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: ++++------+------+------+---