEN4HZ4@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: RASMOL digest 253 Date: Mon, 23 Sep 2002 09:45:29 -0400 To: rasmol@lists.umass.edu http://proteinexplorer.org At 9/22/02, you wrote: >Hey, I am trying to remember the website to use the protein explorer. Can >you refresh my memory. > > > >----- Original Message ----- >From: "RASter display of MOLecular structure" >To: "RASter display of MOLecular structure" >Sent: Sunday, September 22, 2002 12:00 AM >Subject: RASMOL digest 253 > > >> >> RASMOL Digest 253 >> >> Topics covered in this issue include: >> >> 1) Re: Bug in MolUSc and MOI with Chime 2.6 SP4 >> by Paul Pillot >> 2) Protein Explorer 1.982 works with Chime 2.6 SP4 >> by Eric Martz >> 3) FW: Chime compatibility >> by Lewis Edgel >> 4) Re: FW: Chime compatibility >> by southey@ux1.cso.uiuc.edu >> 5) Chime 2.0.3 works in Protein Explorer 1.982 >> by Eric Martz >> 6) F-actin structure? >> by timothy driscoll >> 7) Re: F-actin structure? >> by Eric C Niederhoffer >> 8) Re: F-actin structure? >> by Eric Martz >> 9) Re: F-actin structure? >> by timothy driscoll >> 10) Re: F-actin structure? >> by timothy driscoll >> 11) Re: F-actin structure? >> by Eric C Niederhoffer >> 12) F-actin >> by Eric C Niederhoffer >> 13) BIOMT transformations >> by timothy driscoll >> 14) Mechanism of Interaction - v 1.3 >> by Jean-Philippe Demers >> 15) Mechanism of Interaction - v 1.3 >> by Jean-Philippe Demers >> 16) Re: F-actin structure? >> by Dr Nicholas Keep >> 17) Re: BIOMT transformations >> by Dr Nicholas Keep >> 18) Re: Mechanism of Interaction - v 1.3 >> by timothy driscoll >> 19) Re: Mechanism of Interaction - v 1.3 >> by "James W. Caras" >> 20) Unsubscribe >> by Baagi Mmereki >> 21) Fwd: Re: F-actin structure? >> by Eric Martz >> 22) Re: Fwd: Re: F-actin structure? >> by Dr Nicholas Keep >> 23) Fwd: Re: b factors ('color temperature' scale) >> by Eric Martz >> > >------------------------------------------- >Introducing NetZero Long Distance >Unlimited Long Distance only $29.95/ month! >Sign Up Today! www.netzerolongdistance.com > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il 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-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Student Interface to the Biology Workbench available Date: Mon, 23 Sep 2002 11:24:42 -0500 (CDT) To: biowb@ncsa.uiuc.edu, rasmol@lists.umass.edu Cc: jake@ncsa.uiuc.edu, bievenue@shodor.org Hi, This is the first public announcement of the Student Interface to the Biology Workbench. Although the basic interface has been available, this announcement by delayed due to significant changes have been made to the interface (such as changing the programming language from Java to Python and the incorporation of new tools). Consequently text and images from older examples may not completely reflect the current version and hopefully the intended content remains obvious in such cases. Please forward this message to any interested parties and I am sorry for any duplicate or unwanted messages. Thanks Bruce Southey Lead developer of SIB The Student Interface to the Biology Workbench (SIB) is an educational orientated interface to the Biology Workbench interface (http://workbench.sdsc.edu) developed as part of the Biology Student Workbench (http://peptide.ncsa.uiuc.edu). We have developed SIB for people who have little experience with bioinformatics and associated tools. In particular, the development of SIB is been orientated towards high school and undergraduate education. The current URL for the homepage is: http://deltas.animal.uiuc.edu/sibdoc/index.html In addition to a link to SIB, this page contains information about the status of SIB, a general getting started guide and a small tutorial using SIB. In addition, other information is provided that may be useful for some people. The current URL for the actual SIB interface is: http://peptide.ncsa.uiuc.edu/cgi-bin/sib.py The general mode of operation is: 1.Select the sequence(s) that you want. 2.Make sure you select the required number of sequences for that tool or a warning will appear. NDJINN doesn't require this step and will ignore any sequence(s) selected. Instead just enter a query string into the appropriate box. Select the desired databases OR one entry from genome databases for NDJINN, BLASTN, BLASTP, FASTA or PSIBLAST tools. You will be warned if did not select any database or too many databases. The more databases you select the longer the process will take. 3.Click the button of the Tool that you want to run. The Student Interface to the Biology Workbench uses the same information as the Biology Workbench. This means that any Biology Workbench user can access their account information from either interface. This means that any change made will immediately appear when the same user with the other interface accesses the account. The bioinformatics tools and databases were selected based on Biology Student Workbench tutorials. Tool options are set to the Biology Workbench default values to reduce confusion by the users. An additional 14 tools have been implemented and can be requested via email. These tools were not made available due to the overlapping features of more powerful tools. Currently the Biology Workbench maintains over 60 general databases and over 140 genome databases. Additional databases maintained by the Biology Workbench can be added upon request via email. In addition, new features are present in SIB that is not included in the original Biology Workbench: 1)Multiple background colors can be chosen, including white. 2)Extract tool. This tool allows the user to extract a region from a larger DNA or protein sequence. For example, annotation of a sequence provides specific region such as the gene or motif that is defined by the minimum and maximum residues. The user just needs to select the sequence, enter the minimum and maximum values and click on the 'Extract' button. 3)Transfer tool. This tool allows a user to transfer sequences and alignments from one Biology Workbench session to another session. In addition, one user can transfer sequences and alignments to another authorized user. 4) Create Form tool: We have developed a procedure for a teacher (or user) to share sequences and alignments with their students. The user selects a set of sequences that they which to share and creates a web page. This web page is then saved where all parties can access it and any user can just enter their Biology Workbench username and password to import these sequences to the session of their choice. Two examples are linked at the SIB homepage. Please notify me (Bruce Southey, southey@uiuc.edu) if you encounter any problems or error messages and include any information that will help me understand the problem. We would like to thank Mary, Sam, Kathy, Gary and Maureen for identifying problems. A special thanks goes to those participants in workshops who bravely and successfully used the previous versions of SIB. We also acknowledge the financial support provided by US Department of Education's Preparing Tomorrow's Teachers to Use Technology Program and NSF's Division of Undergraduate Education. Finally, we acknowledge the Biology Workbench team for creating and maintenance of the Biology Workbench site. Thanks, The Biology Student Workbench team ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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, browsers, and Netscape 7 Date: Thu, 26 Sep 2002 15:39:53 -0400 To: rasmol@lists.umass.edu at 11:06 PM EDT on (Thursday) 12 September 2002 James W. Caras said: > I also have seen both PCs and Macs on OS9 running Chime on Netscape 7. I > have had people report that structure tutorials making use of LiveConnect > function with this setup. > hi Jamie, I've been successful installing Chime in N7 under OS9. Chime loads fine, recognizes MIME types and the menu features work (the ones I've tested, at least so far). I can open a local pdb file. About:Plug-ins shows all is well with the world. unfortunately, I am unable to use any LiveConnect-enabled sites with this browser. all of them throw the javascript error "executeScript() is not a function." according to Netscape, though, N7 should run LiveConnect communications just like 3 and 4. do you have any public sites that use executeScript() and run in Mac N7? > As for Mac OSX, I have had no luck, but cannot imagine that the fix would > be that hard. We just need to squeak a bit louder. > my two cents: no luck here, either. it appears to be a problem with Chime registration by N7 (X). IOW, it ain't registering. I've tried putting Chime in the main Library:Internet Plug-ins folder, my user Library:Internet Plugins folder, and even in a new Plug-ins folder in the Netscape 7 folder (according to the Netscape documentation, this is where plug-ins or their aliases must reside). I also added the "chemical/x-pdb" MIME to my N7 helper apps. I copied the Chime files and tried the installer. tried Chime 2.0a just for kicks. nada. I thought it might be a file type issue - except that, strangely enough, OS X recognizes Chime is a file of type Plug-in, and even says it knows to use N7 to open it. this is the same situation for X plug-ins that actually work, like QT, so apparently it is browser-level trouble. best scenario would be if it is just an installation/registration issue - maybe an updated installer would work without requiring any changes to the Chime source at all... okay, faint hope, I'm sure ;-) -tim -- molvisions - molecular graphics & visualization http://www.molvisions.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-- User-Agent: Microsoft-Entourage/10.1.0.2006 ++++------+------+------+------+------+------+------+------+------+------+ From: "James W. Caras" Subject: Re: Chime, browsers, and Netscape 7 Date: Thu, 26 Sep 2002 16:38:27 -0500 To: rasmol@lists.umass.edu Hi Tim and fellow Chimers- More on the OSX/chime/Netscape 7 problem; > do you have any public sites that use executeScript() and run in Mac N7? I have not tried any of my LiveConnect-requiring structure exercises with OS9/NS7 yet, but a media copy-editor I work with explained to me that this was her configuration and she was able to go though the exercise just fine. (But again, this was a copyeditor and I don't know if she knew what she was supposed to be seeing. I think it fair to assume she pushed a few buttons though, and didn't report any error warnings to me.) I will try things out this evening with my Powerbook (OS9) and let you know. I do know that my exercises are much less complex in the javascript/liveconnect arena than what I have seen you do, so maybe my exercises are squeaking by. > my two cents: no luck here, either. it appears to be a problem with Chime > registration by N7 (X). IOW, it ain't registering. I've tried putting > Chime in the main Library:Internet Plug-ins folder, my user Library:Internet > Plugins folder, and even in a new Plug-ins folder in the Netscape 7 folder > (according to the Netscape documentation, this is where plug-ins or their > aliases must reside). I also added the "chemical/x-pdb" MIME to my N7 > helper apps. I copied the Chime files and tried the installer. tried Chime > 2.0a just for kicks. nada. I too have been through everything you tried. I assumed that if I were really creative and manually moved things around and forced recognition I could get it to work. Why shouldn't it? I figured the problem was with the way plug-ins were shared in the common library folders and that Chime just didn't know where it was. And yes, Netscape appears to know it has Chime and be all ready to go. I think this is a job for some hacker on Mozilla.org. I truly believe this problem could be fixed with a repair of one or a few lines of browser code. I bet we could find someone through their forums to take up our cause. Once it is fixed with Mozilla, the fix will end up in Netscape 8. Any Mozilla crusaders out there? Best Regards, Jamie On 9/26/02 2:39 PM, "timothy driscoll" wrote: > at 11:06 PM EDT on (Thursday) 12 September 2002 James W. Caras said: > >> I also have seen both PCs and Macs on OS9 running Chime on Netscape 7. I >> have had people report that structure tutorials making use of LiveConnect >> function with this setup. >> > > hi Jamie, > > I've been successful installing Chime in N7 under OS9. Chime loads fine, > recognizes MIME types and the menu features work (the ones I've tested, at > least so far). I can open a local pdb file. About:Plug-ins shows all is > well with the world. > > unfortunately, I am unable to use any LiveConnect-enabled sites with this > browser. all of them throw the javascript error "executeScript() is not a > function." according to Netscape, though, N7 should run LiveConnect > communications just like 3 and 4. > > do you have any public sites that use executeScript() and run in Mac N7? > > >> As for Mac OSX, I have had no luck, but cannot imagine that the fix would >> be that hard. We just need to squeak a bit louder. >> > my two cents: no luck here, either. it appears to be a problem with Chime > registration by N7 (X). IOW, it ain't registering. I've tried putting > Chime in the main Library:Internet Plug-ins folder, my user Library:Internet > Plugins folder, and even in a new Plug-ins folder in the Netscape 7 folder > (according to the Netscape documentation, this is where plug-ins or their > aliases must reside). I also added the "chemical/x-pdb" MIME to my N7 > helper apps. I copied the Chime files and tried the installer. tried Chime > 2.0a just for kicks. nada. > > I thought it might be a file type issue - except that, strangely enough, OS > X recognizes Chime is a file of type Plug-in, and even says it knows to use > N7 to open it. this is the same situation for X plug-ins that actually > work, like QT, so apparently it is browser-level trouble. > > best scenario would be if it is just an installation/registration issue - > maybe an updated installer would work without requiring any changes to the > Chime source at all... okay, faint hope, I'm sure ;-) > > > -tim ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. /|||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: timothy driscoll Subject: Re: Chime, browsers, and Netscape 7 Date: Thu, 26 Sep 2002 20:22:34 -0400 To: rasmol@lists.umass.edu at 4:38 PM EDT on (Thursday) 26 September 2002 James W. Caras said: > > do you have any public sites that use executeScript() and run in Mac N7? > > > I will try things out this evening with my Powerbook (OS9) and let you > know. I do know that my exercises are much less complex in the > javascript/liveconnect arena than what I have seen you do, so maybe my > exercises are squeaking by. > if you visit you'll see a very simple executeScript() example. OMMs it behaves thusly: *works in NC 4.79 (and lower) for mac OS 9.2.2 as Classic (10.1.5); *works in NC 4.79 (and lower) for mac OS 9.2.2; *works in NC 4.79 (and lower) for win2k; *does not work in N7 for mac OS X 10.1.5 (not seeing the plug-in, also js error "executeScript is not a function"); *does not work in N7 for mac OS 9.2.2 as Classic (js error "executeScript is not a function"); *does not work in N7 for OS 9.2.2 (js error "executeScript is not a function"); *does not work in N7 for win2k (js error "executeScript is not a function"); *does not work in mac IE. *does not work in win2k IE. if you have a chance, I'd be interested in seeing your results for this page. > > Any Mozilla crusaders out there? > not this one ;-) -tim -- molvisions - molecular graphics & visualization http://www.molvisions.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-- User-Agent: Microsoft-Entourage/10.1.0.2006 ++++------+------+------+------+------+------+------+------+------+------+ From: "James W. Caras" Subject: Re: Chime, browsers, and Netscape 7 Date: Fri, 27 Sep 2002 10:05:00 -0500 To: rasmol@lists.umass.edu Hi Tim and all- On my Powerbook G3 running OS 9.2, I installed Netscape 7 (classic), then went to MDL and downloaded the latest Chime and installed it. I went to the Boyer Biochemistry site and everything ran flawlessly. The Boyer textbook site uses the standard small-frame, hidden-button, execute immediately scheme. My javascript/liveconnect used in this site is based around what others have done long, long ago (likely the earliest incarnations executeScript) but in trying to understand things I generally re-write the javascript so that it makes sense to me. I went to your demo site at Molvisions and the executeScript did not work, and the javascript debugger did report the error that it is not a function. My uninformed guess is that this error is not really related to NS or Chime, but an error of this type I have often seen (too many times!) with my own javascript coding. I did look at the source and didn't even see the executeScript function (could this be it?), nor an external javascript call that might carry it, but then again you had some server-side includes that might have the executeScript built in (I am not yet familiar with this stuff). Anyway, the good news is that Netscape 7 is a go on both platforms, sans OS X. I have not tried downloading NS 7-classic on my G4/OSX box and running it under classic. If it works, it would be a good temporary solution for providing OS X users with a modern browser compatible with Chime. (Coding web pages that look good for NS4 really bites.) Hope I helped. Jamie On 9/26/02 7:22 PM, "timothy driscoll" wrote: > at 4:38 PM EDT on (Thursday) 26 September 2002 James W. Caras said: > >>> do you have any public sites that use executeScript() and run in Mac N7? >> >> >> I will try things out this evening with my Powerbook (OS9) and let you >> know. I do know that my exercises are much less complex in the >> javascript/liveconnect arena than what I have seen you do, so maybe my >> exercises are squeaking by. >> > > if you visit you'll see > a very simple executeScript() example. OMMs it behaves thusly: > > *works in NC 4.79 (and lower) for mac OS 9.2.2 as Classic (10.1.5); > *works in NC 4.79 (and lower) for mac OS 9.2.2; > *works in NC 4.79 (and lower) for win2k; > > *does not work in N7 for mac OS X 10.1.5 (not seeing the plug-in, also js > error "executeScript is not a function"); > *does not work in N7 for mac OS 9.2.2 as Classic (js error "executeScript is > not a function"); > *does not work in N7 for OS 9.2.2 (js error "executeScript is not a > function"); > *does not work in N7 for win2k (js error "executeScript is not a function"); > > *does not work in mac IE. > *does not work in win2k IE. > > if you have a chance, I'd be interested in seeing your results for this > page. > > >> >> Any Mozilla crusaders out there? >> > not this one ;-) > > > -tim ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. /|||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: timothy driscoll Subject: Re: Chime, browsers, and Netscape 7 Date: Fri, 27 Sep 2002 11:55:51 -0400 To: rasmol@lists.umass.edu at 10:05 AM EDT on (Friday) 27 September 2002 James W. Caras said: > Hi Tim and all- > > On my Powerbook G3 running OS 9.2, I installed Netscape 7 (classic), then > went to MDL and downloaded the latest Chime and installed it. I went to > the Boyer Biochemistry site and everything ran flawlessly. > thanks for providing a test site - my N7-Mac also runs this site without trouble. (I was suspicious of my browser installation, but apparently it's fine!) however, read on... > The Boyer textbook site uses the standard small-frame, hidden-button, > execute immediately scheme. My javascript/liveconnect used in this site is > based around what others have done long, long ago (likely the earliest > incarnations executeScript) but in trying to understand things I generally > re-write the javascript so that it makes sense to me. > the Boyer site appears to use immediate-mode buttons exclusively - not executeScript() - so it doesn't really tell us whether executeScript() functions under N7. > I went to your demo site at Molvisions and the executeScript did not > work, and the javascript debugger did report the error that it is not a > function. My uninformed guess is that this error is not really related to > NS or Chime, but an error of this type I have often seen (too many > times!) with my own javascript coding. > hmm. I suppose it could be some js difference between NC4 flavors and the rest of the civilized world (shocking, I know). I'm looking into this and will post the results when I have them. > I did look at the source and didn't even see the executeScript function > (could this be it?), nor an external javascript call that might carry it, > but then again you had some server-side includes that might have the > executeScript built in (I am not yet familiar with this stuff). > the executeScript() calls are in the anchor tags for the links themselves; for example: a href="javascript:document.mol.executeScript('color red')" it's actually very simple code - on purpose. > Anyway, the good news is that Netscape 7 is a go on both platforms > well if I have to use IMBIF to run N7-Mac, I will - no great moral decision there ;-) regards, -tim -- molvisions - molecular graphics & visualization http://www.molvisions.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: timothy driscoll Subject: Chime and N7 Date: Fri, 27 Sep 2002 23:22:08 -0400 To: "LIST: rasmol" greetings, for all interested chime developers out there, I've finished some tests on Chime in N7 and here are my results. all tests used Chime 2.6SP3 unless noted. all results verified on two separate computers. ********************* test site. ********************* tests. 1. ability to send a single command to Chime via executeScript(). 2. ability to send a single command to Chime via IMBIF in an IFRAME. 3. ability to send a single command to Chime via IMBIF in a "standard" frameset. ********************* results. platform: windows 2000. browser: N7. executeScript() fails. IMBIF from IFRAME fails. IMBIF from standard frameset works. browser: NC4. executeScript() works. IMBIF from IFRAME fails. IMBIF from standard frameset works. browser: IE6 (Chime 2.6SP3 & SP4). executeScript() fails. IMBIF from IFRAME works. IMBIF from standard frameset works. platform: Mac OS 9.2.2 (Classic or boot). browser: N7. executeScript() fails. IMBIF from IFRAME fails. IMBIF from standard frameset works. browser: NC4. executeScript() works. IMBIF from IFRAME fails. IMBIF from standard frameset works. platform: Mac OS 10.1.5. browser: N7. plug-in fails to load. browser: IE5.5. plug-in fails to load. ********************* conclusions. 1. N7 (mac & win) and IE6 (win only) support IMBIF, but not executeScript(). 2. Netscape (any version, either platform) does not support the IFRAME tag. 3. for best cross-compatibility, use IMBIF in a standard frameset. this will ensure functionality in Win IE6, N7, and NC4, and Mac N7 and NC4. (nothing works in Mac IE or in OSX yet). for the sticklers, here are the exact errors: 1. when executeScript() fails, javascript console reports "executeScript() is not a function." 2. when IMBIF fails, javascript console reports the iframe "has no properties." and here are my systems: mac os 10.1.5: G4, 2x500MHz, 512MB RAM. mac os 9.2.2 primary: G4, 2x500MHz, 512MB RAM. (OS 10.1.5 installed.) mac os 9.2.2 secondary: G3, 350 MHz, 192MB RAM. win 2000 (5.0 SP2): x86-based ibm netvista, 667 MHz, 129MB RAM. hope this is useful, tim -- molvisions - molecular graphics & visualization http://www.molvisions.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-- johno@mdli.com ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime download URL Date: Sun, 29 Sep 2002 10:22:00 -0400 To: rasmol@lists.umass.edu Cc: webmaster@mdlchime.com, bdickey@mdli.com, chime-team@mdli.com, Recently the URL www.mdlchime.com stopped working, but the URL www.mdlchime.com/chime continues to work. I have asked Bob Dickey at MDL to add a redirect from the short URL to the long one since I have dozens of links at my websites to the short version, including in thousands of downloaded copies of Protein Explorer etc. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il 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-- John Olson ++++------+------+------+------+------+------+------+------+------+------+ From: Robert Dickey Subject: RE: Chime download URL Date: Sun, 29 Sep 2002 11:32:36 -0700 To: "'Eric Martz'" , rasmol@lists.umass.edu Cc: webmaster@mdli.com, Robert Dickey , chime-team@mdli.com, I just added the redirect, and it seems to work, so let me know if you still have a problem. Regards, Bob Dickey -----Original Message----- Sent: Sunday, September 29, 2002 7:22 AM johno@mdli.com From: Eric Martz [mailto:emartz@microbio.umass.edu] Subject: Chime download URL To: rasmol@lists.umass.edu Cc: webmaster@mdlchime.mdli.com; bdickey@mdli.com; chime-team@mdli.com; Recently the URL www.mdlchime.com stopped working, but the URL www.mdlchime.com/chime continues to work. I have asked Bob Dickey at MDL to add a redirect from the short URL to the long one since I have dozens of links at my websites to the short version, including in thousands of downloaded copies of Protein Explorer etc. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il 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-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Re: Chime and N7 Date: Mon, 30 Sep 2002 08:42:08 -0500 (CDT) To: "LIST: rasmol" Hi, Paul Pillot had previously (early this year) told me that Netscape/Mozilla doesn't support the executeScript method. Hence the issues with Protein Explorer. However, there doesn't seem to be much on the web on this function. Regards Bruce On Fri, 27 Sep 2002, timothy driscoll wrote: > greetings, > > for all interested chime developers out there, I've finished some tests on > Chime in N7 and here are my results. all tests used Chime 2.6SP3 unless > noted. all results verified on two separate computers. > > > ********************* > test site. > > > > ********************* > tests. > 1. ability to send a single command to Chime via executeScript(). > 2. ability to send a single command to Chime via IMBIF in an IFRAME. > 3. ability to send a single command to Chime via IMBIF in a "standard" > frameset. > > > ********************* > results. > > platform: windows 2000. > browser: N7. > executeScript() fails. > IMBIF from IFRAME fails. > IMBIF from standard frameset works. > > browser: NC4. > executeScript() works. > IMBIF from IFRAME fails. > IMBIF from standard frameset works. > > browser: IE6 (Chime 2.6SP3 & SP4). > executeScript() fails. > IMBIF from IFRAME works. > IMBIF from standard frameset works. > > > platform: Mac OS 9.2.2 (Classic or boot). > browser: N7. > executeScript() fails. > IMBIF from IFRAME fails. > IMBIF from standard frameset works. > > browser: NC4. > executeScript() works. > IMBIF from IFRAME fails. > IMBIF from standard frameset works. > > > platform: Mac OS 10.1.5. > browser: N7. > plug-in fails to load. > > browser: IE5.5. > plug-in fails to load. > > > > ********************* > conclusions. > > 1. N7 (mac & win) and IE6 (win only) support IMBIF, but not executeScript(). > 2. Netscape (any version, either platform) does not support the IFRAME tag. > 3. for best cross-compatibility, use IMBIF in a standard frameset. this > will ensure functionality in Win IE6, N7, and NC4, and Mac N7 and NC4. > (nothing works in Mac IE or in OSX yet). > > > for the sticklers, here are the exact errors: > 1. when executeScript() fails, javascript console reports "executeScript() > is not a function." > 2. when IMBIF fails, javascript console reports the iframe "has no > properties." > > and here are my systems: > mac os 10.1.5: G4, 2x500MHz, 512MB RAM. > mac os 9.2.2 primary: G4, 2x500MHz, 512MB RAM. (OS 10.1.5 installed.) > mac os 9.2.2 secondary: G3, 350 MHz, 192MB RAM. > win 2000 (5.0 SP2): x86-based ibm netvista, 667 MHz, 129MB RAM. > > > > hope this is useful, > > tim > -- > molvisions - molecular graphics & visualization > http://www.molvisions.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-Accept-Language: en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Hens Borkent Subject: ChimeSPx and N7, IE6, ... Date: Mon, 30 Sep 2002 16:34:03 +0200 To: rasmol@lists.umass.edu Chimers, In view of the recent discussion on Chime on the Mac, in particular Timothy Driscoll's mail of September 27th: With so many combinations of operating systems, browsers and chime versions, there seems to be a need for annotated testing material in two directions: - a number of sites using different techniques to offer chime functionality, scripting methods etc, where one can check ones browser capability, - a list of testers using different OS's, browser versions and chime versions, to whom one can mail a URL for 'certification'. Is this part of what James Caras is compiling, or has somebody else collected information of this type? Is there an obvious site where such information should or could be offered (apart from mdlchime.com)? Kind regards, Hens Borkent -- 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 g8UEZP901143 ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Chime and N7 Date: Mon, 30 Sep 2002 10:33:54 -0400 To: rasmol@lists.umass.edu at 8:42 AM EDT on (Monday) 30 September 2002 southey@ux1.cso.uiuc.edu said: > Hi, > Paul Pillot had previously (early this year) told me that Netscape/Mozilla > doesn't support the executeScript method. Hence the issues with Protein > Explorer. However, there doesn't seem to be much on the web on this > function. > > Regards > Bruce > hi Bruce, more like N7/Mozilla doesn't recognize the function. here's something I found about LiveConnect and plug-ins in the N7 documentation: " If a legacy Communicator 4.x plug-in binary is installed within Mozilla or Netscape, its basic features will function as expected because of the backward compatibility of the Mozilla Plug-in API supported by Netscape. " -- this sounds like Chime in N7, doesn't it? -- " However, if the plug-in has a Java API callable from JavaScript via LiveConnect, these calls within will fail silently until the plug-in binary is upgraded to support the Mozilla Plug-in API. Contact the plug-in vendor to determine when an upgraded plug-in binary will be available for download.  " -- without knowing anything official, I might guess that a patch of Chime is required for executeScript() to run in N7. I will ask at the MDL site about it. -tim -- molvisions - molecular graphics & visualization http://www.molvisions.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: timothy driscoll Subject: Re: ChimeSPx and N7, IE6, ... Date: Mon, 30 Sep 2002 11:28:34 -0400 To: rasmol@lists.umass.edu at 4:34 PM EDT on (Monday) 30 September 2002 Hens Borkent said: > With so many combinations of operating systems, browsers and chime > versions, there seems to be a need for annotated testing material in two > directions: > - a number of sites using different techniques to offer chime > functionality, scripting methods etc, where one can check ones browser > capability, > - a list of testers using different OS's, browser versions and chime > versions, to whom one can mail a URL for 'certification'. > > Is this part of what James Caras is compiling, or has somebody else > collected information of this type? > Is there an obvious site where such information should or could be > offered (apart from mdlchime.com)? > I do not know of a central repository for such information, though you can find a lot of it on Eric Martz's Chime site. there are, of course, many Web sites that use Chime at varying levels. I have a "short list" of such sites that I generally use for testing, though this is far from ideal (lots of uncontrolled variables). IMHO your ideas have a lot of merit. if nothing comes from other list members, I would be willing to recruit volunteers for a "distributed testing facility" and host the central node here at my own site. let's see what others say... -tim -- molvisions - molecular graphics & visualization http://www.molvisions.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-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Roberts, Rebecca" Subject: OpenGL or DirectX or VMRL Date: Mon, 30 Sep 2002 14:18:32 -0400 To: rasmol@lists.umass.edu Hello all, Does anyone know if PE or similar program supports full-screen OpenGL or DirectX. Alternatively, does anyone know of a way to export the images in VRML (virtual reality modeling language)? Thanks, Rebecca ---------------------------------------- Dr. Rebecca A. Roberts Assistant Professor Department of Biology Ursinus College Collegeville PA 19426 (610) 489-4111 ext 2665 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <5FF81408E6DBD211AEAD00104B93CAFE053057F2@exchange.ursinus.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re: OpenGL or DirectX or VMRL Date: Mon, 30 Sep 2002 21:45:26 +0200 To: rasmol@lists.umass.edu PE and chime are based upon the RasMol program, which cannot produce OpenGl or DirectX renderings. You must use other molecular visualisation softwares to do that (on windows for example you can try Accelrys wablabviewer, or MolMol; both produce vrml outputs). You can find many informations on other molecular modelisation software to this adress : http://www.molvisindex.org good luck ! Paul ----- Original Message ----- Sent: Monday, September 30, 2002 8:18 PM From: "Roberts, Rebecca" Subject: OpenGL or DirectX or VMRL To: > Hello all, > > Does anyone know if PE or similar program supports full-screen OpenGL or > DirectX. Alternatively, does anyone know of a way to export the images in > VRML (virtual reality modeling language)? > > Thanks, > > Rebecca > > ---------------------------------------- > Dr. Rebecca A. Roberts > Assistant Professor > Department of Biology > Ursinus College > Collegeville PA 19426 > (610) 489-4111 ext 2665 > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- johno@mdli.com ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: "Breaking" news about Chime downloads Date: Mon, 30 Sep 2002 20:50:06 -0400 To: rasmol@lists.umass.edu Cc: webmaster@mdlchime.com, bdickey@mdli.com, chime-team@mdli.com, I have been informed by Robert Dickey, Chime project lead at MDL, that the server MDL uses for Chime installer downloads was hacked by vandals. MDL has taken it down until further notice. This explains why, at the present time, there is no response at www.mdlchime.com. However, their ftp site remains operational and the current Chime installers for both Windows and Mac are available there at ftp://ftp.mdli.com/pub/chime26 Robert is quite aware that this is a serious inconvenience to many. He assures me they will try to redirect the URL www.mdlchime.com to the ftp site ASAP, during the time while they are working on a permanent solution to a less vulnerable download server. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il 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 ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: RasTop newsletter Date: Mon, 30 Sep 2002 23:28:28 -0700 To: rasmol@lists.umass.edu, pdb-l@rcsb.org * new update, version 2.0.2 * RasTop in French by Naoum Salame * Using RasTop on Mac and Linux * Contributing to RasTop/RasMol # RasTop, version 2.0.2 This a minor update available at www.geneinfinity.org/rastop/download . A number of bugs have been corrected. Many thanks to Naoum Salame for suggesting gui improvments and reporting a large number of errors. RasTop is now multi-user with a separate preference file created automatically for each individual. Saving of pdb files are now coordinate dependent, allowing the building of composite pdb files (thanks to Andrew Horsfield for suggesting this improvment). #Rastop In French by Naoum Salame Naoum Salame from the INRP (Institut National de Recherche Pédagogique) is editing a French version of RasTop 2.0. Check his website dedicated to RasTop at http://www.inrp.fr/Acces/biotic/rastop/accueil.htm and download the impressive "RasTop en Francais". #Using RasTop on Mac and Linux - Tsvika Greener is using RasTop successfully on Linux RH7.3 X86 using Wine (http://www.codeweavers.com/technology/wine/download.php). Thanks Tsvika for the info; - Mentionned 6 months ago on the list but worth to know, RasTop works perfectly on Mac OS9 using VirtualPC - Thanks to Patrick Dansette (CNRS, Paris) and Joel Sussman (Weissman Institute); - Simple curiosity, but I guess Wine should work on OS X. Share your experience with us! #Contributing to RasMol Want to help the community, some code spleeping in a drawer or -worst- exe file distributed freely for the academic community without source? No matter, donnate your code (C only) to the community; surfaces, shapes, and volume are welcome. Want to plug them in? Just go! Thanks for your interest and support, Philippe Valadon september 2002 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <5FF81408E6DBD211AEAD00104B93CAFE053057F2@exchange.ursinus.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Giulio Vistoli Subject: Re: OpenGL or DirectX or VMRL Date: Tue, 01 Oct 2002 08:43:44 +0200 To: rasmol@lists.umass.edu Dear Rebecca, You can use VEGA (http://users.unimi.it/ddl) that supports OpenGL and exports the images in VRML Best regards Giulio Vistoli --------- Giulio Vistoli Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano Italia Tel. +39-02-50317522 Fax +39-02-50317565 giulio.vistoli@unimi.it http://users.unimi.it/ddl ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Gopalan Vivek Subject: regarding 'distributed testing facility' Date: Tue, 01 Oct 2002 15:38:59 +0800 To: rasmol@lists.umass.edu Hi all, I've developed a Chime application 'XdomView' for visualization of protein structural domains and intron positions of the homologous genes mapped on the protein structure. It is available at http://surya.bic.nus.edu.sg/xdom. I've only tested it in windows OS with Netscape 4.7 and IE 6.0. Since I've no access to Mac OS or any other systems where Chime works, I don't have any idea how my application works on these systems. I strongly believe that development of an "distributed testing facility" for Chime applications will surely help people like me and others who rely on Chime for visualisation. Thanking you Gopalan Vivek Bioinformatics Centre Block MD7 #02-07 Biochemistry Department National University of Singapore Singapore 119260 http://surya.bic.nus.edu.sg/~vivek Off Tel : (65) 6874 4459 Off Fax : (65) 6778 2466 ----- Original Message ----- Sent: Monday, September 30, 2002 11:28 PM From: "timothy driscoll" Subject: Re: ChimeSPx and N7, IE6, ... To: > at 4:34 PM EDT on (Monday) 30 September 2002 Hens Borkent said: > > > With so many combinations of operating systems, browsers and chime > > versions, there seems to be a need for annotated testing material in two > > directions: > > - a number of sites using different techniques to offer chime > > functionality, scripting methods etc, where one can check ones browser > > capability, > > - a list of testers using different OS's, browser versions and chime > > versions, to whom one can mail a URL for 'certification'. > > > > Is this part of what James Caras is compiling, or has somebody else > > collected information of this type? > > Is there an obvious site where such information should or could be > > offered (apart from mdlchime.com)? > > > > I do not know of a central repository for such information, though you can > find a lot of it on Eric Martz's Chime site. > > there are, of course, many Web sites that use Chime at varying levels. I > have a "short list" of such sites that I generally use for testing, though > this is far from ideal (lots of uncontrolled variables). > > IMHO your ideas have a lot of merit. if nothing comes from other list > members, I would be willing to recruit volunteers for a "distributed testing > facility" and host the central node here at my own site. > > let's see what others say... > > > -tim > -- > molvisions - molecular graphics & visualization > http://www.molvisions.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-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: XdomView app Date: Tue, 01 Oct 2002 14:04:44 +0200 To: rasmol@lists.umass.edu Re: Gopalan Vivek's site - http://surya.bic.nus.edu.sg/xdom I could not get a working connection. At the root directory -http://surya.bic.nus.edu.sg - I did get an Apache Server startup page. This sounds very interesting and look forward to access at such time as it is functional. Lewis Edgel Centralv. 3B 2tr 19476 Upplands Vaesby Sweden ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <016c01c26913$c1ee4bf0$1ed4fea9@Tranquilo> ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: Re: RasTop newsletter Date: Tue, 01 Oct 2002 08:32:23 -0400 To: rasmol@lists.umass.edu You wrote: ># RasTop, version 2.0.2 >available at www.geneinfinity.org/rastop/download The above URL is incorrect, I believe. http://www.geneinfinity.org/rastop/download.htm works, however. 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: XdomView app Date: Tue, 01 Oct 2002 10:31:12 -0400 To: rasmol@lists.umass.edu at 2:04 PM EDT on (Tuesday) 1 October 2002 Lewis Edgel said: > Re: Gopalan Vivek's site - http://surya.bic.nus.edu.sg/xdom > > I could not get a working connection. At the root directory > -http://surya.bic.nus.edu.sg - I did get an Apache Server startup page. > 01 oct 2002 10:30 EST - wake forest, nc. site loads for me, IE5 Mac OSX. might have been trannsient outage. try again, Lewis? -tim -- molvisions - molecular graphics & visualization http://www.molvisions.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-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: rasmol@lists.umass.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: RE: XdomView app Date: Tue, 01 Oct 2002 20:06:38 +0200 To: Gopalan Vivek Cc: rasmol@lists.umass.edu A second visit to your site was a success. For reference, I use Explorer 5.5 service pack 2, running on Windows 2000 version 5.0 build 2195. Lewis Edgel -----Original Message----- Sent: den 1 oktober 2002 16:27 From: Gopalan Vivek [mailto:vivek@bic.nus.edu.sg] Subject: Re: XdomView app To: lewis.edgel@telia.com Dear edgel, I checked the XdomView link in IE and Netscape browsers in my computer and found that it is working normal. As a caution, I've removed all the javascripts and style-sheet cmds in the program's homepage. I have also added a small image file in the mainpage so that it facilitates less downloading time. The web page link is http://surya.bic.nus.edu.sg/xdom/ If you still couldn't enter into the XdomView's homepage, kindly send us the version and name of the browser that you are using to access the program so that we can fix the error easily. Thank you very much for your valuable comments. Gopalan Vivek ----- Original Message ----- Sent: Tuesday, October 01, 2002 8:04 PM From: "Lewis Edgel" Subject: XdomView app To: > Re: Gopalan Vivek's site - http://surya.bic.nus.edu.sg/xdom > > I could not get a working connection. At the root > directory -http://surya.bic.nus.edu.sg - I did get an Apache Server startup > page. > > This sounds very interesting and look forward to access at such time as it > is functional. > > Lewis Edgel > Centralv. 3B 2tr > 19476 Upplands Vaesby > Sweden > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <016c01c26913$c1ee4bf0$1ed4fea9@Tranquilo> ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Subject: getting rastop 2.02 Date: Tue, 01 Oct 2002 08:17:32 -0700 To: rasmol@lists.umass.edu, pdb-l@rcsb.org Of course add htm at the end of the given url: http://www.geneinfinity.org/rastop/download.htm Thanks to Frieda Reichsman. 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-- johno@mdli.com ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Hooray for the new Chime site with old versions Date: Sat, 05 Oct 2002 13:32:21 -0400 To: webmaster@mdlchime.com, bdickey@mdli.com, chime-team@mdli.com, Cc: rasmol@lists.umass.edu Dear Bob and MDL Chime Team: I just noticed that you have your new Chime download site working at http://www.mdlchime.com Thanks for making Chime available promptly after the unfortunate attacks the old Chime server suffered recently. Hooray for making the old versions available, including SGI Irix Chime 0.9z. Also I appreciate the link to the ftp site. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il 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: Microsoft-Entourage/10.1.0.2006 ++++------+------+------+------+------+------+------+------+------+------+ From: "James W. Caras" Subject: writing new chime structure in a frame Date: Wed, 09 Oct 2002 22:55:26 -0500 To: rasmol@lists.umass.edu Hello all- Has anybody had any luck writing a new chime page into an existing frame using javascript (without changing the url of the frame...that would be too easy)? I have tried using the open(), then a few write() commands that list the proper html and the embed code, then the close() command, to no avail. I can write a normal web page into the frame this way, but when I try embedding a pdb file in it there is a blank spot where the chime structure is but no structure, no chime functionality. I know this works for embedded video. It should be so simple.... Any help would be greatly appreciated. Jamie ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. /|||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-- User-Agent: Microsoft-Entourage/10.1.0.2006 ++++------+------+------+------+------+------+------+------+------+------+ From: "James W. Caras" Subject: Re: Chime and N7 Date: Wed, 09 Oct 2002 23:05:56 -0500 To: rasmol@lists.umass.edu Hi All- One note regarding Tim's thorough and extremely helpful testing on different platforms: I generally write Chime structure pages using (what Tim refers to as) IMBIF from standard frameset (never really played around with executeScript). My pages work on IE 5 for Mac OS 9. Also, a minor note (in my experience is that Communicator 4.7 is identical to Netscape Navigator 4.08. So we can update the "compatibility conclusions" drawn: 1. N7 (mac & win) and IE6 (win only) support IMBIF, but not executeScript(). 2. Netscape (any version, either platform) does not support the IFRAME tag. 3. For best cross-compatibility, use IMBIF in a standard frameset. This will ensure functionality in Win IE6, N7, and NC4, and Mac N7, N4, NC4, and IE5. 4. Nothing works in OSX-native Mac IE or Netscape7 yet). On 9/27/02 10:22 PM, "timothy driscoll" wrote: > greetings, > > for all interested chime developers out there, I've finished some tests on > Chime in N7 and here are my results. all tests used Chime 2.6SP3 unless > noted. all results verified on two separate computers. > > > ********************* > test site. > > > > ********************* > tests. > 1. ability to send a single command to Chime via executeScript(). > 2. ability to send a single command to Chime via IMBIF in an IFRAME. > 3. ability to send a single command to Chime via IMBIF in a "standard" > frameset. > > > ********************* > results. > > platform: windows 2000. > browser: N7. > executeScript() fails. > IMBIF from IFRAME fails. > IMBIF from standard frameset works. > > browser: NC4. > executeScript() works. > IMBIF from IFRAME fails. > IMBIF from standard frameset works. > > browser: IE6 (Chime 2.6SP3 & SP4). > executeScript() fails. > IMBIF from IFRAME works. > IMBIF from standard frameset works. > > > platform: Mac OS 9.2.2 (Classic or boot). > browser: N7. > executeScript() fails. > IMBIF from IFRAME fails. > IMBIF from standard frameset works. > > browser: NC4. > executeScript() works. > IMBIF from IFRAME fails. > IMBIF from standard frameset works. > > > platform: Mac OS 10.1.5. > browser: N7. > plug-in fails to load. > > browser: IE5.5. > plug-in fails to load. > > > > ********************* > conclusions. > > 1. N7 (mac & win) and IE6 (win only) support IMBIF, but not executeScript(). > 2. Netscape (any version, either platform) does not support the IFRAME tag. > 3. for best cross-compatibility, use IMBIF in a standard frameset. this > will ensure functionality in Win IE6, N7, and NC4, and Mac N7 and NC4. > (nothing works in Mac IE or in OSX yet). > > > for the sticklers, here are the exact errors: > 1. when executeScript() fails, javascript console reports "executeScript() > is not a function." > 2. when IMBIF fails, javascript console reports the iframe "has no > properties." > > and here are my systems: > mac os 10.1.5: G4, 2x500MHz, 512MB RAM. > mac os 9.2.2 primary: G4, 2x500MHz, 512MB RAM. (OS 10.1.5 installed.) > mac os 9.2.2 secondary: G3, 350 MHz, 192MB RAM. > win 2000 (5.0 SP2): x86-based ibm netvista, 667 MHz, 129MB RAM. > > > > hope this is useful, > > tim ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. /|||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-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: RE: writing new chime structure in a frame Date: Thu, 10 Oct 2002 08:14:42 +0200 To: rasmol@lists.umass.edu Without seeing your code, I am not sure what you want. Can I assume that you have tried to use a simple "redirect" command? It has been two years since I taught HTML /Javascript, but I seem to recall a student having several HTML pages linked inside of a frame. I got out the Peach Pit Press "Javascript for the World Wide Web" (Negrino, Smith) 3rd Ed. and found in Chapter 2, pages 18-19, a description for embedding redirection inside of a link. What this function does, is allow the user to be redirected without being aware of the transition. I think your university has a copy of this book in the library.( The ISBN code is 0-201-35463-2.)If you find I am mistaken, email me the contents of your webpage(lewis.edgel@telia.com) and I will see what I can do for you. If I am successful, I will send you a copy of the code. -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of James W. Caras Sent: den 10 oktober 2002 05:55 From: owner-rasmol@lists.umass.edu Subject: writing new chime structure in a frame To: rasmol@lists.umass.edu Hello all- Has anybody had any luck writing a new chime page into an existing frame using javascript (without changing the url of the frame...that would be too easy)? I have tried using the open(), then a few write() commands that list the proper html and the embed code, then the close() command, to no avail. I can write a normal web page into the frame this way, but when I try embedding a pdb file in it there is a blank spot where the chime structure is but no structure, no chime functionality. I know this works for embedded video. It should be so simple.... Any help would be greatly appreciated. Jamie ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. /|||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: timothy driscoll Subject: Re: Chime and N7 Date: Thu, 10 Oct 2002 06:51:30 -0400 To: rasmol@lists.umass.edu at 11:05 PM EDT on (Wednesday) 9 October 2002 James W. Caras said: > > I generally write Chime structure pages using (what Tim refers to as) > IMBIF from standard frameset (never really played around with > executeScript). My pages work on IE 5 for Mac OS 9. Also, a minor note > (in my experience is that Communicator 4.7 is identical to Netscape > Navigator 4.08. > hi Jamie, two minor notes: 1. the IMBIF acronym originated with Eric Martz, just to give credit where credit is due ;-) 2. there are differences in javascript implementation between NN 4.0x and NC 4.5-4.8, though I never bothered to track down the details. in fact, there are differences within the NC 4.7x sub-versions (?) themselves! for example, NC 4.76 chokes on either a window.move() or window.resizeTo() - but only 4.76. argh. > 4. Nothing works in OSX-native Mac IE or Netscape7 yet). > :-( thanks for the update about Mac IE5! regards, tim -- molvisions - molecular graphics & visualization http://www.molvisions.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-MIMEOLE: Produced By Microsoft Exchange V6.0.6249.0 Thread-Topic: writing new chime structure in a frame Thread-Index: AcJwECIbQ/KGfgl3RAeAvnMLJ3JQoQAURGGg Content-Class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: "Jennifer L. Muzyka" Subject: RE: writing new chime structure in a frame Date: Thu, 10 Oct 2002 09:34:08 -0400 To: rasmol@lists.umass.edu Jamie- I've done this in the spectroscopy project I worked on this summer and talked about at the BCCE meeting. You can find the pages at: http://web.centre.edu/muzyka/organic/table/unknownsFrames.htm The javascript code is in a separate file called tools.js. You can probably download it from the server. If you have trouble finding it, let me know and I'll email you a copy of the javascript code. -Jennifer -----Original Message----- Sent: Wednesday, October 09, 2002 11:55 PM From: James W. Caras [mailto:caras@mail.utexas.edu] Subject: writing new chime structure in a frame To: rasmol@lists.umass.edu Hello all- Has anybody had any luck writing a new chime page into an existing frame using javascript (without changing the url of the frame...that would be too easy)? I have tried using the open(), then a few write() commands that list the proper html and the embed code, then the close() command, to no avail. I can write a normal web page into the frame this way, but when I try embedding a pdb file in it there is a blank spot where the chime structure is but no structure, no chime functionality. I know this works for embedded video. It should be so simple.... Any help would be greatly appreciated. Jamie ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. ,-. /|||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: timothy driscoll Subject: Re: writing new chime structure in a frame Date: Thu, 10 Oct 2002 10:56:00 -0400 To: rasmol@lists.umass.edu at 10:55 PM EDT on (Wednesday) 9 October 2002 James W. Caras said: > Hello all- > > Has anybody had any luck writing a new chime page into an existing frame > using javascript (without changing the url of the frame...that would be > too easy)? > hi Jamie, I usually build the html in a variable, then write the variable. not sure if that makes any difference, but... you can see a simple example at , follow the link to the "new Chime instance in a frameset." feel free to use the code, of course. how this example works: the original frameset has a Chime instance written into the html document of the bottom frame. a link in the top frame calls a function written in the frameset document (parent). this function writes a new html document to the bottom frame. the new html document contains a new instance of Chime, with a different background, color scheme. notice there is no redirection; the new js code overwrites the existing html. I've tested this example successfully in the following browsers: Mac (OS9): NN 4.08, NC 4.5, NC 4.79, N7, iCab (!). Win (2k): NC 4.5, NC 4.79, N7, IE6.0 SP1. hth, tim -- molvisions - molecular graphics & visualization http://www.molvisions.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-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 boundary="Boundary_(ID_S87Y8NySsaL7mbHrI+dVOg)" Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Robert Bateman Subject: workshop announcement Date: Thu, 10 Oct 2002 18:14:17 -0500 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_S87Y8NySsaL7mbHrI+dVOg) I would like to announce a molecular visualization workshop which is part of an NSF CCLI grant project. The initial announcement can be found at http://orca.st.usm.edu/~rbateman/kinemage/workshop.htm I will be glad to answer questions, but please send them to me directly rather than through the list. Bob 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) --Boundary_(ID_S87Y8NySsaL7mbHrI+dVOg)

I would like to announce a molecular visualization workshop which is part of an NSF CCLI grant project. The initial announcement can be found at http://orca.st.usm.edu/~rbateman/kinemage/workshop.htm

 

I will be glad to answer questions, but please send them to me directly rather than through the list.

Bob

 

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)

 

--Boundary_(ID_S87Y8NySsaL7mbHrI+dVOg)-- boundary="Boundary_(ID_NUNJ90A6cJ+ABzXNQEr6ug)" ++++------+------+------+------+------+------+------+------+------+------+ From: "A.Malcolm Campbell" Subject: Re: workshop announcement Date: Fri, 11 Oct 2002 10:45:18 -0400 To: rasmol@lists.umass.edu --Boundary_(ID_NUNJ90A6cJ+ABzXNQEr6ug) Robert, I am very impressed with the online JavaMage images. This would be a great teaching tool. I am in the process of developing proteomics lab to go with my genomics lab. I want students to interact with molecules. We just got a grant to buy 3D goggles. Any chance Kinemage will project in sterographics at some point in the future?? I would love to come to your workshop. Unfortunately, I have classes on that friday and MS is a long way to travel for just half a day. Any chance there might be a workshop at Duke? This would be much easier for me. Finally, I would like to encourage you and your group to consider publishing in Cell Biology Education (CBE; www.cellbioed.org). The name of the journal is a bit of a misnomer because we cover all aspects of life science education. Because we are an electronic journal, we are also looking to publish peer reviewed works in areas not served by paper journals. Your online visualization (JavaMage) or other topics sound ideal. One requirement for publishing in CBE is that each submitted work must have been assessed. I saw from your web site that this is not a problem for your work. Please take a few minutes to check out CBE. Our second issue is out and our third one is being formatted. We have a fast turnaround time, and authors have been very pleased with the thoughtful reviews of their submissions. Thanks for your time and your hard work. Great stuff! Malcolm ________________________________________________________ A. Malcolm Campbell Associate Professor of Biology Davidson College Director of GCAT (www.bio.davidson.edu/GCAT) Co-Editor-In-Chief Cell Biology Education (www.cellbioed.org) PO Box 7118 (US Mail) 209 Ridge Road (shipping) Davidson College Davidson, NC 28035 704-894-2692 (phone) 704-894-2512 (fax) www.bio.davidson.edu/campbell --Boundary_(ID_NUNJ90A6cJ+ABzXNQEr6ug) Robert, I am very impressed with the online JavaMage images. This would be a great teaching tool. I am in the process of developing proteomics lab to go with my genomics lab. I want students to interact with molecules. We just got a grant to buy 3D goggles. Any chance Kinemage will project in sterographics at some point in the future?? I would love to come to your workshop. Unfortunately, I have classes on that friday and MS is a long way to travel for just half a day. Any chance there might be a workshop at Duke? This would be much easier for me. Finally, I would like to encourage you and your group to consider publishing in Cell Biology Education (CBE; www.cellbioed.org). The name of the journal is a bit of a misnomer because we cover all aspects of life science education. Because we are an electronic journal, we are also looking to publish peer reviewed works in areas not served by paper journals. Your online visualization (JavaMage) or other topics sound ideal. One requirement for publishing in CBE is that each submitted work must have been assessed. I saw from your web site that this is not a problem for your work. Please take a few minutes to check out CBE. Our second issue is out and our third one is being formatted. We have a fast turnaround time, and authors have been very pleased with the thoughtful reviews of their submissions. Thanks for your time and your hard work. Great stuff! Malcolm Helvetica ________________________________________________________ A. Malcolm Campbell Associate Professor of Biology Davidson College Director of GCAT (www.bio.davidson.edu/GCAT) Co-Editor-In-Chief Cell Biology Education (www.cellbioed.org) PO Box 7118 (US Mail) 209 Ridge Road (shipping) Davidson College Davidson, NC 28035 704-894-2692 (phone) 704-894-2512 (fax) www.bio.davidson.edu/campbell --Boundary_(ID_NUNJ90A6cJ+ABzXNQEr6ug)-- boundary="Boundary_(ID_bTcokyiXZrlsPDtNPpzS5w)" ++++------+------+------+------+------+------+------+------+------+------+ From: "A.Malcolm Campbell" Subject: unintentional email to list Date: Fri, 11 Oct 2002 10:46:48 -0400 To: rasmol@lists.umass.edu --Boundary_(ID_bTcokyiXZrlsPDtNPpzS5w) To the list: Sorry. I hit reply instead of emailing Robert directly. Malcolm ________________________________________________________ A. Malcolm Campbell Associate Professor of Biology Davidson College Director of GCAT (www.bio.davidson.edu/GCAT) Co-Editor-In-Chief Cell Biology Education (www.cellbioed.org) PO Box 7118 (US Mail) 209 Ridge Road (shipping) Davidson College Davidson, NC 28035 704-894-2692 (phone) 704-894-2512 (fax) www.bio.davidson.edu/campbell --Boundary_(ID_bTcokyiXZrlsPDtNPpzS5w) To the list: Sorry. I hit reply instead of emailing Robert directly. Malcolm Helvetica ________________________________________________________ A. Malcolm Campbell Associate Professor of Biology Davidson College Director of GCAT (www.bio.davidson.edu/GCAT) Co-Editor-In-Chief Cell Biology Education (www.cellbioed.org) PO Box 7118 (US Mail) 209 Ridge Road (shipping) Davidson College Davidson, NC 28035 704-894-2692 (phone) 704-894-2512 (fax) www.bio.davidson.edu/campbell --Boundary_(ID_bTcokyiXZrlsPDtNPpzS5w)-- johno@mdli.com ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Old Chime download URL broken Date: Fri, 11 Oct 2002 13:33:37 -0400 To: webmaster@mdlchime.com, bdickey@mdli.com, chime-team@mdli.com, Cc: rasmol@lists.umass.edu The URL www.mdli.com/download/chime gives Error code: Unauthorized CGI Error code: Forbidden CGI Error code: Not Found CGI Error code: Server Error CGI Since this is used in many older Chime download links including some on my various sites, would it be possible to redirect this again to www.mdlchime.com? I assume that you will at least restore the documentation for script commands and embed tags when you can get to it. Beyond downloading the installer, these were the most crucial parts of your Chime site, in my opinion. Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il 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: Outage of Protein Explorer, MolVisIndex, DNA etc. yesterday Date: Fri, 11 Oct 2002 13:56:54 -0400 To: rasmol@lists.umass.edu Yesterday there was a power failure at the San Diego Supercomputer Center that caused many services to be inaccessible for several hours. These included Protein Explorer, MolVisIndex.Org, DNA Structure, etc. I myself was teaching at the time and needed access to all 3 of these, and I suspect many others were similarly inconvenienced. The condition has been corrected. Overall, SDSC provides extremely reliable and well-maintained servers, and their staff has been very responsive and helpful. I have provided explicit links to the UMass copies of Protein Explorer and my DNA Structure Tutorial at http://www.umass.edu/microbio/chime in case of such an event in the future. (MolVisIndex.Org involves CGI and so SDSC is its sole source.) -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il 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-- (by way of Eric Martz ) ++++------+------+------+------+------+------+------+------+------+------+ From: Robert Dickey Subject: RE: Old Chime download URL broken Date: Sat, 12 Oct 2002 14:52:52 -0400 To: rasmol@lists.umass.edu The URL (www.mdli.com/download/chime) has been redirected to www.mdlchime.com The new Chime site does not currently use the MS-Access and SQL-Server tables that contained the embed tag and script information. When the new MDL Web site goes into production, this information will be added. Regards, Bob Dickey ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Chime in IE5-Mac Date: Mon, 14 Oct 2002 17:19:09 -0400 To: rasmol@lists.umass.edu at 11:05 PM EDT on (Wednesday) 9 October 2002 James W. Caras said: > I generally write Chime structure pages using (what Tim refers to as) > IMBIF from standard frameset (never really played around with > executeScript). My pages work on IE 5 for Mac OS 9. > hi Jamie (or anyone), I've had no luck getting Chime to function in IE5 for Mac OS9, even with very simple sites that work in NN, NC, N7, IE for win, and iCab. is there an installation trick for Mac IE? I seem to recall an earlier discussion on this list about un-zipping the Chime.zip file for IE, but I can't find it in the list archives. thanks, tim -- molvisions - molecular graphics & visualization http://www.molvisions.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: timothy driscoll Subject: Chime in Win N7 error Date: Tue, 15 Oct 2002 10:47:29 -0400 To: "LIST: rasmol" hi Chime developers, anyone seen this before? I keep getting an error loading a multi-frame Chime page in N7. the error throws two messages: "Unable to allocate frame buffer" and "Chime Fatal Error - Chime could not allocate enough memory to display molecule in 3D." I am using the immediate-mode button to send commands to Chime; the commands are assembled as javascript strings and do not contain any incompatible "baddies." the buttons are written by javascript into a regular frame set to width 1% (so not an IFRAME). I'm running N7 on Win2k. the same page refuses to load Chime in N7 for Mac OS9, but without throwing any errors - just the traditional Netscape blank stare ;-) in both cases, the rest of the page loads without incident. any ideas? -tim -- molvisions - molecular graphics & visualization http://www.molvisions.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-Accept-Language: en References: <5.0.0.25.1.20001024145347.009ec8d0@ocean.otr.usm.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: 3D visualization Date: Tue, 15 Oct 2002 10:12:54 -0400 To: rasmol@lists.umass.edu Does anyone use Chime for 3D immersive visualization? We would appreciate recommendations for software and hardware for 3D (stereo) visualization of molecules. Thanks, Joan Slonczewski Professor of Biology Kenyon College 202 North College Road Gambier, OH 43022 Phone 740-427-5397 http://www2.kenyon.edu/depts/biology/slonc/slonc.htm slonczewski@kenyon.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 V5.00.2919.6700 boundary="Boundary_(ID_tRci7ynGWVr0BVwyfewjjQ)" X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: "Pan, Li" Subject: Question: how to use color feature in Rasmol Date: Sun, 03 Nov 2002 22:50:06 -0500 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_tRci7ynGWVr0BVwyfewjjQ) Hi, there: I am doing some research about new numerical methods for molecular simulation. I use Rasmol as a post-process tool to visualize my numerical results. Now I want to use colours to group atoms of different stress values. For example, the stress of atoms which are close to dislocation area are high while the stress of atoms which are far away from dislocation area are low. Then, the atoms with high stress are one colour and atoms with low stress are another colour or I use several colours to point out several groups of atoms from high stress level to low stress level. Could Rasmol do that and what's the format of the input file. If you have any idea, please reply this email. Thank you very much. Regards, Li Pan --Boundary_(ID_tRci7ynGWVr0BVwyfewjjQ)
Hi, there:
 
     I am doing some research about new numerical methods for molecular simulation. I use Rasmol as a post-process tool to visualize my numerical results. Now I want to use colours to group atoms of different stress values. For example, the stress of atoms which are close to dislocation area are high while the stress of atoms which are far away from dislocation area are low. Then, the atoms with high stress are one colour and atoms with low stress are another colour or I use several colours to point out several groups of atoms from high stress level to low stress level. Could Rasmol do that and what's the format of the input file.
 
     If you have any idea, please reply this email. Thank you very much.
 
Regards,
Li Pan    
--Boundary_(ID_tRci7ynGWVr0BVwyfewjjQ)-- X-Accept-Language: en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: File commands Date: Wed, 06 Nov 2002 09:58:22 -0500 To: rasmol@lists.umass.edu We're having trouble displaying part of this file: http://biology.kenyon.edu/courses/biol63/2MYS.pdb Chains b and c don't show in ribbons or sticks, only spacefill. Any suggestions? Joan Slonczewski Professor of Biology Kenyon College 202 North College Road Gambier, OH 43022 Phone 740-427-5397 http://www2.kenyon.edu/depts/biology/slonc/slonc.htm slonczewski@kenyon.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: timothy driscoll Subject: Re: File commands Date: Wed, 06 Nov 2002 10:16:04 -0500 To: rasmol@lists.umass.edu at 9:58 AM EDT on (Wednesday) 6 November 2002 Joan Slonczewski said: > We're having trouble displaying part of this file: > http://biology.kenyon.edu/courses/biol63/2MYS.pdb > Chains b and c don't show in ribbons or sticks, only spacefill. > Any suggestions? hi Joan, 2mys chains b and c contain only alpha carbons. AFAIK, spacefill and backbone are the only display styles that work on such chains. hth, -tim -- molvisions - molecular graphics & visualization http://www.molvisions.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-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Gorga, Frank" Subject: RE: File commands Date: Wed, 06 Nov 2002 10:35:01 -0500 To: "'rasmol@lists.umass.edu'" Joan, Take a careful look at the pdb file... it contains only alpha carbons for chains B and C... I suspect that this, and the (necessary) lack of connect records is the cause of the problems. Note that ball & stick also works, but it shows only the balls. Both spacefill and the balls of ball&sticks work fine with disconnected atoms; most other views need connect records. Notice, also, that the backbone command (which "connects the dots" of alpha carbons )works for all three chains. Hope that this helps, --- 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: Wednesday, November 06, 2002 9:58 AM From: Joan Slonczewski [mailto:slonczewski@kenyon.edu] Subject: File commands To: rasmol@lists.umass.edu We're having trouble displaying part of this file: http://biology.kenyon.edu/courses/biol63/2MYS.pdb Chains b and c don't show in ribbons or sticks, only spacefill. Any suggestions? Joan Slonczewski Professor of Biology Kenyon College 202 North College Road Gambier, OH 43022 Phone 740-427-5397 http://www2.kenyon.edu/depts/biology/slonc/slonc.htm slonczewski@kenyon.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: Pokescope stereo viewer Date: Wed, 06 Nov 2002 11:48:36 -0500 To: rasmol@lists.umass.edu, pdb-l@rcsb.org Recently I purchased a Pokescope stereo viewer (about $40, www.pokescope.com) for looking at split-image divergent (wall-eyed) stereo image pairs. It folds into a small plastic cube about 3.5 x 5.5 x 5.5 cm (1.4 x 2.25 x 2.25 in) that easily fits in a pocket. When folded, all optical surfaces are covered and protected. I took it into a class of seven students. None of these students had previous stereo viewing experience, and nobody had learned how to view split stereo images unaided. Everyone in the class was able to achieve 3D perception of stereo molecular images in Chime immediately. One person took a little longer, but succeeded -- this person said that her vision does not usually achieve 3D perception in ordinary life. I was very impressed at the ease of use. I have learned to view split image stereo images unaided so I do not need this viewer for myself. However, when I want to show a stereo image to others, it will be the quickest, easiest, and most portable solution. Also it would be a good solution for those who find unaided 3D perception difficult with split-image pairs. I also own a head-mounting ("hat") style "Nu 3D Vu" viewer which is of equally high quality but considerably more cumbersome and less portable. It does have the advantage that both hands remain free (while one hand must be used to hold the Pokescope), and it has a somewhat wider field of view. It is best for convergent (cross-eyed) pairs, but will work with divergent pairs if the separation is not too great. When you tilt your head, the viewer tilts and you lose the illusion of 3D. So you must hold your head quite still, which quickly becomes uncomfortable. Because the Pokescope is not attached to your head, slight tilts of the head (without tilting the viewer) retain the illusion of 3D, making it a bit more comfortable and contributing to its ease of use. Reading glasses can be worn with either viewer. -Eric Martz (I have no financial interest in this product.) P.S. Protein Explorer's Stereo button makes divergent or convergent image pairs depending on the setting in the Preferences. Protein Explorer displays the RasMol/Chime commands it generates when its buttons are pressed, making it a good way to learn the command language. stereo -5 # divergent (walleyed) or stereo +5 # convergent (crosseyed) For more information on viewing stereo, please see Protein Explorer's Help/Index/Glossary http://molvis.sdsc.edu/protexpl/igloss.htm#stereo and/or Gale Rhodes' page http://www.usm.maine.edu/~rhodes/0Help/StereoView.html /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il 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-Accept-Language: en References: <9F5E83E17008D31193DD0090274E75051319DA80@mailhost.bridgew.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: Re: File commands Date: Wed, 06 Nov 2002 12:31:11 -0500 To: rasmol@lists.umass.edu Frank, Thanks for the help--something too obvious to look for(!) Joan "Gorga, Frank" wrote: > Joan, > > Take a careful look at the pdb file... it contains only alpha carbons for > chains B and C... I suspect that this, and the (necessary) lack of connect > records is the cause of the problems. > > Note that ball & stick also works, but it shows only the balls. Both > spacefill and the balls of ball&sticks work fine with disconnected atoms; > most other views need connect records. Notice, also, that the backbone > command (which "connects the dots" of alpha carbons )works for all three > chains. > > Hope that this helps, > > --- 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: Joan Slonczewski [mailto:slonczewski@kenyon.edu] > Sent: Wednesday, November 06, 2002 9:58 AM > To: rasmol@lists.umass.edu > Subject: File commands > > We're having trouble displaying part of this file: > http://biology.kenyon.edu/courses/biol63/2MYS.pdb > Chains b and c don't show in ribbons or sticks, only spacefill. > Any suggestions? > Joan Slonczewski > Professor of Biology > Kenyon College > 202 North College Road > Gambier, OH 43022 > Phone 740-427-5397 > http://www2.kenyon.edu/depts/biology/slonc/slonc.htm > slonczewski@kenyon.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-Accept-Language: en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: Re: File commands Date: Wed, 06 Nov 2002 12:31:38 -0500 To: rasmol@lists.umass.edu Tim, Thanks for the help--something too obvious to look for(!) Joan timothy driscoll wrote: > at 9:58 AM EDT on (Wednesday) 6 November 2002 Joan Slonczewski said: > > > We're having trouble displaying part of this file: > > http://biology.kenyon.edu/courses/biol63/2MYS.pdb > > Chains b and c don't show in ribbons or sticks, only spacefill. > > Any suggestions? > > hi Joan, > > 2mys chains b and c contain only alpha carbons. AFAIK, spacefill and > backbone are the only display styles that work on such chains. > > hth, > > -tim > -- > molvisions - molecular graphics & visualization > http://www.molvisions.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-Accept-Language: en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: Composite model? Date: Wed, 13 Nov 2002 09:27:14 -0500 To: rasmol@lists.umass.edu We'd like to do a model of the phage T4 injector, but the PDB file we have shows only one of the three dimer sections; the three dimers are supposed to be interleaved, creating a beta triplex "needle." Is there any simple way to superimpose three models offset 120 degrees? http://biology.kenyon.edu/slonc/T4_1k28.pdb Joan Slonczewski Professor of Biology Kenyon College 202 North College Road Gambier, OH 43022 Phone 740-427-5397 http://www2.kenyon.edu/depts/biology/slonc/slonc.htm slonczewski@kenyon.edu ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-MSMail-priority: Normal References: <3DD26142.965837D3@kenyon.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: Re: Composite model? Date: Wed, 13 Nov 2002 15:41:29 +0100 To: rasmol@lists.umass.edu Try the Probable Quaternary Structure server from the EBI. I submitted the pdb id 1k28, and there is one model accessible on this page : http://pqs.ebi.ac.uk/pqs-bin/macmol.pl?filename=1k28 I took a look to it, and it looks very nice... Paul Pillot ----- Original Message ----- Sent: Wednesday, November 13, 2002 3:27 PM From: "Joan Slonczewski" Subject: Composite model? To: > We'd like to do a model of the phage T4 injector, but the PDB file we have shows > only one of the three dimer sections; the three dimers are supposed to be > interleaved, creating a beta triplex "needle." Is there any simple way to > superimpose three models offset 120 degrees? > http://biology.kenyon.edu/slonc/T4_1k28.pdb > > Joan Slonczewski ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <3DD26142.965837D3@kenyon.edu> <001801c28b22$c103dd00$bbaf0f50@zig> ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: Re: Composite model? Date: Wed, 13 Nov 2002 11:37:05 -0500 To: rasmol@lists.umass.edu Thanks, Paul; the file looks great. This is a good site to know about. Joan Paul Pillot wrote: > Try the Probable Quaternary Structure server from the EBI. > I submitted the pdb id 1k28, and there is one model accessible on this page > : http://pqs.ebi.ac.uk/pqs-bin/macmol.pl?filename=1k28 > I took a look to it, and it looks very nice... > > Paul Pillot > > ----- Original Message ----- > From: "Joan Slonczewski" > To: > Sent: Wednesday, November 13, 2002 3:27 PM > Subject: Composite model? > > > We'd like to do a model of the phage T4 injector, but the PDB file we have > shows > > only one of the three dimer sections; the three dimers are supposed to be > > interleaved, creating a beta triplex "needle." Is there any simple way to > > superimpose three models offset 120 degrees? > > http://biology.kenyon.edu/slonc/T4_1k28.pdb > > > > Joan Slonczewski > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Composite model? Date: Wed, 13 Nov 2002 12:37:33 -0500 To: rasmol@lists.umass.edu Cc: henrick@ebi.ac.uk At 11/13/02, Joan Slonczewski wrote: >We'd like to do a model of the phage T4 injector, but the PDB file we have shows >only one of the three dimer sections... Paul Pillot has pointed out the solution at the Probable Quaternary Structure (PQS) server of European Bioinformatics Institute. Protein Explorer (PE) makes it easy to find PQS: click on the Molecule Information (or Mol Info) link within PE to access external resources. One link in the Mol Info window takes you directly to the PQS page for the PDB code you are exploring. Also, the phage T4 injector 1K28 is featured in the Atlas of Macromolecules that accompanies Protein Explorer, http://molvis.sdsc.edu/atlas/atlas.htm#magnif where the full trimer is offered. In general I have used PQS extensively in this Atlas; in some cases (virus capsids) I offer an alpha-carbon only PDB file stripped down from PQS to keep the PDB file manageable in size. The 4th figure at the top of the Atlas (http://molvis.sdsc.edu/atlas) is a snapshot of the putative bacterial cell-wall puncturing device of T4, a truly amazing and magnificent protein machine. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il 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-- charset=us-ascii X-Accept-Language: en,pdf ++++------+------+------+------+------+------+------+------+------+------+ From: Jeff Cohlberg Subject: B-Z transition -- a challenge? Date: Wed, 13 Nov 2002 12:11:48 -0800 To: rasmol@lists.umass.edu An invitation to people who are good at making animations: I would love to see an animation of the B-Z transition in DNA, in which the guanine bases rotate from anti to syn and the entire cytidine residues including the riboses flip over, resulting in a switch from a right-handed to a left-handed helix without disrupting base pairs. This is something which is a bit of a struggle to visualize from schematic diagrams and even harder to convey to students. Does anyone know of such an animation? -- I don't. If one of the ace animators in this e-mail group could come up with an animation like this, it would be a great teaching tool. I don't know whether or not Chime is the best tool for constructing something like this. Jeff Cohlberg -- Jeffrey A. Cohlberg, Professor Department of Chemistry and Biochemistry California State University, Long Beach 1250 Bellflower Blvd. Long Beach, CA 90840 phone (562) 985-4944 fax (775) 248-1263 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: defined sets in Chime immediate-mode button? Date: Fri, 15 Nov 2002 16:03:35 -0500 To: "LIST: rasmol" hi all, I ran into a strange behavior today in Chime, and I'm curious if anyone can confirm it. I'm writing an interface that uses an immediate-mode button to send scripts to Chime. I pre-assemble each script as a javascript string and then write the button, again using javascript. it's fairly straightforward, and the method works fine for most everything. today, though, I included some defined sets in my script; for example, define fab (:a,:c,1-223b,1-223d) unfortunately, after defining the set, I can't manipulate it using my immediate-mode button interface. I tried this kind of syntax: define fab (:a,:c,1-223b,1-223d);select all;color red;select fab;color blue but no blue. however, if I try this: select all;color red;select (:a,:c,1-223b,1-223d);color blue it works as expected. I also tested command line access, again passing commands to the immediate-mode button and then on to Chime. first I tried defining the set in the initial script and then accessing it via command line. zippo. then I tried both defining it and accessing it via command line. nada as well. so I'm forced to conclude that defined sets don't appear to "work" thru an immediate-mode button. anyone else experience this, or have proof positive to refute me? it's a PITA compatibility issue, since defined sets make user access to Chime much easier, but immediate-mode buttons are necessary to support modern browsers. something about cake. :tim -- molvisions - molecular graphics & visualization http://www.molvisions.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: timothy driscoll Subject: Re: defined sets in Chime immediate-mode button? Date: Fri, 15 Nov 2002 16:12:58 -0500 To: "LIST: rasmol" at 4:03 PM EDT on (Friday) 15 November 2002 timothy driscoll said: > I ran into a strange behavior today in Chime, and I'm curious if anyone > can confirm it. I'm writing an interface that uses an immediate-mode > button to send scripts to Chime. I pre-assemble each script as a > javascript string and then write the button, again using javascript. > it's fairly straightforward, and the method works fine for most > everything. today, though, I included some defined sets in my script; > for example, > > define fab (:a,:c,1-223b,1-223d) > > unfortunately, after defining the set, I can't manipulate it using my > immediate-mode button interface. oh Lord, I am an idiot. disregard my last post, about defined sets thru immediate-mode button. it really does work. if I tell you what I did wrong, you'd only laugh harder. have an enjoyable weekend, :tim -- molvisions - molecular graphics & visualization http://www.molvisions.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-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: Roy Carambula Subject: RE: defined sets in Chime immediate-mode button? Date: Fri, 15 Nov 2002 16:42:12 -0500 To: "'rasmol@lists.umass.edu'" Tim, That's the way it works. You would have never found the problem until you had posted it. Good weekend. Roy -----Original Message----- Sent: Friday, November 15, 2002 4:13 PM From: timothy driscoll [mailto:listsub@molvisions.com] Subject: Re: defined sets in Chime immediate-mode button? To: LIST: rasmol at 4:03 PM EDT on (Friday) 15 November 2002 timothy driscoll said: > I ran into a strange behavior today in Chime, and I'm curious if anyone > can confirm it. I'm writing an interface that uses an immediate-mode > button to send scripts to Chime. I pre-assemble each script as a > javascript string and then write the button, again using javascript. > it's fairly straightforward, and the method works fine for most > everything. today, though, I included some defined sets in my script; > for example, > > define fab (:a,:c,1-223b,1-223d) > > unfortunately, after defining the set, I can't manipulate it using my > immediate-mode button interface. oh Lord, I am an idiot. disregard my last post, about defined sets thru immediate-mode button. it really does work. if I tell you what I did wrong, you'd only laugh harder. have an enjoyable weekend, :tim -- molvisions - molecular graphics & visualization http://www.molvisions.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-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "E.M.Crabb" Subject: Accessibility and buttons Date: Wed, 20 Nov 2002 12:49:16 +0000 To: "'rasmol@lists.umass.edu'" Hello all I am writing to the list to see if we can get some advice on the issue of accessibility. We have produced a Chime tutorial for our students on olfactory receptors which I have recently adapted to work using Internet Explorer. However we have a problem with the embed buttons - does anyone know a way to tab around these? An example of the code I have used to embed the molecules is shown below, however the buttons can not be highlighted when using the tab key. Is the only way round this to embed the actual molecule itself in the text rather than using buttons? Any suggestions would be gratefully received. Thank you Eleanor Dr Eleanor Crabb Multimedia Producer Science Web and Interactive Multimedia Group Science Faculty The Open 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-Originating-IP: [12.91.235.93] X-OriginalArrivalTime: 20 Nov 2002 15:01:59.0937 (UTC) FILETIME=[C6D0C710:01C290A5] ++++------+------+------+------+------+------+------+------+------+------+ From: "Pat O'Hern" Subject: Re: Accessibility and buttons Date: Wed, 20 Nov 2002 15:01:59 +0000 To: rasmol@lists.umass.edu >>However we have a problem with the embed buttons - does anyone >>know a way to tab around these? Hi, Eleanor- I'm not certain I understand your problem exactly, but I'm visualizing a block of text then a button, then another block of text then anotehr button, etc. You want your visually disabled learners to be able to skip over the buttons and get on with the rest of the text. If that is so, you might want to consider putting an "invisible" image before each command. I use a 1 X 1 pixel spacer .gif with border=0 as an image link/anchor tag. When selected, the link takes the user down to the corresponding anchor at the start of the next block of text. That way you can include an "alt" description and even a long description of what the molecuar image shows and the student can jump down to the next paragraph of text. Pat O'Hern Patricia A. O'Hern, Ph.D. CyberScience Design Computer-based Training and Accessibility Engineering 318 N. Decatur Lane Decatur, GA 30033 Ph: (404) 508-0375 FX: (404) 508-0128 www.cybersciencedesign.com pat.ohern@cybersciencedesign.com _________________________________________________________________ The new MSN 8: advanced junk mail protection and 2 months FREE* http://join.msn.com/?page=features/junkmail ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: "E.M.Crabb" Subject: RE: Accessibility and buttons Date: Wed, 20 Nov 2002 16:57:36 +0000 To: "'rasmol@lists.umass.edu'" Hello Thank you very much for your comments - this will certainly help with providing an alt comment for each molecule. Apologies however for not making myself clear. The problem is that we can find no way that students can load the molecule without actually clicking on the square buttons generated using the embed tag using a mouse. Is there a way that students can do this by using the tab key to move around the page and when a button is highlighted they could run the molecule by then pressing enter. We find that pressing tab does not highlight the buttons. Any ideas? Eleanor > -----Original Message----- > From: Pat O'Hern [SMTP:pat_ohern@hotmail.com] > Sent: 20 November 2002 15:02 > To: rasmol@lists.umass.edu > Subject: Re: Accessibility and buttons > > >>However we have a problem with the embed buttons - does anyone > >>know a way to tab around these? > > Hi, Eleanor- > > I'm not certain I understand your problem exactly, but I'm visualizing a > block of text then a button, then another block of text then anotehr > button, > etc. You want your visually disabled learners to be able to skip over the > buttons and get on with the rest of the text. > > If that is so, you might want to consider putting an "invisible" image > before each command. I use a 1 X 1 pixel spacer .gif with border=0 > > as an image link/anchor tag. When selected, the link takes the user down > to > the corresponding anchor at the start of the next block of text. That way > you can include an "alt" description and even a long description of what > the > molecuar image shows and the student can jump down to the next paragraph > of > text. > > Pat O'Hern > > > > Patricia A. O'Hern, Ph.D. > CyberScience Design > Computer-based Training > and Accessibility Engineering > 318 N. Decatur Lane > Decatur, GA 30033 > Ph: (404) 508-0375 > FX: (404) 508-0128 > www.cybersciencedesign.com > pat.ohern@cybersciencedesign.com > > > > > _________________________________________________________________ > The new MSN 8: advanced junk mail protection and 2 months FREE* > http://join.msn.com/?page=features/junkmail > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Accessibility and buttons Date: Wed, 20 Nov 2002 19:40:43 +0100 To: rasmol@lists.umass.edu I think there's a way to do a such thing : you could write form buttons (as in every HTML document which contains a form), and assign to the onClick event a javascript function which sends a script to chime. It's possible but a little tricky to do... I think that if you've never been playing around Chime and javascript, you should use Jean-Philippe Demers Mechanism Of Interaction. You can found it at http://www3.sympatico.ca/diane.demers/moi/ It provides every function you'll need to interact with chime via javascript rather than with embed buttons. Paul ----- Original Message ----- Sent: Wednesday, November 20, 2002 5:57 PM From: "E.M.Crabb" Subject: RE: Accessibility and buttons To: > Hello > > Thank you very much for your comments - this will certainly help with > providing an alt comment for each molecule. Apologies however for not making > myself clear. The problem is that we can find no way that students can load > the molecule without actually clicking on the square buttons generated using > the embed tag using a mouse. Is there a way that students can do this by > using the tab key to move around the page and when a button is highlighted > they could run the molecule by then pressing enter. We find that pressing > tab does not highlight the buttons. Any ideas? > > Eleanor ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: ca References: ++++------+------+------+------+------+------+------+------+------+------+ From: Gabriel Pons Subject: Re: lipoproteins Date: Thu, 21 Nov 2002 09:31:18 +0100 To: rasmol@lists.umass.edu hello all: I am preparing classes on lipoproteins and I have found a pdb file model on discoidal HDL. Anybody knows anyother files on esferical particles as LDL or VLDL, much more common? Thanks Gabriel Pons > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: ca References: ++++------+------+------+------+------+------+------+------+------+------+ From: Gabriel Pons Subject: Re: construct a file on a modular protein Date: Thu, 21 Nov 2002 09:34:50 +0100 To: rasmol@lists.umass.edu Hello all: I woul like to try to put together the differents domains cristallyzed from LDL receptor. Is there anay program to do that? It has to be done manually? is there any place where I could find some instructions to edit the coordinates and unite the residues ? Thanks Gabriel Pons ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: [12.91.235.87] X-OriginalArrivalTime: 21 Nov 2002 12:41:59.0775 (UTC) FILETIME=[625786F0:01C2915B] ++++------+------+------+------+------+------+------+------+------+------+ From: "Pat O'Hern" Subject: Re: lipoproteins Date: Thu, 21 Nov 2002 12:41:59 +0000 To: rasmol@lists.umass.edu I believe that there is a pdb file for apolipoprotein E. Pat Patricia A. O'Hern, Ph.D. CyberScience Design Computer-based Training and Accessibility Engineering 318 N. Decatur Lane Decatur, GA 30033 Ph: (404) 508-0375 FX: (404) 508-0128 www.cybersciencedesign.com pat.ohern@cybersciencedesign.com _________________________________________________________________ Add photos to your messages with MSN 8. Get 2 months FREE*. http://join.msn.com/?page=features/featuredemail ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <20010306123939-r01010600-e92f3014@216.254.100.238> ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: Chime view, restrict 2 chains Date: Thu, 21 Nov 2002 10:18:30 -0500 To: rasmol@lists.umass.edu Tim, Could you perhaps answer this question about how to "restrict" view to two chains? The molecule is a tetramer of individual dimers (AB, CD, EF, GH) and we'd like to see just A and B without the others; but "restrict" seems to let us see only A or B: http://biology.kenyon.edu/slonc/TGF1_phos.pdb Thanks, Joan Joan Slonczewski Professor of Biology Kenyon College 202 North College Road Gambier, OH 43022 Phone 740-427-5397 http://www2.kenyon.edu/depts/biology/slonc/slonc.htm slonczewski@kenyon.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-Accept-Language: en References: <20010306123939-r01010600-e92f3014@216.254.100.238> <3DDCF946.30BA2653@kenyon.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: John Mills Subject: Re: Chime view, restrict 2 chains Date: Thu, 21 Nov 2002 15:36:56 +0000 To: rasmol@lists.umass.edu Try: select *a or *b restrict selected John Mills Joan Slonczewski wrote: > Tim, > Could you perhaps answer this question about how to "restrict" view to two chains? > The molecule is a tetramer of individual dimers (AB, CD, EF, GH) and we'd like to > see just A and B without the others; but "restrict" seems to let us see only A or B: > > http://biology.kenyon.edu/slonc/TGF1_phos.pdb > Thanks, > Joan > > Joan Slonczewski > Professor of Biology > Kenyon College > 202 North College Road > Gambier, OH 43022 > Phone 740-427-5397 > http://www2.kenyon.edu/depts/biology/slonc/slonc.htm > slonczewski@kenyon.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: timothy driscoll Subject: Re: Chime view, restrict 2 chains Date: Thu, 21 Nov 2002 10:52:45 -0500 To: rasmol@lists.umass.edu at 3:36 PM EDT on (Thursday) 21 November 2002 John Mills said: > Try: > > select *a or *b > restrict selected > > John Mills > oops - just answered before reading your reply, John. yes, this works, too! :tim -- molvisions - molecular graphics & visualization http://www.molvisions.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: timothy driscoll Subject: Re: Chime view, restrict 2 chains Date: Thu, 21 Nov 2002 10:52:03 -0500 To: rasmol@lists.umass.edu at 10:18 AM EDT on (Thursday) 21 November 2002 Joan Slonczewski said: > Tim, > Could you perhaps answer this question about how to "restrict" view to two > chains? > The molecule is a tetramer of individual dimers (AB, CD, EF, GH) and we'd > like to > see just A and B without the others; but "restrict" seems to let us see only > A or B: > hi Joan, restrict (:a,:b) works for me; if this is not what you want, let me know... :tim -- molvisions - molecular graphics & visualization http://www.molvisions.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: <20010306123939-r01010600-e92f3014@216.254.100.238> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Chime view, restrict 2 chains Date: Fri, 22 Nov 2002 15:51:21 -0500 To: rasmol@lists.umass.edu At 11/21/02, Joan Slonczewski wrote: >Tim, >Could you perhaps answer this question about how to "restrict" view to two chains? >The molecule is a tetramer of individual dimers (AB, CD, EF, GH) and we'd like to >see just A and B without the others; but "restrict" seems to let us see only A or B: Tim's and John's replies already answered Joan's question, but I wanted to point out that this sort of thing can be done in Protein Explorer from menus (at the QuickViews page). The goal of Protein Explorer is to enable you to do such things without having to remember RasMol command syntax. To select two arbitrary chains: Method 1: SELECT Chain A Use QuickViews Plus to change the SELECT logic to "+" (add new selections to existing selection) SELECT Chain B (now both chains are selected) Method 2: SELECT Clicked Check "one chain per click" Click on the 2 chains desired Click "Stop" selection by clicking (Stop link is at top of middle frame) To restrict: DISPLAY Only (... only what is currently selected) Also I wanted to add that if there are 8 chains in the PDB file, zooming in on 2 of them may not allow satisfactory rotation (they may slide off center). This can be fixed by saving a separate PDB file that contains only the 2 chains of interest. If the biological unit is a dimer, this will usually be available from Probable Quaternary Structures: In Protein Explorer, click "Mol Info", then (under External resources) Probable Quaternary Structures. There will be a link to display the dimer in Protein Explorer, or RasMol etc. If PQS does not offer what you want, step by step instructions for using RasMol to save the desired chains with nearby ligand/hetero atoms are offered: In Protein Explorer, click "Mol Info", then (under External resources) Fewer or Single Chains. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il 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-X-Sender: yaya@epsilon.pair.com ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: MacOS X RasMol_2.7.2.1 binaries Date: Sun, 24 Nov 2002 17:07:47 -0500 (EST) To: rasmol@lists.umass.edu, pdb-l@rcsb.org RasMol 2.7.2.1 binaries for MacOS 10.2.2 (Darwin 6.2) using XDarwin 4.2.1.1 are now available from the Accessible Retired Computers in Biology (ARCiB) website: http://arcib.dowling.edu Information about installation is available in the FAQ on the RasMol website: http://www.RasMol.org -- 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 ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: MacOS X RasMol_2.7.2.1 binaries Date: Mon, 25 Nov 2002 07:34:37 -0500 To: rasmol@lists.umass.edu at 5:07 PM EDT on (Sunday) 24 November 2002 Herbert J. Bernstein said: > RasMol 2.7.2.1 binaries for MacOS 10.2.2 (Darwin 6.2) using XDarwin > 4.2.1.1 are now available from the Accessible Retired Computers in Biology > (ARCiB) website: > > http://arcib.dowling.edu > > Information about installation is available in the FAQ on the RasMol > website: > > http://www.RasMol.org > > -- H. J. Bernstein > hi Herb, thanks for the link, and the binaries! :tim -- molvisions - molecular graphics & visualization http://www.molvisions.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: Animated simulation of inhibitor binding to HIV protease Date: Sun, 01 Dec 2002 22:47:06 -0500 To: rasmol@lists.umass.edu, pdb-l@rcsb.org Beginning in 1998, I have simulated protein conformational changes by "morphing", that is, interpolating between two empirically-determined conformations. (Some were with the assistance of Krebs and Gerstein's morph server, http://molmovdb.mbb.yale.edu/molmovdb/). Such morphs can be played as animations using Protein Explorer (http://proteinexplorer.org -- see in particular http://molvis.sdsc.edu/protexpl/morfdoc.htm ) with the advantage that they can be rotated, even while animating, to view from any perspective. Also, buttons are provided to change the rendering and color scheme. I have just released a new simulation of ligand binding to protein that, unlike the previous ones, is derived from a single empirically determined structure. The example chosen is that of the Ritonavir inhibitor binding to HIV protease (1HXW). This fictional simulation, intended for educational use, was made by pulling the ligand from the complex with concurrent real-time energy minimization by molecular mechanics, using MDL Sculpt (http://www.mdli.com/products/sculpt.html). The result shows satisfying adjustments of backbones, sidechains, and water to accomodate the inhibitor as it "slides in". An animated multi-gif of the result can be viewed at http://molvis.sdsc.edu/atlas/an_hivpi.gif documented at http://molvis.sdsc.edu/protexpl/morfdoc.htm where you can also get the multiple-model PDB file containing the simulation frames, and several animations saved from Protein Explorer. The latter can be played back without running Protein Explorer, but do require that you have MDL Chime installed (www.mdlchime.com). For example, here is a saved animation of the simulation rendered in spacefill: http://molvis.sdsc.edu/atlas/hivpi_m2.htm These simulations are also listed in the Atlas of Macromolecules (http://molvis.sdsc.edu/atlas). Animation by PE is now smoother in Internet Explorer. NOTE FOR PE DOWNLOADERS: The above enhancements have been added to the on-line Protein Explorer 1.982, but are not yet included in the downloadable package. However, you can save the simulation PDB file* and/or animation HTML files from the on-line version. -Eric Martz *Once you see the ensemble of models in PE, click on "MDL" below the molecule (bottom right corner), and pick File, Save Molecule As. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il 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-- boundary="Boundary_(ID_1lg45FZCcQW6escki+9x0w)" ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: Re: Animated simulation of inhibitor binding to HIV protease Date: Mon, 02 Dec 2002 08:17:17 -0500 To: rasmol@lists.umass.edu --Boundary_(ID_1lg45FZCcQW6escki+9x0w) On Sunday, December 1, 2002, at 10:47 PM, Eric Martz wrote: > > An animated multi-gif of the result can be viewed at > > http://molvis.sdsc.edu/atlas/an_hivpi.gif > Just got back from T-giving travels, and had to tell you that this an-gif is outrageously cool! Frieda Frieda Reichsman, PhD 30 South Whitney Street Molecules in Motion Amherst MA 01002 Interactive Molecular Structures 413-253-2405 http://www.moleculesinmotion.com http://www.bio.umass.edu/biochem/mydna --Boundary_(ID_1lg45FZCcQW6escki+9x0w) On Sunday, December 1, 2002, at 10:47 PM, Eric Martz wrote: An animated multi-gif of the result can be viewed at http://molvis.sdsc.edu/atlas/an_hivpi.gif Just got back from T-giving travels, and had to tell you that this an-gif is outrageously cool! Frieda Helvetica Frieda Reichsman, PhD 30 South Whitney Street Molecules in Motion Amherst MA 01002 Interactive Molecular Structures 413-253-2405 http://www.moleculesinmotion.com http://www.bio.umass.edu/biochem/mydna --Boundary_(ID_1lg45FZCcQW6escki+9x0w)-- X-Authentication-warning: hydrogen.leitl.org: eugen owned process doing -bs ++++------+------+------+------+------+------+------+------+------+------+ From: Eugen Leitl Subject: Large protein and protein complex structures Date: Mon, 02 Dec 2002 14:24:35 +0100 (CET) To: rasmol@lists.umass.edu I think I've seen a reference to a depository of large protein structures (virus capsids, protein complexes, etc) passing across this list several weeks ago. I thought I bookmarked it, but can't find it out of hand. Can you help me? TIA, Eugen Leitl ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Large protein and protein complex structures Date: Mon, 02 Dec 2002 10:43:32 -0500 To: rasmol@lists.umass.edu At 12/2/02, you wrote: > >I think I've seen a reference to a depository of large protein structures >(virus capsids, protein complexes, etc) passing across this list several >weeks ago. I thought I bookmarked it, but can't find it out of hand. > >Can you help me? > >TIA, > >Eugen Leitl EBI's Probable Quaternary Structures http://pqs.ebi.ac.uk/ In Protein Explorer, click on Mol. Info. and there is a link to it. Protein Explorer also offers a less technical summary of how PQS works, and a number of examples illustrating the kinds of things it finds. Go to the Help/Index/Glossary and look up Probable Quaternary Structures (http://molvis.sdsc.edu/protexpl/igloss.htm#pqs). Virus capsids (as received from PQS) tend to be 50-100 megabytes. I've stripped a few down to alpha carbons only, and you can find them under Viruses in the Atlas of Macromolecules (http://molvis.sdsc.edu/atlas/atlas.htm#virions). SV40 was 70 megs, 12 megs for alpha carbons only, and gzipped to 3 megs (suitable for Chime, can be saved from Chime for use in RasMol or other PDB software). /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf: http://consurf.tau.ac.il 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-X-Sender: ++++------+------+------+------+------+------+------+------+------+------+ From: southey@ux1.cso.uiuc.edu Subject: Serving pdb files from Linux Date: Mon, 02 Dec 2002 11:56:27 -0600 (CST) To: rasmol@lists.umass.edu Hi, I am trying to create html pages with pdb files embedded using a Linux server via the code: However I can not get the page to display when served via my server with the chime plugin (SP3 or SP4). (Except two old non-supported browsers.) http://deltas.animal.uiuc.edu/pdbtest.html In IE I get the error "The data that the plugin requested, did not download successfully" on my win98 machine running IE 5.5 or win2000 running IE 5.0. Under Netscape 4.79 I get "click here to get the plugin" - one that is already installed. Has anybody had this problem before and know a solution? The pdb files where downloaded as either "save as..." or directly via the Chime plugin command (on a windows and a linux machine). Thanks, 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-MIMEOLE: Produced By Microsoft Exchange V6.0.5762.3 Thread-Topic: Serving pdb files from Linux Thread-Index: AcKaLK0ZsS9DGPBTRW2qi3TiEDGUIAAAyhxQ content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: Anthony Lewis Subject: RE: Serving pdb files from Linux Date: Mon, 02 Dec 2002 18:28:50 +0000 To: rasmol@lists.umass.edu Hello, Could this be something to do with the MIME type not being "registered" on the server you are using. As I understand it, the server needs to send the client details of the type of file it's sending and this is achieved using the MIME type. So if the server doesn't know what the files is, it can't then tell the client/browser what to do with it. I'm sure this is a simplistic description and that others will be able to provide more precise details. Anyway, I hope it helps, Anthony Lewis -----Original Message----- Sent: 02 December 2002 17:56 From: southey@ux1.cso.uiuc.edu [mailto:southey@ux1.cso.uiuc.edu] Subject: Serving pdb files from Linux To: rasmol@lists.umass.edu Hi, I am trying to create html pages with pdb files embedded using a Linux server via the code: However I can not get the page to display when served via my server with the chime plugin (SP3 or SP4). (Except two old non-supported browsers.) http://deltas.animal.uiuc.edu/pdbtest.html In IE I get the error "The data that the plugin requested, did not download successfully" on my win98 machine running IE 5.5 or win2000 running IE 5.0. Under Netscape 4.79 I get "click here to get the plugin" - one that is already installed. Has anybody had this problem before and know a solution? The pdb files where downloaded as either "save as..." or directly via the Chime plugin command (on a windows and a linux machine). Thanks, 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-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: rlight Subject: RE: Serving pdb files from Linux Date: Mon, 02 Dec 2002 13:33:16 -0500 To: rasmol@lists.umass.edu Interesting. I'm running windows XP. FYI: With netscape 7.0, I get the structures loaded. With IE 6.0, I get black frames, but no structures and no messages. With netscape 4.7, I get only the h1 text, no blank frames or structures. Robley Lightr ************************************************************* Robley J. Light Professor of Chemistry and Biochemistry Department of Chemistry Phone: (850) 644-3844 and Biochemistry Email: rlight@chem.fsu.edu Florida State University Fax: (850) 644-8281 Tallahassee, FL 32306-4390 Home Page: http://chemweb.chem.fsu.edu/editors/rlight > -----Original Message----- > From: owner-rasmol@lists.umass.edu > [mailto:owner-rasmol@lists.umass.edu] On Behalf Of > southey@ux1.cso.uiuc.edu > Sent: Monday, December 02, 2002 12:56 PM > To: rasmol@lists.umass.edu > Subject: Serving pdb files from Linux > > > Hi, > I am trying to create html pages with pdb files embedded > using a Linux server via the code: > > > > However I can not get the page to display when served via my > server with the chime plugin (SP3 or SP4). (Except two old > non-supported browsers.) > http://deltas.animal.uiuc.edu/pdbtest.html In IE I get the error "The data that the plugin requested, did not download successfully" on my win98 machine running IE 5.5 or win2000 running IE 5.0. Under Netscape 4.79 I get "click here to get the plugin" - one that is already installed. Has anybody had this problem before and know a solution? The pdb files where downloaded as either "save as..." or directly via the Chime plugin command (on a windows and a linux machine). Thanks, Bruce Southey --- Incoming mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.423 / Virus Database: 238 - Release Date: 11/25/2002 --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.423 / Virus Database: 238 - Release Date: 11/25/2002 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Serving pdb files from Linux Date: Mon, 02 Dec 2002 13:56:47 -0500 To: rasmol@lists.umass.edu hi Bruce, at 6:28 PM EDT on (Monday) 2 December 2002 Anthony Lewis said: > Hello, > > Could this be something to do with the MIME type not being "registered" on > the server you are using. As I understand it, the server needs to send the > client details of the type of file it's sending and this is achieved using > the MIME type. So if the server doesn't know what the files is, it can't > then tell the client/browser what to do with it. > I agree. you have to configure your server to return files with the pdb suffix as the "chemical/x-pdb" MIME. for a complete list of MIME types handled by Chime, you can look at About:Plugins in any Netscape that has Chime installed. I'm sorry but I don't know how to enable plugins on a Linux server. I also recall having to clear my server cache, and stop-restart the Web server module (I'm running OS XS here) for the changes to take effect. if that doesn't work, you might try explicitly defining the file type in your embed tag: though I admit, I don't know when this actually makes a difference. anecdotally, it sometimes appears to fix plugin problems for me. ? hth, :tim > > > -----Original Message----- > From: southey@ux1.cso.uiuc.edu [mailto:southey@ux1.cso.uiuc.edu] > Sent: 02 December 2002 17:56 > To: rasmol@lists.umass.edu > Subject: Serving pdb files from Linux > > > Hi, > I am trying to create html pages with pdb files embedded using a Linux > server via the code: > > > > However I can not get the page to display when served via my server with > the chime plugin (SP3 or SP4). (Except two old non-supported browsers.) > > http://deltas.animal.uiuc.edu/pdbtest.html > > In IE I get the error "The data that the plugin requested, did not > download successfully" on my win98 machine running IE 5.5 or win2000 > running IE 5.0. Under Netscape 4.79 I get "click here to get the plugin" > - one that is already installed. > > Has anybody had this problem before and know a solution? > The pdb files where downloaded as either "save as..." or directly via the > Chime plugin command (on a windows and a linux machine). > > > Thanks, > Bruce Southey > -- molvisions - molecular graphics & visualization http://www.molvisions.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: Serving pdb files from Linux Date: Mon, 02 Dec 2002 14:07:47 -0600 (CST) To: rasmol@lists.umass.edu Thanks! Yes, I needed to set the web server to serve these files. Basically it means changing some configuration file(s). With Apache (version 2), I managed to get .mol files to work using AddType directive (AddType chemical/x-mdl-molfile .mol) in the httpd.conf file. But I have to find the conflict with the .pdb files. Thanks, Bruce On Mon, 2 Dec 2002, timothy driscoll wrote: > hi Bruce, > > at 6:28 PM EDT on (Monday) 2 December 2002 Anthony Lewis said: > > Hello, > > > > Could this be something to do with the MIME type not being "registered" on > > the server you are using. As I understand it, the server needs to send the > > client details of the type of file it's sending and this is achieved using > > the MIME type. So if the server doesn't know what the files is, it can't > > then tell the client/browser what to do with it. > > > I agree. you have to configure your server to return files with the pdb > suffix as the "chemical/x-pdb" MIME. for a complete list of MIME types > handled by Chime, you can look at About:Plugins in any Netscape that has > Chime installed. I'm sorry but I don't know how to enable plugins on a > Linux server. > > I also recall having to clear my server cache, and stop-restart the Web > server module (I'm running OS XS here) for the changes to take effect. > > if that doesn't work, you might try explicitly defining the file type in > your embed tag: > > > > though I admit, I don't know when this actually makes a difference. > anecdotally, it sometimes appears to fix plugin problems for me. ? > > > hth, > > :tim > > > > > > > -----Original Message----- > > From: southey@ux1.cso.uiuc.edu [mailto:southey@ux1.cso.uiuc.edu] > > Sent: 02 December 2002 17:56 > > To: rasmol@lists.umass.edu > > Subject: Serving pdb files from Linux > > > > > > Hi, > > I am trying to create html pages with pdb files embedded using a Linux > > server via the code: > > > > > > > > However I can not get the page to display when served via my server with > > the chime plugin (SP3 or SP4). (Except two old non-supported browsers.) > > > > http://deltas.animal.uiuc.edu/pdbtest.html > > > > In IE I get the error "The data that the plugin requested, did not > > download successfully" on my win98 machine running IE 5.5 or win2000 > > running IE 5.0. Under Netscape 4.79 I get "click here to get the plugin" > > - one that is already installed. > > > > Has anybody had this problem before and know a solution? > > The pdb files where downloaded as either "save as..." or directly via the > > Chime plugin command (on a windows and a linux machine). > > > > > > Thanks, > > Bruce Southey > > > -- > molvisions - molecular graphics & visualization > http://www.molvisions.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: timothy driscoll Subject: RE: Serving pdb files from Linux Date: Mon, 02 Dec 2002 15:26:53 -0500 To: rasmol@lists.umass.edu at 2:07 PM EDT on (Monday) 2 December 2002 southey@ux1.cso.uiuc.edu said: > Thanks! > > Yes, I needed to set the web server to serve these files. Basically it > means changing some configuration file(s). With Apache (version 2), I > managed to get .mol files to work using AddType directive (AddType > chemical/x-mdl-molfile .mol) in the httpd.conf file. But I have to find > the conflict with the .pdb files. > ah-ha. you might have a conflict with Palm, since PDAs use the pdb extension for their apps and it is likely to come pre-configured. regards, :tim -- molvisions - molecular graphics & visualization http://www.molvisions.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: Serving pdb files from Linux Date: Mon, 02 Dec 2002 14:44:24 -0600 (CST) To: Paul Pillot Cc: rasmol@lists.umass.edu Hi, Yes it's a cool structure - one I never expected! I created a bioinformatics tutorial to some teachers who were using it in the wet lab. Here the link if anyone wants it: http://deltas.animal.uiuc.edu/sibdoc/GreenFP_SIB.pdf If you are into transgenic art, see Alba at: http://www.ekac.org/ There are also red and yellow versions. It is also neat because the flurophore involves 3 ammino acids (ser65, tyr66 and gly67 - you can find them :-)). These are essential for the fluorescence for example changing tyr66 to his shifts the spectrum to ultraviolet. So it also provides other useful activities. Regards Bruce On Mon, 2 Dec 2002, Paul Pillot wrote: > Perhaps you've fixed your server's bug, but FYI it runs fine for me with > IE6.0 (Win Me) > I've never seen you green fluorescent protein before. Thanks, it's a very > nice structure ! > > Paul > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: GFP (was Re: Serving pdb files from Linux) Date: Mon, 02 Dec 2002 16:28:35 -0500 To: rasmol@lists.umass.edu at 2:44 PM EDT on (Monday) 2 December 2002 southey@ux1.cso.uiuc.edu said: > Hi, > > Yes it's a cool structure - one I never expected! I created a > bioinformatics tutorial to some teachers who were using it in the wet lab. > Here the link if anyone wants it: > http://deltas.animal.uiuc.edu/sibdoc/GreenFP_SIB.pdf > > If you are into transgenic art, see Alba at: > http://www.ekac.org/ > > There are also red and yellow versions. It is also neat because the > flurophore involves 3 ammino acids (ser65, tyr66 and gly67 - you can find > them :-)). These are essential for the fluorescence for example changing > tyr66 to his shifts the spectrum to ultraviolet. So it also provides > other useful activities. > > Regards > Bruce > > On Mon, 2 Dec 2002, Paul Pillot wrote: > > > Perhaps you've fixed your server's bug, but FYI it runs fine for me with > > IE6.0 (Win Me) > > I've never seen you green fluorescent protein before. Thanks, it's a very > > nice structure ! > > > > Paul > > GFP is a beautiful structure, and a very cool protein in the lab, too. I've just reposted my old, old (old) GFP in Chime presentation; you can view it online at be warned that it has been tested in Netscape Communicator 4.x only; while it may function in other browsers, I can make no guarantee at this point. it is quite an old module (did I say that already?) ;-) anyone interested in a "modern" version of this Chime module is welcome to email me offlist. it does not yet exist, but I could upgrade it... regards, :tim -- molvisions - molecular graphics & visualization http://www.molvisions.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: Roche Genetics CD-ROM Date: Tue, 03 Dec 2002 09:11:17 -0600 (CST) To: rasmol@lists.umass.edu Hi My apologize in advance for this but it is free and some of you may be interested in it. My only interest is in the educational value and not the company etc. Roche Genetics (http://www.rochegenetics.com) has put out a free CD-ROM on genetics that you can request a copy from: http://www.roche.com/home/science/science-gengen/science-gengen-cdrom.htm It includes sections on introduction to genetics, finding disease causing genes, and pharmacogenetics. It uses a combination of Macromedia's Shockwave and flash so you need a browser that supports these. You can also get a couple of other languages. I got mine in the USA with the latest copy of Scientific American. I could provide the .iso for those who can not wait and can burn their own. Regards Bruce ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: "Kathleen M. Gorski" Subject: Re: Roche Genetics CD-ROM Date: Tue, 03 Dec 2002 10:25:04 -0500 To: rasmol@lists.umass.edu My copy of this CD was picked up at a pharmacy! It's a great (free) teaching tool. kathy gorski ******************** A little integrity is better than any career. - Ralph Waldo Emerson in "The Conduct of Life" Kathleen M. Gorski, Ph.D. Science Teacher, Academic Technology Coordinator Kingswood-Oxford Middle School 695 Prospect Avenue West Hartford, CT 06105-4245 email: gorski.k@k-o.org phone: 860-233-3500 x3301 fax: 860-233-1151 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Roche Genetics CD-ROM Date: Tue, 03 Dec 2002 10:39:43 -0500 To: rasmol@lists.umass.edu at 9:11 AM EDT on (Tuesday) 3 December 2002 southey@ux1.cso.uiuc.edu said: > Hi > My apologize in advance for this but it is free and some of you may be > interested in it. My only interest is in the educational value and not > the company etc. > > Roche Genetics (http://www.rochegenetics.com) has put out a free CD-ROM on > genetics that you can request a copy from: > > http://www.roche.com/home/science/science-gengen/science-gengen-cdrom.htm > looks neat - I requested a copy of my own. (I'm trying to curb my need for instant gratification by actually waiting the 2-3 weeks ;-) thanks for the link, Bruce! :tim -- molvisions - molecular graphics & visualization http://www.molvisions.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: timothy driscoll Subject: BBEdit plug-in for scripting? Date: Wed, 04 Dec 2002 17:00:11 -0500 To: "LIST: rasmol" greetings Mac Chime/RasMol scripters: something that I really miss when writing Chime or RasMol scripts, especially long and convoluted ones, is syntax coloring. it is possible to write a language module for BBEdit to handle syntax coloring for the Chime/RasMol command language. for those who don't know, BBEdit is a popular text/html editor for the Mac. it already handles over 20 other languages - including, btw, python and actionscript. AFAIK writing a language module is not quite a no-brainer. so I am doing a little pre-market survey: does anyone else use BBEdit to write scripts? if so, would syntax coloring be a desired feature for you? 'cause if it's just me, well, maybe it ain't worth the time ;-) feel free to reply off-list. regards, :tim -- molvisions - molecular graphics & visualization http://www.molvisions.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-- <913F8FBFBCDEAC439132B6C806C89FF002BDD1EB@niaid-mail2.niaid.nih.gov> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: ?fix for too much memory? Date: Wed, 04 Dec 2002 18:59:34 -0500 To: David Margulies Cc: rasmol@lists.umass.edu At 12/4/02, David Margulies wrote: Eric: Is there any fix for the too much memory problem, i.e. > 1Gb on Mac G4 dp for chime/ protein explorer? It would be nice not to have to remove memory wouldn't you say? Dear David: As stated on my Troubleshooting page http://molvis.sdsc.edu/protexpl/troubles.htm#macmemory the only other solution I've been told about is to upgrade to OSX and run Chime/PE in the classic environment. As I think you know, I am not a Mac user myself. I've copied this to the list in case anyone has suggestions to add. -Eric ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Lewis Edgel Subject: RE: ?fix for too much memory? Date: Thu, 05 Dec 2002 10:27:46 +0100 To: rasmol@lists.umass.edu Here's a shot in the dark... have not played with the newer OS from Apple... I seem to recall that you can set the memory allocation for each program running on operating system series 7-8. Perhaps, you could contact Apple's educational support people to see if this is a possibility - IF you have not already explored this. I do recall your earlier posting on the matter, but am not sure which flavour of OS exhibited the problem. My wife uses a G4 to process test results from a Becton-Dickenson flow-cytometer and found the solution suggested by Mr. Martz allowed her to run the BD program (not OSX compatible) as well as the majority of the programs from the machine the G4 replaced (Powermac 7300/200). I agree OSX running in classic mode seems the most painless solution for the majority of compatibility problems. Lewis Edgel -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Eric Martz Sent: Thursday, December 05, 2002 1:00 AM From: owner-rasmol@lists.umass.edu Subject: Re: ?fix for too much memory? To: David Margulies Cc: rasmol@lists.umass.edu At 12/4/02, David Margulies wrote: Eric: Is there any fix for the too much memory problem, i.e. > 1Gb on Mac G4 dp for chime/ protein explorer? It would be nice not to have to remove memory wouldn't you say? Dear David: As stated on my Troubleshooting page http://molvis.sdsc.edu/protexpl/troubles.htm#macmemory the only other solution I've been told about is to upgrade to OSX and run Chime/PE in the classic environment. As I think you know, I am not a Mac user myself. I've copied this to the list in case anyone has suggestions to add. -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-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-GB; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en, en-us X-MailScanner: Found to be clean X-MailScanner-SpamCheck: not spam, SpamAssassin (score=-0.8, required 10, SIGNATURE_LONG_SPARSE, SPAM_PHRASE_02_03, USER_AGENT, USER_AGENT_MOZILLA_UA, X_ACCEPT_LANG) ++++------+------+------+------+------+------+------+------+------+------+ From: Nicholas Keep Subject: Defining rasscript files for Mac using Explorer Date: Thu, 05 Dec 2002 09:54:18 +0000 To: rasmol@lists.umass.edu Can anyone help. We use rasmol scripts in our online courses and have covered installation for many combinations http://tsmb02.cryst.bbk.ac.uk/tech/rasmol However one of our students wants to know how to define rasmol scripts running internet explorer on a Mac! (I know this is not the best solution) How do you tell a mac to associate a file extension with 'rasmol -script' rather than just 'rasmol'. Any suggesions welcomed Nick -- Dr Nicholas H. Keep School of Crystallography, Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.keep@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G083 Office) 020-7631-6868 (Rosalind Franklin Laboratory) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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,fr-FR X-MailScanner: Found to be clean References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Dr. Sydney SHALL" Subject: Re: BBEdit plug-in for scripting? Date: Thu, 05 Dec 2002 11:28:03 +0000 To: rasmol@lists.umass.edu I use BBEdit, and I would appreciate it. Sydney timothy driscoll wrote: > greetings Mac Chime/RasMol scripters: > > something that I really miss when writing Chime or RasMol scripts, > especially long and convoluted ones, is syntax coloring. it is possible to > write a language module for BBEdit to handle syntax coloring for the > Chime/RasMol command language. for those who don't know, BBEdit is a > popular text/html editor for the Mac. it already handles over 20 other > languages - including, btw, python and actionscript. > > AFAIK writing a language module is not quite a no-brainer. so I am doing a > little pre-market survey: does anyone else use BBEdit to write scripts? if > so, would syntax coloring be a desired feature for you? 'cause if it's just > me, well, maybe it ain't worth the time ;-) > > feel free to reply off-list. > > regards, > > :tim > -- > molvisions - molecular graphics & visualization > http://www.molvisions.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-- charset=us-ascii X-Accept-Language: en,fr-FR X-MailScanner: Found to be clean References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Dr. Sydney SHALL" Subject: Re: ?fix for too much memory? Date: Thu, 05 Dec 2002 11:35:17 +0000 To: rasmol@lists.umass.edu Lewis Edgel wrote: > Here's a shot in the dark... have not played with the newer OS from Apple... > I seem to recall that you can set the memory allocation for each program > running on operating system series 7-8. Perhaps, you could contact Apple's > educational support people to see if this is a possibility - IF you have not > already explored this. I do recall your earlier posting on the matter, but > am not sure which flavour of OS exhibited the problem. > This is correct. In MAC OS 8.x or 9.x one can, indeed one usually needs to, set the memory allocation for each program. In MAC OS X this is not possible easily. They (Apple) claim that the the operating system will automatically apportion the correct amount of memory to each running program. If this is correct could the problem be virtual memory, which I believe, but I do not know, is handled quite differently in MAC OS X. Sydney > > My wife uses a G4 to process test results from a Becton-Dickenson > flow-cytometer and found the solution suggested by Mr. Martz allowed her to > run the BD program (not OSX compatible) as well as the majority of the > programs from the machine the G4 replaced (Powermac 7300/200). I agree OSX > running in classic mode seems the most painless solution for the majority of > compatibility problems. > > Lewis Edgel > > -----Original Message----- > From: owner-rasmol@lists.umass.edu > [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Eric Martz > Sent: Thursday, December 05, 2002 1:00 AM > To: David Margulies > Cc: rasmol@lists.umass.edu > Subject: Re: ?fix for too much memory? > > At 12/4/02, David Margulies wrote: > > Eric: > Is there any fix for the too much memory problem, i.e. > 1Gb on Mac G4 dp > for chime/ protein explorer? It would be nice not to have to remove memory > wouldn't you say? > > Dear David: > > As stated on my Troubleshooting page > http://molvis.sdsc.edu/protexpl/troubles.htm#macmemory > > the only other solution I've been told about is to upgrade to OSX and run > Chime/PE in the classic environment. As I think you know, I am not a Mac > user myself. I've copied this to the list in case anyone has suggestions to > add. > > -Eric > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Mary Jane Shultz Subject: Visualization conference Date: Fri, 06 Dec 2002 17:24:52 -0500 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_IUyPCaV2jssQMbiJU+VIqw) Greetings from the Chair of the 2003 Gordon Conference on Visualization in Science and Education. For those not familiar with the conference, the focus is on creating visualizations that are accurate AND that help students in learning concepts. (For more information, see the web site: http://www.soton.ac.uk/~ecchemed/grc/). I am posting to this list because I am trying to find someone who is involved with molecular-level visualizations in biology or chemistry who is concerned with the question of whether the visualizations help students learn or how they help students learn? If this sounds like you, please email me Mary.shultz@tufts.edu (Note: no c in Shultz) We can then talk further. Looking forward to hearing from you! Thanks Mary Shultz --Boundary_(ID_IUyPCaV2jssQMbiJU+VIqw) Content-description: Card for Mary Jane Shultz Content-disposition: attachment; filename=Mary.Shultz.vcf begin:vcard n:;Mary tel;fax:(617) 627-3443 tel;work:(617) 627-3477 x-mozilla-html:FALSE adr:;;mshultz1@emerald.tufts.edu;;;; version:2.1 email;internet:Mary.shultz@tufts.edu fn:Mary end:vcard --Boundary_(ID_IUyPCaV2jssQMbiJU+VIqw)-- charset=us-ascii X-Accept-Language: en X-OriginalArrivalTime: 07 Dec 2002 15:57:24.0336 (UTC) FILETIME=[55558F00:01C29E09] References: <3DF123B4.D74EF022@tufts.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Brian WHite Subject: Re: Visualization conference Date: Sat, 07 Dec 2002 10:57:22 -0500 To: rasmol@lists.umass.edu That sounds like me. I recently published a paper on this in biochem mol bio education. How can I help? Brian Mary Jane Shultz wrote: > Greetings from the Chair of the 2003 Gordon Conference on Visualization > in Science and Education. For those not familiar with the conference, > the focus is on creating visualizations that are accurate AND that help > students in learning concepts. (For more information, see the web site: > http://www.soton.ac.uk/~ecchemed/grc/). I am posting to this list > because I am trying to find someone who is involved with molecular-level > visualizations in biology or chemistry who is concerned with the > question of whether the visualizations help students learn or how they > help students learn? If this sounds like you, please email me > Mary.shultz@tufts.edu > (Note: no c in Shultz) > We can then talk further. Looking forward to hearing from you! > > Thanks > Mary Shultz -- Prof. Brian White Biology Department University of Massachusetts, Boston 100 Morrissey Blvd Boston MA 02125 (617) 287-6630 fax:(617) 287-6650 brian.white@ems.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-- Content-disposition: inline X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id gB7KAqd12916 ++++------+------+------+------+------+------+------+------+------+------+ From: Joseph Mazurkiewicz Subject: Re: Visualization conference Date: Sat, 07 Dec 2002 15:04:15 -0500 To: rasmol@lists.umass.edu Dear Dr. Shultz: I just saw your posting to the RasMol Email List and am interested in your GRC Conference on Visualization in Science and Education. I had just joined the RasMol List after replying to a colleague's query about PDB files and the visualization of ribbon diagrams of serotonin receptors. I run an imaging core facility at the Albany Medical College (AMC), providing confocal microscopy and electron microscopy for researchers at AMC and am a member of his Ph.D. student's thesis advisory committee, so it was appropriate that he ask me about things that do with imaging paradigms. After doing a little web surfing and subsequently re-acquainting myself with RasMol and MDL Chime, and their utility in visualizing receptor structure through ribbon-, stick-diagrams, etc. I answered his question. In addition, I was reminded of their utility in teaching basic chemical concepts in protein and nucleic acid structure when I browsed the Umass education/RasMol web site. Aside from my research in neuroscience, I run the Medical Cell Biology and Genetics Theme, the first course that the 1st year medical students take, in which we present some of the very basic concepts in biochemistry and molecular biology, including protein structure and function, and cellular signaling. So you can see why the topic of the conference interests me. Another approach to the use of visualization of biological events in education is the use of visual research results in the teaching of cell biology. A collaborator and I use fluorescence imaging in live-cell, time-lapse confocal microscopy to visualize the involvement of GFP-tagged PKC isoforms in signaling activity during phagocytosis of fluorescently tagged targets. The combination of molecular biologic, biochemical, and imagin techniques permits us to directly assess the effect of site-directed mutations to PKC on cell responses during signaling in our research. Additionally, the movies we've collected in our research are used in teaching basic concepts in phagocytosis to the medical students by illustrating the actual movement of the signaling molecule, PKC, to the site of active phagocytosis at the plasma membrane where the target is engulfed and visualizing the re-arrangement of the GFP-PKC during target the process of internalization. In examining your "visual", the flow diagram on the Conference web site, I seem to sit at two of the apices of your triangle: scientist and educator. I am, however, especially interested in the aspect of the program where participants will discuss evaluation of such endeavors, although I do not consider myself an evaluator in the context of that diagram. I would be willing to share our experiences in the educational aspect and discuss the visualization tool we use, but would be there to learn about the evaluation process. In medical education we are constantly being told to reduce the time that medical students are in lectures, yet be sure the material we present is both up-to-date and complete. The question arises, does the presentation of concepts visually satisfy all those needs? Is that methodology effective? Your conference is the first I've seen that attempts to develop tools to answer such questions. Looking forward to hearing from you. Joe >>> Mary.Shultz@tufts.edu 12/06/02 17:28 PM >>> Greetings from the Chair of the 2003 Gordon Conference on Visualization in Science and Education. For those not familiar with the conference, the focus is on creating visualizations that are accurate AND that help students in learning concepts. (For more information, see the web site: http://www.soton.ac.uk/~ecchemed/grc/). I am posting to this list because I am trying to find someone who is involved with molecular-level visualizations in biology or chemistry who is concerned ith the ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <200212021645.gB2Gjnd13872@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: Browser trouble Date: Mon, 09 Dec 2002 12:35:50 -0500 To: rasmol@lists.umass.edu Cc: slonczewski@kenyon.edu We're finding that some of our new Chime tutorials don't work in XP IE 6; in fact even a plain PDB doesn't work. Can anyone give us a clue? Also, I would appreciate it if people using XP IE or Netscape 7 could take a look at our page and let us know how the old tutorials work: http://biology.kenyon.edu/BMB/chime.htm Thanks a lot, Joan Joan Slonczewski Professor of Biology Kenyon College 202 North College Road Gambier, OH 43022 Phone 740-427-5397 http://www2.kenyon.edu/depts/biology/slonc/slonc.htm slonczewski@kenyon.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: Wayne Decatur Subject: invented Chime? Date: Mon, 09 Dec 2002 11:24:01 -0800 (PST) To: rasmol@lists.umass.edu Well, with NEetscape 4.8something the Ebola tutorial work fine and with IE 5.5 the Ebola tutoral did eventually work although it was quite slow starting up. I thought my IE was locked up. Also, on your website it says Eric Martz invented Chime. This wasn't my understanding? Wayne --- Joan Slonczewski wrote: > We're finding that some of our new Chime tutorials > don't work in XP IE 6; in > fact even a plain PDB doesn't work. Can anyone give > us a clue? > > Also, I would appreciate it if people using XP IE > or Netscape 7 could take a > look at our page and let us know how the old > tutorials work: > http://biology.kenyon.edu/BMB/chime.htm > > Thanks a lot, > Joan > > Joan Slonczewski > Professor of Biology > Kenyon College > 202 North College Road > Gambier, OH 43022 > Phone 740-427-5397 > http://www2.kenyon.edu/depts/biology/slonc/slonc.htm > slonczewski@kenyon.edu > > > __________________________________________________ Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now. http://mailplus.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-- X-WebMail-UserID: southey@staff.uiuc.edu X-EXP32-SerialNo: 00003242 ++++------+------+------+------+------+------+------+------+------+------+ From: southey Subject: RE: Browser trouble Date: Mon, 09 Dec 2002 20:15:09 -0600 To: Joan Slonczewski , rasmol Hi, Using a Mozilla and IE 6.0 with Chime SP4 on Win XP pro I think they just take some time for loading. So you might have to wait a few minutes. I have not gone all the examples etc. Regards Bruce >===== Original Message From Joan Slonczewski ===== >We're finding that some of our new Chime tutorials don't work in XP IE 6; in >fact even a plain PDB doesn't work. Can anyone give us a clue? > >Also, I would appreciate it if people using XP IE or Netscape 7 could take a >look at our page and let us know how the old tutorials work: >http://biology.kenyon.edu/BMB/chime.htm > >Thanks a lot, >Joan > >Joan Slonczewski >Professor of Biology >Kenyon College >202 North College Road >Gambier, OH 43022 >Phone 740-427-5397 >http://www2.kenyon.edu/depts/biology/slonc/slonc.htm >slonczewski@kenyon.edu > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 boundary="Boundary_(ID_2IcYQDHNVkUInWbt/jTSoQ)" X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Giulio Vistoli Subject: Announcing VEGA1.4.3 Date: Wed, 11 Dec 2002 11:49:13 +0100 To: pdb-l@rcsb.org, rasmol@lists.umass.edu, chemweb@ic.ac.uk This is a multi-part message in MIME format. --Boundary_(ID_2IcYQDHNVkUInWbt/jTSoQ) Dear collegues, As a christmas gift, we are glad to announce the new release of VEGA1.4.3 (http://www.ddl.unimi.it/) our well known program to convert, manage and visualize of 3D structures for several platforms (Win32, Linux, Irix, AmigaOs). New features of release 1.4.3: - Alchemy loader & saver. - MDL Molfile saver. - CSV and Raw surface format. - Gromacs .xtc support for the trajectory analysis. - Multi-model PDB support for the trajectory analysis. - ILM calculation in the trajectory analysis. - The IFF file format was expanded in order to support the surface maps. - Win32: new geometry transformation engine. - Win32: added By segment coloring method. - Win32: surface calculation for selected atoms. - Win32: trajectory analysis for selected atoms. - Win32: interactive selection of the conformations trough the graph editor. - Win32: added the Data De/compressor Engine support in the graph editor. - Win32: now the graph editor supports Gromacs log files. - Win32: REBOL/View instead of REBOL/Core scripting language. - Win32: new extended commands (BioDock, GraphAdd, GraphCalc, GraphClose, GraphDelete, GraphGet, GraphLabelX, GraphLabelY, GraphLoad, GraphNew, GraphOpen, GraphSave, GraphSet, GraphTitle, GraphWin, MonitorPower). - Win32: new system variables (CPUs, GLRenderer, GLVendor, GLVersion, GraphLabelX, GraphLabelY, GraphPoints, GraphPosX, GraphPosY, GraphSizeX, GraphSizeY, GraphTitle, GraphVisible, TmpFile, TmpDir). - Win32: WinDD 1.4. Giulio Vistoli & Alessandro Pedretti --------------- Giulio Vistoli Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano Italia Tel. +39-02-50317545 Fax +39-02-50317565 giulio.vistoli@unimi.it http://www.ddl.unimi.it --Boundary_(ID_2IcYQDHNVkUInWbt/jTSoQ)
Dear collegues,

As a christmas gift, we are glad to announce the new release of VEGA1.4.3
(http://www.ddl.unimi.it/) our well known program to convert, manage and
visualize of 3D structures for several platforms (Win32, Linux, Irix,
AmigaOs).

 New features of release 1.4.3:

- Alchemy loader & saver.
- MDL Molfile saver.
- CSV and Raw surface format.
- Gromacs .xtc support for the trajectory analysis.
- Multi-model PDB support for the trajectory analysis.
- ILM calculation in the trajectory analysis.
- The IFF file format was expanded in order to support the surface maps.
- Win32: new geometry transformation engine.
- Win32: added By segment coloring method.
- Win32: surface calculation for selected atoms.
- Win32: trajectory analysis for selected atoms.
- Win32: interactive selection of the conformations trough the graph editor.
- Win32: added the Data De/compressor Engine support in the graph editor.
- Win32: now the graph editor supports Gromacs log files.
- Win32: REBOL/View instead of REBOL/Core scripting language.
- Win32: new extended commands (BioDock, GraphAdd, GraphCalc, GraphClose,
GraphDelete, GraphGet, GraphLabelX, GraphLabelY, GraphLoad, GraphNew,
GraphOpen, GraphSave, GraphSet, GraphTitle, GraphWin, MonitorPower).
- Win32: new system variables (CPUs, GLRenderer, GLVendor, GLVersion,
GraphLabelX, GraphLabelY, GraphPoints, GraphPosX, GraphPosY, GraphSizeX,
GraphSizeY, GraphTitle, GraphVisible, TmpFile, TmpDir).
- Win32: WinDD 1.4.

Giulio Vistoli & Alessandro Pedretti
---------------
Giulio Vistoli
Istituto di Chimica Farmaceutica e Tossicologica
Viale Abruzzi, 42
I-20131 Milano
Italia
Tel. +39-02-50317545
Fax +39-02-50317565
giulio.vistoli@unimi.it
http://www.ddl.unimi.it
--Boundary_(ID_2IcYQDHNVkUInWbt/jTSoQ)-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: rlight Subject: RE: Browser trouble Date: Wed, 11 Dec 2002 14:24:59 -0500 To: rasmol@lists.umass.edu They load very, very slowly under IE 6 (Windows XP), giving the "not responding" signal, but eventually loads and seems to work. I only looked at a couple. Seems to work well with Netscape 7 Robley Light ************************************************************* Robley J. Light Professor of Chemistry and Biochemistry Department of Chemistry Phone: (850) 644-3844 and Biochemistry Email: rlight@chem.fsu.edu Florida State University Fax: (850) 644-8281 Tallahassee, FL 32306-4390 Home Page: http://chemweb.chem.fsu.edu/editors/rlight > -----Original Message----- > From: owner-rasmol@lists.umass.edu > [mailto:owner-rasmol@lists.umass.edu] On Behalf Of Joan Slonczewski > Sent: Monday, December 09, 2002 12:36 PM > To: rasmol@lists.umass.edu > Cc: slonczewski@kenyon.edu > Subject: Browser trouble > > > We're finding that some of our new Chime tutorials don't work > in XP IE 6; in fact even a plain PDB doesn't work. Can > anyone give us a clue? > > Also, I would appreciate it if people using XP IE or > Netscape 7 could take a look at our page and let us know how > the old tutorials work: http://biology.kenyon.edu/BMB/chime.htm > > Thanks a lot, > Joan > > Joan Slonczewski > Professor of Biology > Kenyon College > 202 North College Road > Gambier, OH 43022 > Phone 740-427-5397 > http://www2.kenyon.edu/depts/biology/slonc/slo> nc.htm > > slonczewski@kenyon.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-- > > --- > Incoming mail is certified Virus Free. > Checked by AVG anti-virus system (http://www.grisoft.com). > Version: 6.0.423 / Virus Database: 238 - Release Date: 11/25/2002 > > --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.427 / Virus Database: 240 - Release Date: 12/6/2002 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: KLOTHO missing? Date: Mon, 16 Dec 2002 19:02:33 -0500 To: "LIST: rasmol" hello, I just noticed that KLOTHO, the database for small molecules, is no longer accessible at its traditional URL . the linkouts on that page to do not work from my machine. anyone have any current info on this resource? thanks, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: KLOTHO missing? Try http://www.biocheminfo.org/klotho/ Date: Tue, 17 Dec 2002 07:15:31 -0500 To: Clifford Felder Cc: "LIST: rasmol" at 11:08 AM EDT on (Tuesday) 17 December 2002 Clifford Felder said: > On Mon, 16 Dec 2002, timothy driscoll wrote: > > I just noticed that KLOTHO, the database for small molecules, is no > > longer accessible at its traditional URL > > . anyone have any current info on > > this resource? > Try http://www.biocheminfo.org/klotho/ > Sincerely, Clifford Felder > > thank you! in fact, is the link listed at the old URL; it just wasn't working the few times I tried it before today. now it works. regards, :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-GB; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en, en-us X-MailScanner: Found to be clean X-MailScanner-SpamCheck: not spam, SpamAssassin (score=-1.1, required 10, SIGNATURE_LONG_SPARSE, SPAM_PHRASE_01_02, USER_AGENT, USER_AGENT_MOZILLA_UA, X_ACCEPT_LANG) ++++------+------+------+------+------+------+------+------+------+------+ From: Nicholas Keep Subject: 2.7 Mac Binaries and resources Date: Tue, 17 Dec 2002 17:20:40 +0000 To: rasmol@lists.umass.edu How do you install the2.7 rasmol binaries from www.openrasmol.org, without recompiling. I am not a mac user, but some of our distance learning students are. You clearly need something called a resource file as well as setting the APPL and RSML file type and signature. Having played around for much of the day at some point I tried the right combination of things and got a working version of 2.71.1 (I used cut and paste in ResEdit from various things including the RasMac.rsrc in the gzip and the 2.6 that worked from the sit.hqx file). It all apparently failed but when I came back after lunch one version was working. I was unable to work out which one. Can anyone give me a clear guide to how I should do this. (I was using an old G3 PowerPC) 2.7.1. has indeed fixed the bug that caused some of our rasmol scripts to fail in 2.6b2 on the macs Many thanks Nick -- Dr Nicholas H. Keep School of Crystallography, Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.keep@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G083 Office) 020-7631-6868 (Rosalind Franklin Laboratory) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: pdb format from Cn3D/VAST? Date: Sun, 29 Dec 2002 18:23:10 -0500 To: LIST rasmol hi, I used VAST at the NCBI Web site (http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml) to align two 3d structures. I downloaded the alignment and viewed it using Cn3D, and it looks great. now I'd like to be able to save it as a simple pdb file (text format with atom records) for use in rasmol/chime/spv/wlvp. does anyone know how to do this, or if it is even possible? thanks! :tim -- molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Importance: Normal X-MSMail-priority: Normal X-Original-Recipient: ++++------+------+------+------+------+------+------+------+------+------+ END OF 2002 LIST HISTORY