Beginning Jan 1, 2001: ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: Biomolecules at Kenyon College Date: Thu, 04 Jan 2001 17:39:13 -0500 To: rasmol@lists.umass.edu The "Biomolecules at Kenyon College" site has been revised and has added several new tutorials by students from my class this semester. We would greatly appreciate any feedback and suggestions, especially notification of errors or need for improved design. Thanks also for all the help in responding to our questions; it made a world of difference for the students in the course, and made them feel excited about their projects. Joan Slonczewski http://www2.kenyon.edu/depts/biology/BMB/chime.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-Accept-Language: en References: <0G3C00IMOOUJD4@supai.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: Re: Enter your Chime resources in the World Index Date: Fri, 05 Jan 2001 09:20:02 -0500 To: rasmol@lists.umass.edu Eric, I entered the Kenyon site on your list, and it looked great; this list overall will be useful for our classes. However, the author credits came out different than I expected, due to my inexperience with your system. The credits actually need to say: Author: Kenyon College students; Site Director, Joan Slonczewski [linked to my e-mail] The individual tutorials should have individual student names, but still my own e-mail link as site director. Is there any way I can edit these listings? Thanks, Joan Slonczewski Eric Martz wrote: > This is a reminder that those of you who have authored Chime-based > resources should enter the url's in the World Index of Molecular > Visualization Resources at http://molvis.sdsc.edu/visres You simply fill > out a form there and submit it. > > There are already 60-some resources by 30-some authors there. They are > automatically alphabetically indexed by molecule, topic, keywords, title, > and author. > > I am planning to add some new categories soon, such as for organic > chemistry resources, SwissPDB Viewer resources, sources of molecules, etc. > > -Eric > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > The Protein Explorer: http://www.proteinexplorer.org > World Index of Chime Resources: http://molvis.sdsc.edu/visres > PDB Lite molecule finder: http://www.umass.edu/microbio/rasmol/pdblite.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: copy chime script problem Date: Fri, 05 Jan 2001 13:55:00 -0500 To: rasmol@lists.umass.edu Last year I had my sophomore biochem students do a Chime homework problem. see it at http://www.gvsu.edu/carlsont/comp2.html It involved locating and downloading a pdb file for aspartame from the web and learning how to use chime to modify the image as directed. To prove they completed the assignment, I had them use the copy chime script command to create a chime script needed to regenerate their image and save it in and spt file. This was turned in to me with their pdb file on a disk and I could load the image, execute the script and see their results. The problem I encountered was that on some of the computers on campus, the copy chime script command didn't work. All campus computers run the same software (netscape plus chime) from the same server. We never did find out why some computers had this probelem while others didn't. Has anyone else had this problem or know why it occurs? thanks todd carlsont@gvsu.edu ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <0G3C00IMOOUJD4@supai.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Enter your Chime resources in the World Index Date: Fri, 05 Jan 2001 20:02:01 -0500 To: rasmol@lists.umass.edu Yes, Just click on the Edit link at the World Index site. At 01/05/2001, you wrote: >Eric, >I entered the Kenyon site on your list, and it looked great; this list overall >will be useful for our classes. >However, the author credits came out different than I expected, due to my >inexperience with your system. The credits actually need to say: > >Author: Kenyon College students; Site Director, Joan Slonczewski [linked to my >e-mail] > >The individual tutorials should have individual student names, but still my >own e-mail link as site director. >Is there any way I can edit these listings? > >Thanks, >Joan Slonczewski > >Eric Martz wrote: > >> This is a reminder that those of you who have authored Chime-based >> resources should enter the url's in the World Index of Molecular >> Visualization Resources at http://molvis.sdsc.edu/visres You simply fill >> out a form there and submit it. >> >> There are already 60-some resources by 30-some authors there. They are >> automatically alphabetically indexed by molecule, topic, keywords, title, >> and author. >> >> I am planning to add some new categories soon, such as for organic >> chemistry resources, SwissPDB Viewer resources, sources of molecules, etc. >> >> -Eric >> /* - - - - - - - - - - - - - - - - - - - - - - - - - - - >> The Protein Explorer: http://www.proteinexplorer.org >> World Index of Chime Resources: http://molvis.sdsc.edu/visres >> PDB Lite molecule finder: http://www.umass.edu/microbio/rasmol/pdblite.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 >> - - - - - - - - - - - - - - - - - - - - - - - - - - - */ >> > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org 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: "James W. Caras" Subject: Conference call meeting Date: Mon, 08 Jan 2001 14:29:02 -0600 To: rasmol@lists.umass.edu Hi Todd- I have finally returned from vacation and have my head set on straight, and am sorry for the delay getting back to you. I would like to schedule a conference call with you soon, but the only problem is that my partner is out of town until the 16th, so we will have to wait until he returns. I will get in contact with you then and we can set something up. I don't know if you visited the Kenyon College site mentioned in the RasMol list, but some of them are fantastic! Let me know if you have any questions you need answered before then. Jamie ps. I wrote a tutorial for my lab on the HCV polymerase, and have been working to incorporate some of the suggestions you gave me. I still can't get the Javascript that allows input of the commands working properly, which is very frustrating, but the tutorial is still coming along nicely. My most recent version is at: http://www.sciencetechnologies.com/JohnsonLab/Structures/NS5Btutorial/NS5B.html if you would like to take a look. __________________________________ Dr. James W. Caras Institute for Cellular and Molecular Biology The University of Texas at Austin MBB 3.122 2500 Speedway Austin, TX 78712 (512) 471-0416 caras@mail.utexas.edu http://www.sciencetechnologies.com/HomePaige/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: "James W. Caras" Subject: apologies, yet... Date: Mon, 08 Jan 2001 15:59:51 -0600 To: rasmol@lists.umass.edu My apologies for the email I sent to the rasmol email list that was intended for Todd Carlson. However, if anyone can tell me why my rasmol command line will not work on my HCV polymerase tutorial I would greatly appreciate it. There is a head-sized hole in the wall next to my computer chair, and I have quite a headache. James Caras __________________________________ Dr. James W. Caras Institute for Cellular and Molecular Biology The University of Texas at Austin MBB 3.122 2500 Speedway Austin, TX 78712 (512) 471-0416 caras@mail.utexas.edu http://www.sciencetechnologies.com/HomePaige/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Henry Brzeski Subject: RE: Conference call meeting Date: Tue, 09 Jan 2001 08:30:03 +0000 To: rasmol@lists.umass.edu James > ps. I wrote a tutorial for my lab on the HCV polymerase, and have been > working to incorporate some of the suggestions you gave me. I > still can't > get the Javascript that allows input of the commands working properly, > which is very frustrating, but the tutorial is still coming along > nicely. My most recent version is at: I used Eric's/MDLs basic structure to work a command line. Look at http://www.herts.ac.uk/natsci/Bio/psi/psi.htm to see how mine works. In the final page 'with chime window' you will see that you can load ANY structure and work with it (if you don't know the pdb code you can ask SRS for it). Once the structure is loaded into the window you can modify the display using standard rasmol commands. It all hinges on function sendRasmolScriptToChime( targetchimename, script ) The coding for this is in the chime window. Hope this helps. h Henry Brzeski ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Henry Brzeski Subject: RE: Conference call meeting Date: Tue, 09 Jan 2001 08:44:48 +0000 To: rasmol@lists.umass.edu Dear all My apologies, I did the same as James and sent to the list instead of to him personally. Nevertheless as he said some of the comments may be useful to others. Sorry again for bothering you all. h > I used Eric's/MDLs basic structure to work a command line. Look at > http://www.herts.ac.uk/natsci/Bio/psi/psi.htm to see how mine > works. In the > final page 'with chime window' you will see that you can load ANY > structure > and work with it (if you don't know the pdb code you can ask SRS for it). > Once the structure is loaded into the window you can modify the display > using standard rasmol commands. It all hinges on function > sendRasmolScriptToChime( targetchimename, script ) The coding for > this is in > the chime window. > > Hope this helps. > > h > > Henry Brzeski > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Fwd: Plug-in detection Date: Fri, 09 Mar 2001 13:14:12 -0500 To: rasmol@lists.umass.edu >Date: Mon, 08 Jan 2001 12:28:26 +0100 (MEZ) >From: Andreas Bohne >To: emartz@microbio.umass.edu >Subject: Plug-in detection > >dear eric, > >i have prepaired a javascript which automatically detects if a molecular viewer >is installed. the script switches between [plug-in] and [external helper] >and [none]. >thus a web-designer can avoid error messages on viritors browser's if chime is >not installed. >i had a look in the faq of mdl chime but i did not found any in this context and >hope that i do not tell you old stuff. > >you can find the page at: http://www.dkfz-heidelberg.de/spec/javascript/plugin/ > >i hope you will find it useful and offer this to other useres. > >bye andreas > >+--------------------------------------------------- >| Andreas Bohne >| DKFZ (German Cancer Research Center) >| Central Unit of Spectroscopy >| Molecular Modeling Group >| Im Neuenheimer Feld 280 Tel:+49(0)6221/42-4541 >| D-69120 Heidelberg Fax:+49(0)6221/42-2995 >| E-Mail: a.bohne@dkfz.de >| URL: http://www.dkfz.de/spec/ > Note added by Eric: Protein Explorer tests for platform, browser type and version, Chime and version, and offers help if any of these are not compatible. The code is in file pe.htm included with the entire source when you download PE. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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-Outlook-Express-Macintosh-Edition/5.02.2022 ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Plug-in detection Date: Tue, 09 Jan 2001 14:46:49 -0500 To: rasmol@lists.umass.edu FYI: IE (like NC) has a plugins[] array, but it is always empty even if plug-ins are installed in the browser. One way around this problem is to switch to a helper app, or to none, when the plugins[] array is empty (Netscape always has at least one plug-in installed, so always has at least one member of the plugins[] array). Another is to query the value of navigator.appName for the string "netscape". Unfortunately, neither of these methods will tell you if an IE user has Chime installed. If anyone knows a way to distinguish IE-with-Chime from IE-without-Chime, I'd love to hear it :-) -- Timothy Driscoll molvisions.com - 3D molecular visualization http://www.molvisions.com/ driscoll@molvisions.com Waltham, MA USA 508-864-6516 voice 781-891-4108 fax > From: Eric Martz > Reply-To: rasmol@lists.umass.edu > Date: Fri, 09 Mar 2001 13:14:12 -0500 > To: rasmol@lists.umass.edu > Subject: Fwd: Plug-in detection > >> Date: Mon, 08 Jan 2001 12:28:26 +0100 (MEZ) >> From: Andreas Bohne >> To: emartz@microbio.umass.edu >> Subject: Plug-in detection >> >> dear eric, >> >> i have prepaired a javascript which automatically detects if a molecular > viewer >> is installed. the script switches between [plug-in] and [external helper] >> and [none]. >> thus a web-designer can avoid error messages on viritors browser's if > chime is >> not installed. >> i had a look in the faq of mdl chime but i did not found any in this > context and >> hope that i do not tell you old stuff. >> >> you can find the page at: > http://www.dkfz-heidelberg.de/spec/javascript/plugin/ >> >> i hope you will find it useful and offer this to other useres. >> >> bye andreas >> >> +--------------------------------------------------- >> | Andreas Bohne >> | DKFZ (German Cancer Research Center) >> | Central Unit of Spectroscopy >> | Molecular Modeling Group >> | Im Neuenheimer Feld 280 Tel:+49(0)6221/42-4541 >> | D-69120 Heidelberg Fax:+49(0)6221/42-2995 >> | E-Mail: a.bohne@dkfz.de >> | URL: http://www.dkfz.de/spec/ >> > > Note added by Eric: Protein Explorer tests for platform, browser type and > version, Chime and version, and offers help if any of these are not > compatible. The code is in file pe.htm included with the entire source when > you download PE. > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: copy chime script problem Date: Tue, 09 Jan 2001 15:04:53 -0500 To: rasmol@lists.umass.edu At 01/05/2001, you wrote: >Last year I had my sophomore biochem students do a Chime homework problem. > >see it at http://www.gvsu.edu/carlsont/comp2.html > >It involved locating and downloading a pdb file for aspartame from the web and learning how to use chime to modify the image as directed. To prove they completed the assignment, I had them use the copy chime script command to create a chime script needed to regenerate their image and save it in and spt file. This was turned in to me with their pdb file on a disk and I could load the image, execute the script and see their results. The problem I encountered was that on some of the computers on campus, the copy chime script command didn't work. All campus computers run the same software (netscape plus chime) from the same server. We never did find out why some computers had this probelem while others didn't. Has anyone else had this problem or know why it occurs? > >thanks > > todd > carlsont@gvsu.edu I had the same problem a couple of years ago. During the Copy Chime Script operation, Chime creates a temporary file somewhere and then deletes it. Some computer labs have the expected temporary location write-protected. Although MDL acknowledged that this was the problem, they were never able to tell us where Chime attempts to write the temporary file. I solved the problem by moving to a different computer lab where there were less protections. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2615.200 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: Plug-in detection Date: Thu, 11 Jan 2001 09:36:23 +0100 To: rasmol@lists.umass.edu Dear Chimeleons, I found a way how to detect the presence of Chime in IE5. It is based on the use of a callback function of Chime. If it answers, Chime works. The result can be stored in a cookie and used later pages. It needs only a few line of Javascript. I made a small test page, please, try it and feedback me, is it working OK everywhere? It can be found: http://dragon.klte.hu/~gundat/Chimetest/ (On the first occassion probably the reload/refresh button should be pressed). If somebody is interested in the Javascript code used, the source files can be downloaded as a zip file. Tamas Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ----- Original Message ----- Sent: Tuesday, January 09, 2001 8:46 PM From: Timothy Driscoll Subject: Re: Plug-in detection To: ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Plug-in detection Date: Thu, 11 Jan 2001 12:41:32 -0500 To: tamasgunda@tigris.klte.hu Cc: rasmol@lists.umass.edu At 01/11/2001, you wrote: >I found a way how to detect the presence of Chime in IE5. >Dr Tamas E. Gunda >Research Group for Antibiotics of the Hungarian Acad. Sci. >University of Debrecen, POBox 36 >H-4010 Debrecen, Hungary Very nice, Tamas! Thanks for sharing this, and for making the source downloadable. I confirmed that your page detects Chime in both IE5.0 and Netscape 4.76. Please enter your plugin detection page in "How to create Chime resources" at http://molvisindex.org and your triostin page under chime biochemistry tutorials, ready to use. May I suggest that you mention PDB ID code 185D and cite the Biochemistry paper by Addess and Feigon in which this structure was published? In general I'd like to suggest that authors of Chime tutorials be more careful to indicate PDB ID codes and to cite the experimental work that led to the structures shown. If you have any pages in Hungarian, please list them under the Non-English resources. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Plug-in detection Date: Thu, 11 Jan 2001 14:00:47 -0500 To: rasmol@lists.umass.edu Tamas, Way cool! Thanks! :-) BTW, I've found there is often a significant delay before the Chime plug-in loads. This delay is not associated with starting Java in NC, since the browser continues reading the html document (when Java starts, everything pauses). This may explain why the first visit to your site necessitates a reload/refresh - the browser gets to the installation message in the html doc before the plug-in loads, so it "incorrectly" reports the plug-in as not installed. On reload/refresh, the new cookie is now available and the html doc is written "correctly." One way to fix this is to replace the installation message with a simple gif, and use your function TestChime() to set the installation message gif to the proper message. For example, (without the comments) goes in your html in place of the getCookie() output, and if (chimeyes) { document.install_status.src="installed.gif"; ... } else document.install_status.src="not_installed.gif"; goes in your TestChime() function. If you do this, I also suggest moving the Chime plug-in to the very bottom of the html doc, so "install_status" is created before the TestChime() function is called (this could happen if the plug-in loads before the html page is written). Regards, Tim -- Timothy Driscoll molvisions.com - 3D molecular visualization http://www.molvisions.com/ driscoll@molvisions.com Waltham, MA USA 508-864-6516 voice 781-891-4108 fax > From: "Tamas E. Gunda" > Reply-To: rasmol@lists.umass.edu > Date: Thu, 11 Jan 2001 09:36:23 +0100 > To: rasmol@lists.umass.edu > Subject: Re: Plug-in detection > > Dear Chimeleons, > > I found a way how to detect the presence of Chime in IE5. It is based on the > use of a callback function of Chime. > If it answers, Chime works. The result can be stored in a cookie and used > later pages. > It needs only a few line of Javascript. > I made a small test page, please, try it and feedback me, is it working OK > everywhere? > It can be found: > > http://dragon.klte.hu/~gundat/Chimetest/ > > (On the first occassion probably the reload/refresh button should be pressed). > > If somebody is interested in the Javascript code used, the source files can be > downloaded > as a zip file. > > Tamas > > Dr Tamas E. Gunda > Research Group for Antibiotics of the Hungarian Acad. Sci. > University of Debrecen, POBox 36 > H-4010 Debrecen, Hungary > tel.: (+36-52) 512 900/2472 > fax: (+36-52) 512 914 > e-mail: tamasgunda@tigris.klte.hu > home-page: www.klte.hu/~gundat/gunda.htm > > ----- Original Message ----- > From: Timothy Driscoll > To: > Sent: Tuesday, January 09, 2001 8:46 PM > Subject: Re: Plug-in detection > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: fr,en-US References: <002901c07ba9$95345c20$3b8506c1@chem.klte.hu> ++++------+------+------+------+------+------+------+------+------+------+ From: Jean-Philippe Demers Subject: Re: Plug-in detection Date: Thu, 11 Jan 2001 17:34:00 -0500 To: rasmol@lists.umass.edu This trick is really nice, but I would suggest you that in your EMBED tag, you replace dummy.mol with dummy.pdb, since you are using pdb files. Maybe for you it makes no differences because Chime support both format. However, more then one plugin could be used for only one MIME type, like the CambridgeSoft ChemOffice. If you only pdb files, then it would be better to test for a file with a .pdb extension and if you use both .mol and .pdb files, then maybe you could check for both file types. Jean-Philippe Demers ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Part-time programming jobs Date: Fri, 12 Jan 2001 19:37:08 -0500 To: rasmol@lists.umass.edu, pdb-l@rcsb.org, discuspv@USM.MAINE.EDU Student and professional programmers, especially those familiar with basic protein structure, are invited to check http://www.umass.edu/microbio/jobs.htm for part-time off-site e-jobs involving java server pages, html, javascript, JScript, Chime, and CGI, in support of the Protein Explorer project and related resources. -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en,es-ES ++++------+------+------+------+------+------+------+------+------+------+ From: shalpine@earthlink.net Subject: Comments from list members Date: Fri, 19 Jan 2001 11:59:12 -0800 To: rasmol@lists.umass.edu Dear Dr. Martz: I've been asked to write an article for the Artful Media column in the journal IEEE MultiMedia (Institute for Electrical and Electronics Engineers). The subject will be Molecular Visualization. Molecular Visualization software and the resulting e-community seems to by an example of electronic technology at its best. Yet many outside the general area of biochemistry are not familiar with it. I'm soliciting comments and specific examples from list members regarding both the impact this technology has had on their work, and the impact the electronic community has had on education or on personal attitudes - if any. International (outside US) views will be particularly welcome. I'm also very interested in examples of the technology applied to different subjects such as graphic art. Full credit will be given for any graphics that accompany the article. Interested list members should contact me directly at my email address, shalpine@earthlink.net. (Note: please send links to examples of graphic art or notify me before including any art as an email attachment.) Thank you very much for your help, Susana Susana Maria Halpine Artist-Biochemist Playa del Rey, CA shalpine@earthlink.net http://home.earthlink.net/~shalpine ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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,fr-CA,pl ++++------+------+------+------+------+------+------+------+------+------+ From: Ryszard Brzezinski Subject: hydrophobic core Date: Fri, 19 Jan 2001 15:15:10 -0500 To: Rasmollers community Dear members of the RasMol discussion list! What is the best way to identify, in a protein structure, the amino acids forming the so-called hydrophobic core? Is there any automatic function that allows to identify such residues? To go further, I would try to improve the thermostability of the chitosanase enzyme. One of the known strategies consists in filling the cavities in the hydrophobic core. How can I identify such cavities, calculate their volume and estimate how this volume will change after a given mutation? Thank you! Ryszard Brzezinski Département de Biologie Université de Sherbrooke Sherbrooke (Québec) Canada ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: <3A68A04E.E99482E5@courrier.usherb.ca> ++++------+------+------+------+------+------+------+------+------+------+ From: Matthias Mueller Subject: Re: hydrophobic core Date: Mon, 22 Jan 2001 10:14:08 +0100 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_fCxVWc5w/mm+hV9szvo9EQ) Ryszard Brzezinski wrote: > Dear members of the RasMol discussion list! > > What is the best way to identify, in a protein structure, the amino > acids forming the so-called hydrophobic core? Is there any automatic > function that allows to identify such residues? > To go further, I would try to improve the thermostability of the > chitosanase enzyme. One of the known strategies consists in filling the > cavities in the hydrophobic core. How can I identify such cavities, > calculate their volume and estimate how this volume will change after a > given mutation? > > Thank you! > > Ryszard Brzezinski > Département de Biologie > Université de Sherbrooke > Sherbrooke (Québec) Canada > Hi Ryszard, I think there are several programs available that could identify cavities in proteins. Here are 2 that I know - dowser (http://femto.med.unc.edu/DOWSER/index.html) - solvate (http://www.mpibpc.gwdg.de/abteilungen/071/solvate.html) Bye, Matthias --Boundary_(ID_fCxVWc5w/mm+hV9szvo9EQ) Content-description: Card for Matthias Mueller Content-disposition: attachment; filename=mmuelle4.vcf begin:vcard n:Mueller;Matthias tel;fax:+49 551 2011089 tel;home:+49 177 6200581 tel;work:+49 551 2011141 x-mozilla-html:FALSE org:MPI fuer biophysikalische Chemie adr:;;Am Fassberg 11;37077 Goettingen;;; version:2.1 email;internet:mmuelle4@gwdg.de title:Dipl.-Phys. x-mozilla-cpt:;26688 fn:Matthias Mueller end:vcard --Boundary_(ID_fCxVWc5w/mm+hV9szvo9EQ)-- X-pair-Authenticated: 209.139.110.127 X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id f0NLqOd20309 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: RasMol with Spanish menus and messages Date: Tue, 23 Jan 2001 16:50:47 -0500 To: rasmol@lists.umass.edu, pdb-l@rcsb.org Testers are needed for RasMol_2.7.1.1. This revision adds multilingual capabilities to RasMol 2.7.1. This release handles English and Spanish. It can be found at http://www.bernstein-plus-sons.com/software/RasMol_2.7.1.1. The command to switch to Spanish is "Spanish". The command to switch back to English is "English". At present, Mac, Windows 95/98 and Linux (Mandrake 7.2) precompiled binaries are available. Compilations for other platforms, problem reports, comments and suggestions appreciated. Our thanks to Fernando Gabriel Ranea (Laboratorio de Micología, Museo de Farmacobotánica, Facultad de Farmacia y Bioquímica. Universidad de Buenos Aires (davinci@dinamica.com.ar)) for translating most of the messages into Spanish. Those interested in providing translations into other languages will find the list of messages and menus in http://www.bernstein-plus-sons.com/software/RasMol_2.7.1.1/src/langsel.c In view of the importance of multilingual capabilities in RasMol and the popularity of RasMol 2.7.1, we have interrupted work on RasMol 2.7.2 to ensure availability of these mods against RasMol 2.7.1. Similar mods should be included in an updated release of RasMol 2.7.2 in a few weeks. -- 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 ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: javascript variable in chime commands Date: Thu, 25 Jan 2001 14:48:00 -0500 To: rasmol@lists.umass.edu Hi Does anyone know if it is possible to use a numeric varibale in a javascript routine as a parameter in a chime command. I am trying to enhance some web pages using javascirpt. I have figured out how to pass information from the image to a javascript routine and how to use the javascirpt routine to execute a chime command, but I have not yet figured out how to include a variable from the javascript in the command. Thanks todd carlson GVSU carlsont@gvsu.edu ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: javascript variable in chime commands Date: Thu, 25 Jan 2001 15:25:22 -0500 To: rasmol@lists.umass.edu On 1/25/01 at 2:48 PM, Carlson, Todd wrote: > Hi > > Does anyone know if it is possible to use a numeric varibale in a > javascript routine as a parameter in a chime command. I am trying to > enhance some web pages using javascirpt. I have figured out how to > pass > information from the image to a javascript routine and how to use the > javascirpt routine to execute a chime command, but I have not yet > figured > out how to include a variable from the javascript in the command. > If I understand your question correctly, you can pass arguments from a Chime script to a javascript function in standard fashion: javascript myfunction(1,true,"stringval") If you want to run a Chime script from a javascript function, and incorporate a variable such as user input, something like this is possible: function changeMyColor(colorChoice) { // colorChoice is input from the user var selectedset = "protein"; chimestructure.executeScript("select "+selectedset+";color "+colorChoice); } Or you can use a for loop in javascript to address multiple plug-ins: function changeMyColor(colorChoice) { // colorChoice is input from the user var myScript = "select protein;color "+colorChoice; for (var i=0;i Subject: RE: javascript variable in chime commands Date: Thu, 25 Jan 2001 16:58:00 -0500 To: rasmol@lists.umass.edu, Timothy Driscoll Tim Thanks!! Yes it works. Your examples were for text variables but I was also interested in using numeric variables. But it works the same way. I put together a demo http://www.gvsu.edu/carlsont/test.htm My project is to come up with a javascript routine that would use the move command to manipulate an image on the screen from any orientation to another orientation prescribed by the author. If you use a move command in a Chime tutorial, then the image rotates to the desired final position only if it starts in the desired original position. If the viewer has manipulated the image, then the relative move command will rotate the image to the wrong place. The same problem exists with translations and zoom. I know you can reset the view prior to the move command, but I thought it would be nice to be able to move smoothly to a specific view, independent of the original orientation. I figure this can be done with three steps: 1 pass the current orientation of the image to javascript variables with the "view show user" command. 2 determine the move parameters needed to move from the current orientation to the desired orientation 3. use the executeScript command to execute the move. The hardest part (yet to be done) is step 2. But I have a friend in the Math Dept who specializes in linear algebra applications and has some expreience with xyz coordinate rotations. He is interested in working on the problem. Or, maybe it would be easier to ask the Chime developers to do this for me. todd carlsont@gvsu.edu ______________________________ Reply Separator _________________________________ Author: "Timothy Driscoll" at OFFICE ++++------+------+------+------+------+------+------+------+------+------+ Subject: Re: javascript variable in chime commands Date: 01/25/2001 3:25 PM On 1/25/01 at 2:48 PM, Carlson, Todd wrote: > Hi > > Does anyone know if it is possible to use a numeric varibale in a > javascript routine as a parameter in a chime command. I am trying to > enhance some web pages using javascirpt. I have figured out how to > pass > information from the image to a javascript routine and how to use the > javascirpt routine to execute a chime command, but I have not yet > figured > out how to include a variable from the javascript in the command. > If I understand your question correctly, you can pass arguments from a Chime script to a javascript function in standard fashion: javascript myfunction(1,true,"stringval") If you want to run a Chime script from a javascript function, and incorporate a variable such as user input, something like this is possible: function changeMyColor(colorChoice) { // colorChoice is input from the user var selectedset = "protein"; chimestructure.executeScript("select "+selectedset+";color "+colorChoice); } Or you can use a for loop in javascript to address multiple plug-ins: function changeMyColor(colorChoice) { // colorChoice is input from the user var myScript = "select protein;color "+colorChoice; for (var i=0;i Subject: Netscape upgrade and Explorer failure Date: Mon, 29 Jan 2001 19:20:05 -0500 To: rasmol@lists.umass.edu Hi; For the security requirements I just upgraded my Netscape to the 4.76 version (Mac G4). Now my normally seamless Protein Explorer has died. I can open my local index.htm, get the Explorer pages, but neither the use of local pdb files nor the request for them of the RCSB database ever loads the structure. PE says that it is "busy" but it never does load a structure in the viewer side of the screen. I have full and competent connection to the web. The RCSB page was completely functional through Netscape at the time I was working with PE. The file I was getting was 1PIP (papain). Any thoughts on how I can recover PE function? -- Dr. Jeffrey Atkinson Associate Professor Department of Chemistry Brock University St. Catharines, Ontario Canada L2S 3A1 jatkin@spartan.ac.BrockU.ca http://chemiris.labs.brocku.ca/~chemweb/faculty/atkinson/ phone: 905 688-5550 ext 3967 fax: 905 682-9020 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Jeffrey Atkinson Subject: Netscape upgrade and Explorer failure Date: Mon, 29 Jan 2001 19:25:21 -0500 To: rasmol@lists.umass.edu Hi; With apologies for the double message: The following error comes across the bottom of the screen: Javascript error. Type "Javascript" into location for details. Exactly where is "location"? Any thoughts on how I can recover PE function? -- Dr. Jeffrey Atkinson Associate Professor Department of Chemistry Brock University St. Catharines, Ontario Canada L2S 3A1 jatkin@spartan.ac.BrockU.ca http://chemiris.labs.brocku.ca/~chemweb/faculty/atkinson/ phone: 905 688-5550 ext 3967 fax: 905 682-9020 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: Netscape upgrade and Explorer failure Date: Mon, 29 Jan 2001 21:05:56 -0500 To: rasmol@lists.umass.edu On 1/29/01 at 7:25 PM, Jeffrey Atkinson wrote: > Hi; > > With apologies for the double message: The following error > comes across the bottom of the screen: > > Javascript error. Type "Javascript" into location for details. > > Exactly where is "location"? > > Any thoughts on how I can recover PE function? > -- > Location refers to the location bar of the browser, where the URL appears. You can find it on the main/opening window of PE if you're in the interface already. Remember to type "javascript:" and include the colon (but not the quotes). I use PE with NC 4.76 on a Mac G4 with no troubles. The javascript error details may give a good clue... Tim _________________________________________ Timothy Driscoll molvisions.com - 3D molecular visualization e: driscoll@molvisions.com p: 508-864-6516 f: 781-899-4108 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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 f0U3b5x04110 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: RasMol with Spanish menus and messages Date: Mon, 29 Jan 2001 22:36:08 -0500 (EST) To: rasmol@lists.umass.edu, pdb-l@rcsb.org RasMol_2.7.1.1 is now the default release at http://www.bernstein-plus-sons.com/software/rasmol and the links on the http://www.OpenRasMol.org web page have been updated to reflect this change. This revision adds multilingual capabilities to RasMol 2.7.1. This release handles English and Spanish. The command to switch to Spanish is "Spanish". The command to switch back to English is "English". At present, Mac, Windows 95/98, Linux (Mandrake 7.2) and SGI (IRIX 6.4) precompiled binaries are available. Compilations for other platforms, problem reports, comments and suggestions appreciated. The prior release (RasMol 2.7.1) and its more extensive set of binaries are still available at: http://www.bernstein-plus-sons.com/software/RasMol_2.7.1 Our thanks to Fernando Gabriel Ranea (Laboratorio de Micología, Museo de Farmacobotánica, Facultad de Farmacia y Bioquímica. Universidad de Buenos Aires (davinci@dinamica.com.ar)) for translating most of the messages into Spanish. Those interested in providing translations into other languages will find the list of messages and menus in http://www.bernstein-plus-sons.com/software/RasMol_2.7.1.1/src/langsel.c In view of the importance of multilingual capabilities in RasMol and the popularity of RasMol 2.7.1, we have interrupted work on RasMol 2.7.2 to ensure availability of these mods against RasMol 2.7.1. Similar mods should be included in an updated release of RasMol 2.7.2 in a few weeks. -- 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 ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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 V5.00.2615.200 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: Netscape upgrade and Explorer failure Date: Tue, 30 Jan 2001 11:28:19 +0100 To: rasmol@lists.umass.edu > Hi; > > With apologies for the double message: The following error > comes across the bottom of the screen: > > Javascript error. Type "Javascript" into location for details. > > Exactly where is "location"? > Dr. Jeffrey Atkinson Type it into the "Location:" edit control at the top of the window. After a JScript error NS should write an error message. Otherwise it has no effect, or NS tries to translate it as server name. Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ----- Original Message ----- From: Jeffrey Atkinson ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: Page to help write Chime pages Date: Wed, 31 Jan 2001 13:54:00 -0500 To: rasmol@lists.umass.edu When surfing yesterday I ran across a page which would help you write a web page with a chime image in it. You fill in the form with the necessary information (pdb file, image parameters, etc) and it would generate the necessary code automatically. Unfortunately I forgot to bookmark this and I can't find it again (ug). Does anyone know of the page I am talking about? I have been asked to put together a presentation to teach chemists how to write simple chime pages and a feature like this might be usefull. thanks 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-- References: <0G81001B9J5L3E@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Steven Vik Subject: Re: Page to help write Chime pages Date: Wed, 31 Jan 2001 16:07:20 -0600 To: rasmol@lists.umass.edu > > When surfing yesterday I ran across a page which would help you write a >web > page with a chime image in it. You fill in the form with the necessary > > information (pdb file, image parameters, etc) and it would generate the > > necessary code automatically. Unfortunately I forgot to bookmark this >and > I can't find it again (ug). Does anyone know of the page I am talking > about? I have been asked to put together a presentation to teach >chemists > how to write simple chime pages and a feature like this might be >usefull. > > thanks > > todd carlson > dept of chemistry > gvsu > You might have been looking at the Robert Horton site: http://www.attotron.com/pub/cs/ -Steve Vik -- ***************************************************************** Steven B. Vik Professor Department of Biological Sciences Southern Methodist University Dallas, TX 75275-0376 Phone (214) 768-4228 Fax (214) 768-3955 E-mail svik@mail.smu.edu WWW http://www.smu.edu/~svik or http://svik.atbiology.smu.edu ***************************************************************** ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Scot Wherland Subject: Chime with Opera 5.0 Date: Wed, 31 Jan 2001 15:42:40 -0800 To: rasmol@lists.umass.edu In the search for a better browser, I have been trying Opera 5.0. It has many appealing features. However, Chime does not immediately work. Has anyone made it work? Opera 5.0 is from http://www.opera.com and it uses the Java 2.0 runtime environment. I am using the free version that has a banner ad running. Thanks, - Scot Wherland Voice: 509-335-3360 Prof. of Chemistry FAX: 509-335-8867 Dept. of Chemistry Email: (work): scot_wherland@wsu.edu Washington State University (home): wherland@turbonet.com Pullman, WA 99164-4630 USA ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2615.200 X-MSMail-priority: Normal References: <0G81001B9J5L3E@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: Page to help write Chime pages Date: Thu, 01 Feb 2001 09:05:07 +0100 To: rasmol@lists.umass.edu Todd, I don't know the page, but in such cases it is very useful to use the "history memory" of browsers: just hit the History button in IE or ctrl-H in Netscape. They remember most pages of last 1-2 weeks or more, depending on settings. Maybe this helps. Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ----- Original Message ----- Sent: Wednesday, January 31, 2001 7:54 PM From: Carlson, Todd Subject: Page to help write Chime pages To: > > When surfing yesterday I ran across a page which would help you write a > web > page with a chime image in it. You fill in the form with the necessary > > information (pdb file, image parameters, etc) and it would generate the > > necessary code automatically. Unfortunately I forgot to bookmark this > and > I can't find it again (ug). Does anyone know of the page I am talking > about? I have been asked to put together a presentation to teach > chemists > how to write simple chime pages and a feature like this might be > usefull. > > thanks > > 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 V5.00.2615.200 X-MSMail-priority: Normal References: <200101312343.PAA28084@cheetah.it.wsu.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: Chime with Opera 5.0 Date: Thu, 01 Feb 2001 09:29:58 +0100 To: rasmol@lists.umass.edu Dear Scot, I tried it a few weeks ago, and the Chime plug-in worked well. The only thing I had to do, as far as I remember, that I had Opera to recognize the already installed Netscape plugins. This is an option somewhere in the preferences section. Hope this helps Tamas Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ----- Original Message ----- Sent: Thursday, February 01, 2001 12:42 AM From: Scot Wherland Subject: Chime with Opera 5.0 To: > In the search for a better browser, I have been trying Opera 5.0. It has > many appealing features. > However, Chime does not immediately work. Has anyone made it work? > Opera 5.0 is from http://www.opera.com and it uses the Java 2.0 runtime > environment. I am using the free version that has a banner ad running. > Thanks, > > > - > Scot Wherland Voice: 509-335-3360 > Prof. of Chemistry FAX: 509-335-8867 > Dept. of Chemistry Email: (work): scot_wherland@wsu.edu > Washington State University (home): wherland@turbonet.com > Pullman, WA 99164-4630 USA > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: RE: Page to help write Chime pages Date: Thu, 01 Feb 2001 08:17:00 -0500 To: rasmol@lists.umass.edu, Steven Vik Thanks everyone Steven's suggestion: http://www.attotron.com/pub/cs/ wasn't the one I was looking for, but I like it even better! The browser history hints helped me find the pages I has seen at http://mmlsun2.pha.unc.edu/chime_show.html There are some nice features in these I can use to make scrpting easier. todd ______________________________ Reply Separator _________________________________ Author: "Steven Vik" at OFFICE ++++------+------+------+------+------+------+------+------+------+------+ Subject: Re: Page to help write Chime pages Date: 01/31/2001 5:07 PM > > When surfing yesterday I ran across a page which would help you write a >web > page with a chime image in it. You fill in the form with the necessary > > information (pdb file, image parameters, etc) and it would generate the > > necessary code automatically. Unfortunately I forgot to bookmark this >and > I can't find it again (ug). Does anyone know of the page I am talking > about? I have been asked to put together a presentation to teach >chemists > how to write simple chime pages and a feature like this might be >usefull. > > thanks > > todd carlson > dept of chemistry > gvsu > You might have been looking at the Robert Horton site: http://www.attotron.com/pub/cs/ -Steve Vik -- ***************************************************************** Steven B. Vik Professor Department of Biological Sciences Southern Methodist University Dallas, TX 75275-0376 Phone (214) 768-4228 Fax (214) 768-3955 E-mail svik@mail.smu.edu WWW http://www.smu.edu/~svik or http://svik.atbiology.smu.edu ***************************************************************** ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <200101312343.PAA28084@cheetah.it.wsu.edu> <006501c08c29$29dbeac0$3b8506c1@chem.klte.hu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Paul I. Reisberg" Subject: Re(2): Chime with Opera 5.0 Date: Thu, 01 Feb 2001 17:26:08 -0500 To: rasmol@lists.umass.edu My experience is that OPERA works using the netscape plug-ins as described, however the display options that are set such as display3d= ball&stick don't seem to take effect on loading and the figures always display as wireframe (ribbons seems to work also). A second problem, is that buttons that are added to manipulate the image also fail to function. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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(2): Chime with Opera 5.0 Date: Thu, 01 Feb 2001 17:43:45 -0500 To: rasmol@lists.umass.edu On 2/1/01 at 5:26 PM, preisberg@wellesley.edu (Paul I. Reisberg) wrote: > My experience is that OPERA works using the netscape plug-ins as > described, however the display options that are set such as display3d= > ball&stick don't seem to take effect on loading and the figures always > display as wireframe (ribbons seems to work also). A second problem, is > that buttons that are added to manipulate the image also fail to function. > > > Can anyone comment on support for LiveConnect in the Opera browser? TIA, Tim ________________________________ molvisions.com - 3D molecular visualization e: driscoll@molvisions.com p: 508.864.6516 f: 781.899.4108 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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 boundary="Boundary_(ID_OO8rv/Q3Mc+jOMrNXLPJfQ)" X-MSMail-priority: Normal References: <200101312343.PAA28084@cheetah.it.wsu.edu> <006501c08c29$29dbeac0$3b8506c1@chem.klte.hu> ++++------+------+------+------+------+------+------+------+------+------+ From: Tamas Subject: Re:Chime with Opera 5.0 Date: Sat, 03 Feb 2001 19:39:00 +0100 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_OO8rv/Q3Mc+jOMrNXLPJfQ) Now I rechecked my previous experiences with Opera 5.01 & Chime 2.6. They work, at least there were no problems with my Chime-based pages. I added an Opera test page to my earlier Chime-test url, one can reach it directly http://dragon.klte.hu/~gundat/Chimetest or via Eric's Molvis resources: http://molvis.sdsc.edu/visres/how-to-use/titles.jsp There are some tips too, how to configure Opera to perceive NS plugins (if not done automatically). > My experience is that OPERA works using the netscape plug-ins as > described, however the display options that are set such as display3d= > ball&stick don't seem to take effect on loading and the figures always > display as wireframe (ribbons seems to work also). A second problem, is > that buttons that are added to manipulate the image also fail to function. > I had also the same problem. At last I realized that that in the embed tag I accidentaly left out the name="something" attribute: I put it only in the case of buttons:
Now I rechecked my previous experiences with Opera 5.01 & Chime 2.6. They work, at least
there were no problems with my Chime-based pages. I added an Opera test page to my earlier
Chime-test url, one can reach it directly
or via Eric's Molvis resources:
 
There are some tips too, how to configure Opera to perceive NS plugins (if not done
automatically).  

> My experience is that OPERA works using the netscape plug-ins as
> described, however the display options that are set such as display3d=
> ball&stick don't seem to take effect on loading and the figures always
> display as wireframe (ribbons seems to work also). A second problem, is
> that buttons that are added to manipulate the image also fail to function.
>
I had also the same problem. At last I realized that that in the embed tag  I accidentaly left out
the name="something" attribute:
 
<embed src="file.mol" display3d=sticks ..... name = "something">
 
I put it only in the case of buttons:
 
<embed type="application/x-spt" width=10 height=10 button=push target="something".....
 
Interestingly, this caused no problems in NetScape, but in Opera the buttons went dead.
 
Best regards
 
Tamas
 
------------------
Dr Tamas E. Gunda
Research for Antibiotics
University of Debrecen
H-4010 Debrecen, POBox 36
Hungary
e-mail: tamasgunda@tigris.klte.hu
http://dragon.klte.hu/~gundat
 
 
--Boundary_(ID_OO8rv/Q3Mc+jOMrNXLPJfQ)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Antibody tutorial enhanced + links to other immuno-molecules Date: Sun, 04 Feb 2001 22:39:26 -0500 To: rasmol@lists.umass.edu I have enhanced my Chime-based tutorial on antibody structure. Some of the transitions are now clarified with short movies. Some of the image descriptions were also clarified. The study questions have been revised, and a guide to exploring a Fab:lysozyme complex (1fdl) in Protein Explorer was added. Links were provided at the end of the study questions to display some other molecules of immunological interest in Protein Explorer (MHC, TCR, cytokines, CD4:gp120). http://www.umass.edu/microbio/chime/antibody -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: <0G6W00BEUQ76T3@supai.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Ian Musgrave Subject: Re: Fwd: Plug-in detection Date: Thu, 08 Feb 2001 11:10:59 +1030 To: rasmol@lists.umass.edu G'Day All Sometime ago there was a discussion on this list about programs and web resources for predicting 3-D structure of proteins and/or peptides. As I've just moved cities, I no longer have access to that discussion, did anyone archive it, or can anyone give me pointers to such resources? Cheers! Ian ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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, de-DE, ru References: <0G6W00BEUQ76T3@supai.oit.umass.edu> <3A81EB1B.D0EBA8E4@werple.mira.net.au> ++++------+------+------+------+------+------+------+------+------+------+ From: Eugene.Leitl@lrz.uni-muenchen.de Subject: Re: Fwd: Plug-in detection Date: Thu, 08 Feb 2001 07:50:15 +0100 To: rasmol@lists.umass.edu Ian Musgrave wrote: > > G'Day All > > Sometime ago there was a discussion on this list about programs and web > resources for predicting 3-D structure of proteins and/or peptides. As > I've just moved cities, I no longer have access to that discussion, did > anyone archive it, or can anyone give me pointers to such resources? Try the CCL list archives. http://ccl.net CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@osc.edu ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: fr,en-US References: <0G6W00BEUQ76T3@supai.oit.umass.edu> <3A81EB1B.D0EBA8E4@werple.mira.net.au> ++++------+------+------+------+------+------+------+------+------+------+ From: Jean-Philippe Demers Subject: Fwd: Plug-in detection Date: Thu, 08 Feb 2001 08:28:17 -0500 To: rasmol@lists.umass.edu Someone submitted these URLs and I find them very useful: http://www.bmm.icnet.uk/3djigsaw/form.html http://www.expasy.ch/swissmod/SWISS-MODEL.html http://www.rpc.msoe.edu/3dmd Jean-Philippe Demers ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Does the Quizzer work in IE with Win98? Date: Wed, 14 Feb 2001 15:18:26 -0500 To: rasmol@lists.umass.edu With the help of Tim Driscoll and Jean-Philippe Demers, I am beginning to investigate the feasability of getting Chime sites to work in Internet Explorer. Jean-Philippe pointed out recently here that while LiveConnect doesn't exist in IE, the old 'immediate mode button' method of sending a script to Chime does work in IE. I looked for an older site of mine as a test case, one that uses this method. The Amino Acid Quizzer (http://www.umass.edu/microbio/chime/quizzer) is a good one. It works in IE 5.0 or 5.5, with Chime 2.0.3 or 2.6, in: Windows 95 Windows 98 Second Edition Windows 2000 So far I have been unable to get it to work on my main computer, a notebook running Windows 98 (not second edition). If you have a Windows 98 (not second edition) computer and are willing, please test whether Quizzer works in IE and let us know. I'd like to know if its just my installation of IE, or actually this one version of Windows that is the problem. To find your version of Windows: Right click on 'my computer', click on Properties. Mine says "Microsoft Windows 98, 4.10.1998". (It does not say "Second Edition"). If you send a report, please include the version of Windows (as above), of IE (Help, About IE), and the version of Chime (click on MDL, then About Chime). How to tell if the Quizzer is working: When you enter a number in the slot, that residue should turn green-spacefill and zoom in to ball and stick-CPK. On my computer, I see the immediate-mode button flash momentarily at the top of the right frame, but nothing happens to the molecular image (it just keeps spinning as wireframe on a black background). I've tried everything I can think of* short of upgrading to Win98 Second Edition, which seems to me unlikely to solve it. Thanks very much, -Eric ------------------------------- * What I've tried: -Set IE 5.5 Tools, Internet Options, General, Temporary Internet Files: Settings, Check for newer versions of stored pages: Every Visit (as recommended by Tim Driscoll). -Deleted the files that were obviously for IE 4.0 and 5.0, leaving only 5.5. (Before installing 5.5, I could run either 4.0 or 5.0; afterwards, even if I ran the iexplore.exe directly for 4.0 or 5.0, 5.5 is what ran.) -Ran the IE 5.5 installer for 'typical' installation. Because I had originally installed 5.5 in c:\ie5.5 (not 'program files') it is still there. Perhaps this is a problem but I don't know how to move it. It loads Chime only when Chime is in 'program files\internet explorer\plugins' even tho iexplore.exe is not there. -Ran the Windows Upgrade from IE, Tools, Windows Upgrade. Did the critical upgrades plus a few optionals. -Control Panel, Remove Software, lists MS IE. But the only options are 'add a component' and 'repair'. I completed the repair process. It still doesn't work. Any suggestions? I want to solve this not only so I can test IE on my computer, but also because I may not be the only one who ever encounters this problem if we do start building Chime sites for IE (so I want to be able to tell them what to do ...). /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: Chime documentation Date: Wed, 14 Feb 2001 16:05:00 -0500 To: rasmol@lists.umass.edu I've been putting together some chime pages and found that there seem to be commands that are not documented at the MDL page. Is there a COMPREHENSIVE list of Chmie commands and Embed tags somewhere? I often see people doing some interesting work by using these mystery commands. Thanks. todd carlson ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Chime documentation Date: Wed, 14 Feb 2001 18:29:01 -0500 To: rasmol@lists.umass.edu With the upgrade to Chime 2.6, MDL got nearly everything documented on their new site, www.mdlchime.com. If you know of something they missed, ask and maybe I can help. Also, report it to them at their site (not just here, because they don't monitor this list). -Eric At 02/14/2001, you wrote: > I've been putting together some chime pages and found that there seem >to be > commands that are not documented at the MDL page. Is there a >COMPREHENSIVE > list of Chmie commands and Embed tags somewhere? I often see people >doing > some interesting work by using these mystery commands. Thanks. > > todd carlson /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: RE: Chime documentation Date: Fri, 16 Feb 2001 09:47:00 -0500 To: rasmol@lists.umass.edu, Eric Martz Thanks Eric. I think I may have figured out the problem. The MDL site only has commands specific to Chime, right? The MDL site refers to their list as a complete list of RasMol scripts, which obviously isn't true. I also need a generic RasMol manual to get the complete list. Is the one at http://info.bio.cmu.edu/Courses/BiochemMols/RasFrames/TOC.HTM current and complete? Will all RasMol updates be recognized by Chime? Thanks for the feedback. I have been doing this in a rather haphazzard way and am trying to get myself and my information organized for some more serious efforts. todd Todd Carlson Dept of Chemistry Grand Valley State University Allendale MI 49401 ______________________________ Reply Separator _________________________________ Author: "Eric Martz" at OFFICE ++++------+------+------+------+------+------+------+------+------+------+ Subject: Re: Chime documentation Date: 02/14/2001 6:29 PM With the upgrade to Chime 2.6, MDL got nearly everything documented on their new site, www.mdlchime.com. If you know of something they missed, ask and maybe I can help. Also, report it to them at their site (not just here, because they don't monitor this list). -Eric At 02/14/2001, you wrote: > I've been putting together some chime pages and found that there seem >to be > commands that are not documented at the MDL page. Is there a >COMPREHENSIVE > list of Chmie commands and Embed tags somewhere? I often see people >doing > some interesting work by using these mystery commands. Thanks. > > todd carlson /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: RE: Chime documentation Date: Fri, 16 Feb 2001 09:48:00 -0500 To: rasmol@lists.umass.edu One other thing about the MDL site. It always seems to freeze my internet connection when I go there. Anyone else have this probelm? todd ______________________________ Reply Separator _________________________________ Author: "Eric Martz" at OFFICE ++++------+------+------+------+------+------+------+------+------+------+ Subject: Re: Chime documentation Date: 02/14/2001 6:29 PM With the upgrade to Chime 2.6, MDL got nearly everything documented on their new site, www.mdlchime.com. If you know of something they missed, ask and maybe I can help. Also, report it to them at their site (not just here, because they don't monitor this list). -Eric At 02/14/2001, you wrote: > I've been putting together some chime pages and found that there seem >to be > commands that are not documented at the MDL page. Is there a >COMPREHENSIVE > list of Chmie commands and Embed tags somewhere? I often see people >doing > some interesting work by using these mystery commands. Thanks. > > todd carlson /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: <0G8U00LKTUHI0T@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: David Fahrney Subject: Re: Chime documentation Date: Fri, 16 Feb 2001 10:19:32 -0700 To: rasmol@lists.umass.edu I tried to register at the MDL site yesterday. Although I finally managed to register, the site "crashed" three or four times, so I had to log back in each time. Finally, when I tried to download Chime 2.6 there was a message saying that my system was not suitable for Chime 2.6. Obviously, there are some bugs for MDL to work out in regards to the new Chime site. Dave Fahrney Professor of Biochemistry and Molecular Biology Colorado State University "Carlson, Todd" wrote: > > One other thing about the MDL site. It always seems to freeze my > internet > connection when I go there. Anyone else have this probelm? > > todd > > > ______________________________ Reply Separator > _________________________________ > Subject: Re: Chime documentation > Author: "Eric Martz" at OFFICE > Date: 02/14/2001 6:29 PM > > With the upgrade to Chime 2.6, MDL got nearly everything documented on > their new site, www.mdlchime.com. > If you know of something they missed, ask and maybe I can help. Also, > report it to them at their site (not just here, because they don't monitor > this list). -Eric > > At 02/14/2001, you wrote: > > I've been putting together some chime pages and found that there seem > >to be > > commands that are not documented at the MDL page. Is there a > >COMPREHENSIVE > > list of Chmie commands and Embed tags somewhere? I often see people > >doing > > some interesting work by using these mystery commands. Thanks. > > > > todd carlson > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > The Protein Explorer: http://proteinexplorer.org > World Index of Molecular Visualization Resources: http://molvisindex.org > PDB Lite molecule finder: http://pdblite.org > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: z-slab Date: Tue, 20 Feb 2001 09:47:00 -0500 To: rasmol@lists.umass.edu I see in the RasMol reference manual, there is no z-slab control which allows you to view a slice through the middle of the molecule like there is in kinamage. However, such a feature does exist in RasTop, the windows interface for RasMol. Is this a feature added to RasTop that is not available in RasMol and is this feature possible in Chime? Thanks Todd Carlson Dept of Chemistry GVSU carlsont@gvsu.edu ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Tim Speakeasy Acct Subject: Re: z-slab Date: Tue, 20 Feb 2001 10:11:17 -0500 To: rasmol@lists.umass.edu On 2/20/01 at 9:47 AM, CarlsonT@gvsu.edu (Carlson, Todd) wrote: > > > I see in the RasMol reference manual, there is no z-slab control which > allows you to view a slice through the middle of the molecule like > there is > in kinamage. However, such a feature does exist in RasTop, the windows > > interface for RasMol. Is this a feature added to RasTop that is not > available in RasMol and is this feature possible in Chime? > > Thanks > > Todd Carlson > Dept of Chemistry > GVSU > carlsont@gvsu.edu > Todd, the command you want is slab - for example, slab 50 puts the slab plane in the middle of the molecule. This syntax works in both Chime 2.x and RasMol 2.6x. In addition, the Chime move command includes a slab parameter: move [xrot] [yrot] [zrot] [zoom] [xpos] [ypos] [zpos] [slab] [incr] HTH, Tim _________________________________________ timothy driscoll molvisions.com - 3D molecular visualization e: driscoll@molvisions.com p: 508-864-6516 f: 781-899-4108 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Scot Wherland Subject: RasWin/POVray Date: Tue, 20 Feb 2001 08:36:44 -0800 To: rasmol@lists.umass.edu I have been using RasWin2.7 to write a POVray (ver. 3.1g for Windows) file. The image is pretty, but distorted in the sense that it appears flattened or stretched horizontally. I get the same result with "povray" or "povray3" output. Any ideas? Thanks, Scot - Scot Wherland Voice: 509-335-3360 Prof. of Chemistry FAX: 509-335-8867 Dept. of Chemistry Email: (work): scot_wherland@wsu.edu Washington State University (home): wherland@turbonet.com Pullman, WA 99164-4630 USA ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: RE: z-slab Date: Tue, 20 Feb 2001 11:43:00 -0500 To: rasmol@lists.umass.edu, Tim Speakeasy Acct Sorry, I guess I didn't make myself clear. I know of the slab command, but in other viewing programs (including RasTop) there are two slab planes and you only see the atoms between the planes. This allows you to view a thin slice through the middle of the molecule. With the normal RasMol and Chime slab commands, there is only one slab plane and you see the atoms behind it. todd ______________________________ Reply Separator _________________________________ Author: "Tim Speakeasy Acct" at OFFICE ++++------+------+------+------+------+------+------+------+------+------+ Subject: Re: z-slab Date: 02/20/2001 10:11 AM On 2/20/01 at 9:47 AM, CarlsonT@gvsu.edu (Carlson, Todd) wrote: > > > I see in the RasMol reference manual, there is no z-slab control which > allows you to view a slice through the middle of the molecule like > there is > in kinamage. However, such a feature does exist in RasTop, the windows > > interface for RasMol. Is this a feature added to RasTop that is not > available in RasMol and is this feature possible in Chime? > > Thanks > > Todd Carlson > Dept of Chemistry > GVSU > carlsont@gvsu.edu > Todd, the command you want is slab - for example, slab 50 puts the slab plane in the middle of the molecule. This syntax works in both Chime 2.x and RasMol 2.6x. In addition, the Chime move command includes a slab parameter: move [xrot] [yrot] [zrot] [zoom] [xpos] [ypos] [zpos] [slab] [incr] HTH, Tim _________________________________________ timothy driscoll molvisions.com - 3D molecular visualization e: driscoll@molvisions.com p: 508-864-6516 f: 781-899-4108 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-pair-Authenticated: 12.79.129.22 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: RE: z-slab Date: Tue, 20 Feb 2001 14:03:29 -0500 To: rasmol@lists.umass.edu, Tim Speakeasy Acct The mods to RasMol 2.7.1 in RasTop are under review for inclusion in RasMol 2.7.2.1. This includes the second slab plane. We should have a firm idea of which mods will make it into this release in another week. -- H. J. Bernstein At 11:43 -0500 2/20/01, Carlson, Todd wrote: > >Sorry, I guess I didn't make myself clear. I know of the slab command, but >in >other viewing programs (including RasTop) there are two slab planes and you >only >see the atoms between the planes. This allows you to view a thin slice >through >the middle of the molecule. With the normal RasMol and Chime slab commands, > >there is only one slab plane and you see the atoms behind it. > >todd > >______________________________ Reply Separator >_________________________________ >Subject: Re: z-slab >Author: "Tim Speakeasy Acct" at OFFICE >Date: 02/20/2001 10:11 AM > > >On 2/20/01 at 9:47 AM, CarlsonT@gvsu.edu (Carlson, Todd) wrote: > >> >> >> I see in the RasMol reference manual, there is no z-slab control >which >> allows you to view a slice through the middle of the molecule like >> there is >> in kinamage. However, such a feature does exist in RasTop, the >windows >> >> interface for RasMol. Is this a feature added to RasTop that is not >> available in RasMol and is this feature possible in Chime? >> >> Thanks >> >> Todd Carlson >> Dept of Chemistry >> GVSU >> carlsont@gvsu.edu >> > >Todd, > >the command you want is slab - for example, > >slab 50 > >puts the slab plane in the middle of the molecule. This syntax works in >both >Chime 2.x and RasMol 2.6x. In addition, the Chime move command includes a >slab >parameter: > >move [xrot] [yrot] [zrot] [zoom] [xpos] [ypos] [zpos] [slab] [incr] > > >HTH, > >Tim >_________________________________________ >timothy driscoll >molvisions.com - 3D molecular visualization >e: driscoll@molvisions.com >p: 508-864-6516 >f: 781-899-4108 > > ===================================================== **** 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 ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: <0G92000P693P3R@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Philippe Valadon Subject: Re: z-slab Date: Fri, 05 Jan 2001 10:40:18 -0800 To: rasmol@lists.umass.edu The z-slab or depth plane in RasTop cuts effectively the back of the molecule. It is based on some translations along the z-axis that are not permitted on the command line in rasmol 2.7.1. It should be easy to add the code change into rasmol 2.7.1 to have this feature activated. This remark applies to Chime if, of course, the source code was available. - Philippe --------------------------- *** RasTop *** --------------------------- Philippe Valadon P.O. Box 13014, La Jolla, CA 92039, USA. valadon@ix.netcom.com ----- Original Message ----- Sent: Tuesday, February 20, 2001 6:47 AM From: "Carlson, Todd" Subject: z-slab To: > > > I see in the RasMol reference manual, there is no z-slab control which > allows you to view a slice through the middle of the molecule like > there is > in kinamage. However, such a feature does exist in RasTop, the windows > > interface for RasMol. Is this a feature added to RasTop that is not > available in RasMol and is this feature possible in Chime? > > Thanks > > Todd Carlson > Dept of Chemistry > GVSU > carlsont@gvsu.edu ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2615.200 X-MSMail-priority: Normal References: <200102201637.IAA13034@jaguar.it.wsu.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: RasWin/POVray Date: Wed, 21 Feb 2001 10:31:07 +0100 To: rasmol@lists.umass.edu Do you mean that the image is distorted? Check that in POVRay the image dimensions are set OK. There are several quick options for the rendering you may choose from the menu bar, and some of them has not the usual dimensions. For example - as far as I remember - there are options for 320x200 and 320x240. The latter is the "normal", the formal not (in the case of the usual monitors), and it is easy to choose the wrong one resulting in distorted image. Hope this helps Tamas Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ----- Original Message ----- Sent: Tuesday, February 20, 2001 5:36 PM From: Scot Wherland Subject: RasWin/POVray To: > I have been using RasWin2.7 to write a POVray (ver. 3.1g for Windows) file. > The image is pretty, but distorted in the sense that it appears flattened > or stretched horizontally. I get the same result with "povray" or "povray3" > output. Any ideas? > Thanks, > Scot > > > - > Scot Wherland Voice: 509-335-3360 > Prof. of Chemistry FAX: 509-335-8867 > Dept. of Chemistry Email: (work): scot_wherland@wsu.edu > Washington State University (home): wherland@turbonet.com > Pullman, WA 99164-4630 USA > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Lboro-Filtered: mailer2.lut.ac.uk, Wed, 21 Feb 2001 10:54:59 +0000 ++++------+------+------+------+------+------+------+------+------+------+ From: Vickie McKee Subject: PC to Mac Date: Wed, 21 Feb 2001 10:54:11 +0000 To: rasmol@lists.umass.edu Does anyone have a quick guide to the relationship between chime commands for PC and for mac? I need to produce a mac version of a teaching exercise developed on PC and I don't have easy access to a mac - however, first glance suggests colours, orientation and mouse click action need changing. Vickie **************************************************************** Vickie McKee Chemistry Department Loughborough University Loughborough Leics. LE11 3TU email: v.mckee@lboro.ac.uk http://www-staff.lboro.ac.uk/~cmvm Phone: +44 (0)1509 222565 Fax (Dept): +44 (0)1509 233925 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: RE: z-slab Date: Wed, 21 Feb 2001 08:42:00 -0500 To: rasmol@lists.umass.edu, Philippe Valadon Thanks - I think that answers the question. The rear z-slab was added to RasTop and may be included in the next RasMol update. It is not currently in Chime. Now the follow-up question. What version of RasMol is Chime based on and are modifications in one carried over to the other? I know there are a number of Chime commands that are not found in RasMol. There are apparently RasMol commands not recognized by Chime. Are these programs diverging or will there continue to be coordination? Also, I don't know if this is a related topic, but it has to do with the z-axis. What does the z-translation parameter do in the Chime move command. In RasTop, z-translation seems to equal zoom but in Chime the move command has separate parameters for zoom and z-translation. Zoom works but I can't see that z-translation has any effect. Am I missing something? Thanks todd carlson ______________________________ Reply Separator _________________________________ Author: "Philippe Valadon" at OFFICE ++++------+------+------+------+------+------+------+------+------+------+ Subject: Re: z-slab Date: 01/05/2001 1:40 PM The z-slab or depth plane in RasTop cuts effectively the back of the molecule. It is based on some translations along the z-axis that are not permitted on the command line in rasmol 2.7.1. It should be easy to add the code change into rasmol 2.7.1 to have this feature activated. This remark applies to Chime if, of course, the source code was available. - Philippe --------------------------- *** RasTop *** --------------------------- Philippe Valadon P.O. Box 13014, La Jolla, CA 92039, USA. valadon@ix.netcom.com ----- Original Message ----- Sent: Tuesday, February 20, 2001 6:47 AM > > > I see in the RasMol reference manual, there is no z-slab control which > allows you to view a slice through the middle of the molecule like > there is > in kinamage. However, such a feature does exist in RasTop, the windows > > interface for RasMol. Is this a feature added to RasTop that is not > available in RasMol and is this feature possible in Chime? > > Thanks > > Todd Carlson > Dept of Chemistry > GVSU > carlsont@gvsu.edu From: "Carlson, Todd" Subject: z-slab To: ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Diana Irwin Date: Wed, 21 Feb 2001 12:07:15 +0800 To: rasmol@lists.umass.edu Is it possible to show S-S bonds in Rasmol. They show up in SPDB viewer in my file. Thank you. Diana Irwin ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- charset=us-ascii X-Accept-Language: en,pdf References: ++++------+------+------+------+------+------+------+------+------+------+ From: Jeff Cohlberg Subject: Re: SS bonds in RasMol Date: Wed, 21 Feb 2001 09:38:24 -0800 To: rasmol@lists.umass.edu I don't know if this is the best way to do it, but you can select cystine and sulfur spacefill Jeff Cohlberg Diana Irwin wrote: > Is it possible to show S-S bonds in Rasmol. They show up in SPDB > viewer in my file. > Thank you. > > Diana Irwin -- Jeffrey A. Cohlberg, Professor Department of Chemistry and Biochemistry California State University, Long Beach 1250 Bellflower Blvd. Long Beach, CA 90840 phone (562) 985-4944 fax (209) 821-4471 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: "Dr. Don Harden" Subject: SS BONDS Date: Wed, 21 Feb 2001 14:06:30 -0500 (EST) To: rasmol@lists.umass.edu To turn on SS bonds: ssbonds on In wireframe mode to make them larger: ssbonds 50 To select the cysteine sulphur atoms: select cys.sg On Wed, 21 Feb 2001, Diana Irwin wrote: > Is it possible to show S-S bonds in Rasmol. They show up in SPDB > viewer in my file. > Thank you. > > Diana Irwin > > > ---------------------------------------------------- Dr. Don Harden don-harden@Gsu.EDU Department of Chemistry 547 NSC Georgia State University ph: (404) 651-3580 Atlanta, Ga. 30302 fax: (404) 651-1416 http://chemistry.Gsu.EDU/glactone ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: John Tweedie Subject: Open Page command in Communicator 4.76 with Chime 2.6 Date: Thu, 22 Feb 2001 08:19:44 +1300 To: rasmol@lists.umass.edu I am running Navigator 4.76 on a Beige G3 (266 mH) under system 9.1. At the same time I set these up I also installed Chime 2.6. All seemed to be OK until I tried to open some of my Chime material using the "Open Page" command in Navigator. The page loaded OK but I received a broken PlugIn icon and the "Click here to get the Plug-In message". Accessing the same Chime scripts on a PowerBook 1400c system 8.5, Navigator 4.0 and Chime 2.0a using "Open Page" works fine. This is accessing the same scripts from a Zip disk. The setup on the G3 works fine with the scripts accessed by normal links or by using the Open Location command in Navigator. Any ideas? I am sure it is something simple but I could not find anything relevant with a quick scan of the Chime FAQ's at UMass or MDL. and a search of my accumulated posts through this list. Thanks 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-Originating-IP: 65.161.242.99 ++++------+------+------+------+------+------+------+------+------+------+ From: valadon@ix.netcom.com Subject: RE: z-slab Date: Wed, 21 Feb 2001 15:14:09 -0500 To: rasmol@lists.umass.edu The Z-translation command does not have any effect, both in rasmol and rastop, and, I assume, that it is the same with Chime. A way to simulate a translation along the z-axis would be a zoom centered on the middle of the screen. Just translate the area of interest to the center of the screen, then pick the origin of rotation at the same center, and either zoom in – to get closer, or out – to get farther. I do not know which rasmol version Chime was developped from. As far as I can see they diverged quite a long time ago and I do not know where Chime goes in term of evolution! I consider rasmol 2.7.1.1 developped by Herbert Bernstein as the reference in term of rasmol commands. - Philippe "Carlson, Todd" wrote: > Thanks - I think that answers the question. The rear z-slab was added to RasTop and may be included in the next RasMol update. It is not currently in Chime. Now the follow-up question. What version of RasMol is Chime based on and are modifications in one carried over to the other? I know there are a number of Chime commands that are not found in RasMol. There are apparently RasMol commands not recognized by Chime. Are these programs diverging or will there continue to be coordination? Also, I don't know if this is a related topic, but it has to do with the z-axis. What does the z-translation parameter do in the Chime move command. In RasTop, z-translation seems to equal zoom but in Chime the move command has separate parameters for zoom and z-translation. Zoom works but I can't see that z-translation has any effect. Am I missing something? Thanks todd carlson ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: SS bonds Date: Wed, 21 Feb 2001 15:52:27 -0500 To: rasmol@lists.umass.edu Protein Explorer (http://proteinexplorer.org) is much easier to use, and much more powerful than RasMol. You can do almost everything you'll ever want to do in RasMol without learning a single command -- but if you know RasMol commands, you can enter them, too. For a comparison, see http://www.umass.edu/microbio/chime/explorer/pe_v_ras.htm Protein Explorer displays SS bonds automatically in the first view of any molecule. In its QuickViews menu system, when you click SSBonds, you see the commands sent to Chime to show the disulfide bonds; thereby you can learn what the commands are (both for Chime and for RasMol, in this case). This is a generally good method to learn about RasMol/Chime commands. Moreover, each click of a QuickViews menu item displays help automatically. At 02/21/2001, you wrote: >Is it possible to show S-S bonds in Rasmol. They show up in SPDB >viewer in my file. >Thank you. > >Diana Irwin /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Diana Irwin Subject: Re: SS BONDS Date: Wed, 21 Feb 2001 16:40:03 +0800 To: rasmol@lists.umass.edu >Dear Dr. Harden, Thank you! It is so simple once you know it. Diana Diana C. Irwin Research Support Specialist laboratory of Professor David B. Wilson Molecular Biology and Genetics Cornell University Ithaca, New York 14853 phone 607 255-6476 fax 607 255-2428 email di12@cornell.edu >To turn on SS bonds: > > ssbonds on > >In wireframe mode to make them larger: > > ssbonds 50 > >To select the cysteine sulphur atoms: > > select cys.sg > > >On Wed, 21 Feb 2001, Diana Irwin wrote: > >> Is it possible to show S-S bonds in Rasmol. They show up in SPDB >> viewer in my file. >> Thank you. >> >> Diana Irwin >> >> >> > >---------------------------------------------------- >Dr. Don Harden don-harden@Gsu.EDU >Department of Chemistry 547 NSC >Georgia State University ph: (404) 651-3580 >Atlanta, Ga. 30302 fax: (404) 651-1416 >http://chemistry.Gsu.EDU/glactone > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <3.0.1.32.20010221105411.006aba98@staff-mailin.lboro.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Rob Scarrow Subject: Re: PC to Mac Date: Thu, 22 Feb 2001 10:53:04 -0500 To: rasmol@lists.umass.edu >Does anyone have a quick guide to the relationship between chime commands >for PC and for mac? I need to produce a mac version of a teaching exercise >developed on PC and I don't have easy access to a mac - however, first >glance suggests colours, orientation and mouse click action need changing. > Vickie Dear Vickie, I made the following annotations on the RasMol v2.5 Quick Reference card (designed for PC's) several years ago. I checked quickly and they still work on the Mac vs. 2.6. Rotate X-Y PC: Left button Mac: Mousebutton Translate X-Y PC: Right button Mac: Command key (*) Zoom PC: Shift Left button Mac: Shift/Mousebutton Rotate Z PC: Shift right button Mac: Shift and command keys (*) Z-Clipping PC: Control/left but. Mac: control and command keys (*) (*) - My instincts (as a longtime Mac user) are to try to also hold down the mousebutton when holding down these keys, but you don't need to do this (and in fact it slows things down if you do). Just hold down the command key (and either shift or control) and move the mouse. -- ***** Robert C.Scarrow (Rob) (610)-896-1218 Associate Professor and Chair Department of Chemistry Haverford College 370 Lancaster Avenue Haverford, PA 19041 USA rscarrow@haverford.edu ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <200102201637.IAA13034@jaguar.it.wsu.edu> X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id f1MGIxx22301 ++++------+------+------+------+------+------+------+------+------+------+ From: Scot Wherland Subject: Re: RasWin/POVray Date: Thu, 22 Feb 2001 08:17:12 -0800 To: rasmol@lists.umass.edu Tamas, Thanks for your help. I eventually got an improvement by setting the image dimensions ("up" and "right" in the camera command, to the 1.33 to 1 ratio, not the 1 to 1 ratio assumed by RasWin. The RasWin colors were also quite odd and I have not fixed all of that. In the end I used the straight output from WebLab Viewer for my poster. It was not much worse in quality and much easier to control with more appropriate colors. Scot At 10:31 AM 2/21/01 +0100, you wrote: >Do you mean that the image is distorted? Check that in POVRay the image dimensions are set OK. There are >several quick options for the rendering you may choose from the menu bar, and some of them has not the usual dimensions. >For example - as far as I remember - there are options for 320x200 and 320x240. The latter is the "normal", the formal >not (in the case of the usual monitors), and it is easy to choose the wrong one resulting in distorted image. >Hope this helps > >Tamas  > > > >Dr Tamas E. Gunda >Research Group for Antibiotics of the Hungarian Acad. Sci. >University of Debrecen, POBox 36 >H-4010 Debrecen, Hungary >tel.: (+36-52) 512 900/2472 >fax: (+36-52) 512 914 >e-mail: tamasgunda@tigris.klte.hu >home-page: www.klte.hu/~gundat/gunda.htm > >----- Original Message ----- >From: Scot Wherland >To: >Sent: Tuesday, February 20, 2001 5:36 PM >Subject: RasWin/POVray > > >> I have been using RasWin2.7 to write a POVray (ver. 3.1g for Windows) file. >> The image is pretty, but distorted in the sense that it appears flattened >> or stretched horizontally. I get the same result with "povray" or "povray3" >> output. Any ideas? >> Thanks, >> Scot >> >> >> - >> Scot Wherland       Voice: 509-335-3360 >> Prof. of Chemistry FAX: 509-335-8867 >> Dept. of Chemistry Email: (work): scot_wherland@wsu.edu >> Washington State University         (home): wherland@turbonet.com >> Pullman, WA 99164-4630 USA >> >> >> > > - Scot Wherland Voice: 509-335-3360 Prof. of Chemistry FAX: 509-335-8867 Dept. of Chemistry Email: (work): scot_wherland@wsu.edu Washington State University (home): wherland@turbonet.com Pullman, WA 99164-4630 USA ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2615.200 X-MSMail-priority: Normal References: <200102201637.IAA13034@jaguar.it.wsu.edu> <200102221618.IAA02647@cougar.it.wsu.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: RasWin/POVray Date: Fri, 23 Feb 2001 09:45:21 +0100 To: rasmol@lists.umass.edu >The RasWin colors were also quite odd and I >have not fixed all of that. If the colors are too light or dark, this may be influenced by changing the "global_settings assumed_gamma 2.2" value slightly (usually between 1.5-2.6) Tamas Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.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-- RasMol List ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Fwd: Open Page command in Communicator 4.76 with Chime 2.6 Date: Fri, 23 Feb 2001 15:13:39 -0500 To: Eric Martz , On 2/22/01 at 1:09 PM, emartz@microbio.umass.edu (Eric Martz) wrote: > > >Date: Thu, 22 Feb 2001 08:19:44 +1300 > >From: John Tweedie > >Subject: Open Page command in Communicator 4.76 with Chime 2.6 > >Sender: owner-rasmol@lists.umass.edu > >X-Sender: JTweedie@pop3.massey.ac.nz > >To: rasmol@lists.umass.edu > >Reply-to: rasmol@lists.umass.edu > > > >I am running Navigator 4.76 on a Beige G3 (266 mH) under system 9.1. At > >the same time I set these up I also installed Chime 2.6. All seemed to be > >OK until I tried to open some of my Chime material using the "Open Page" > >command in Navigator. The page loaded OK but I received a broken PlugIn > >icon and the "Click here to get the Plug-In message". > > > > > >Accessing the same Chime scripts on a PowerBook 1400c system 8.5, Navigator > >4.0 and Chime 2.0a using "Open Page" works fine. This is accessing the > >same scripts from a Zip disk. > > > >The setup on the G3 works fine with the scripts accessed by normal links or > >by using the Open Location command in Navigator. > > > >Any ideas? I am sure it is something simple but I could not find anything > >relevant with a quick scan of the Chime FAQ's at UMass or MDL. and a search > >of my accumulated posts through this list. > > > >Thanks > > > >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 > > > > I am not running Chime 2.6 yet, but on my network 2.0a works fine in all versions of NC between 4.5 and 4.76 (Mac G4 and Powerbook G3, both under system 9.04 and, recently, 9.1). I use Open:Page all the time to view local files. Assuming your embed tags follow strict syntax, check About:Plug-ins to make sure spt is mapped to Chime. (BTW, although omitting the TYPE attribute from the EMBED tag will work, sometimes it doesn't, so I suggest including it.) No matter what, my gut reaction is to suggest that you delete all old Chime files, restart with extensions off (Shift-Restart) and reinstall Chime. Also, don't install multiple copies during the same installation (the installer will ask you if you want to Continue or Quit once you've installed the plug-in; choose quit). Always quit the installer and re-run it to install Chime again. I've had faulty installations trying to do more than one at once. HTH, Tim _________________________________________ timothy driscoll molvisions.com - 3D molecular visualization e: driscoll@molvisions.com p: 508-864-6516 f: 781-899-4108 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: jmccray@morehouse.edu (Joseph McCray) Subject: Problems running Protein Explorer on Macintosh iBook laptop Date: Sun, 25 Feb 2001 16:16:15 -0400 To: rasmol@lists.umass.edu Help!! I am trying to load Protein Explorer onto Macintosh iBook laptops for a workshop. It will not run. The iBooks have OS9, Netscape 4.75, and Chime 2.6. When I try to run Protein Explorer, either online or from a downloaded copy I get a message saying that it cannot find the Java applet "java40.jar" and suggesting that I check the Classpath (whatever that is). By clicking ok in this suggestion box I can get PE to start, but nothing appears in the structure window. (By the way, the same error message appears when I run Chime alone on this computer. However, in this case, if I click ok, the structure comes up and appears to respond to the program properly.) Furthermore, I have reinstalled both Netscape 4.75 and Chime 2.6, as well as PE, with the extensions turned off. This only made things worse! Now Netscape shuts down when I try to run PE, saying an error of type 2 has occurred. Does anybody have any suggestions for solving this problem? Is anybody running Protein Explorer 1.8 on a Mac iBook? Thanks for any help. Joseph Dr. Joseph W. McCray, Jr. Associate Professor of Biology Department of Biology Morehouse College Tel.: (404) 681-2800 ext. 2320 Fax: (404) 522-9564 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Jim Perkins Subject: Re: Problems running Protein Explorer on Macintosh iBook laptop Date: Sun, 25 Feb 2001 18:00:10 -0500 To: rasmol@lists.umass.edu >When I try to run Protein Explorer, either online or from a >downloaded copy I get a message saying that it cannot find the Java applet >"java40.jar" and suggesting that I check the Classpath (whatever that is). For some reason, it doesn't seem to be able to find the java40.jar applet. The first thing to do is make sure the applet is correctly installed. It should be located in the following folder, along with a bunch of other .jar applets: Netscape Navigator Folder > Essential Files > Java > Lib If the file is in there, then your computer may be having trouble finding it. Try rebuilding your desktop. If that doesn't work, make sure java is enabled in Netscape. Go to Preferences under the Edit Menu, select "Advanced" and make sure the "Enable Java" button is clicked on. If none of that works, I'm stumped. Jim ___________________________________________________________ James A. Perkins, MS, MFA Assistant Professor of Medical Illustration College of Imaging Arts and Sciences/School of Art Rochester Institute of Technology 73 Lomb Memorial Drive Rochester, NY 14623 716-475-2443 fax: 716-475-6447 japfaa@rit.edu ___________________________________________________________ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Chime - 2 bonds or none? Date: Tue, 27 Feb 2001 08:44:53 -0500 To: RasMol List Hello, I am trying to force Chime 2.x to display a single bond between two atoms 2.2A apart. Neither Chime nor RasMol will do this with the original CONECT records in the pdb file. Adding a single CONECT record like this CONECT 1 2 forces RasMol (v2.7.1) to show a single bond, but not Chime. Adding two CONECT records like this CONECT 1 2 CONECT 2 1 forces Chime to show a double bond, though RasMol still shows only a single bond. Strangely enough, in the original CONECT records for this structure, it *appears* that atoms 1 and 2 should be bonded, though they do not display a bond; for example, these records are already present: CONECT 2 3 1 CONECT 1 2 4 5 6 How can I force Chime to show a *single* bond between these two atoms? And, more abstractly, why doesn't it show one already? [I can send along the actual pdb file if anyone is interested.] TIA, Tim _________________________________________ timothy driscoll molvisions.com - 3D molecular visualization e: driscoll@molvisions.com p: 508-864-6516 f: 781-899-4108 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- charset=us-ascii X-Accept-Language: en,pdf References: <20010227084454-r01010600-5376dde6@216.254.100.238> ++++------+------+------+------+------+------+------+------+------+------+ From: "Edward A. Nater" Subject: Re: Chime - 2 bonds or none? Date: Tue, 27 Feb 2001 08:06:01 -0600 To: rasmol@lists.umass.edu Tim - What we found in our use of Chime is that the CONECT records must be stated in numerical order. That is, the statement CONECT 1 2 will produce the appropriate bond (provided it hasn't been described before) but the statement CONECT 2 1 will not. Chime displays the bonds specified in the CONECT records until it runs into a statement that specifies bonds out of order. At that point it will ignore that particular bond and will proceed to calculate bonds on its own for some period of time. We have yet to figure out what stops it, but eventually it will begin to display bonds as specified until it runs into another record in the wrong numerical order. When it is calculating bonds on its own it will often display ones that are not specified. (we're working with mineral models, so the default covalent radii cause lots of erroneous bonds to be appear). Using the preloadscript="set connect save" command appears to force Chime to display the bonds specified in the CONECT records as long as they are all in appropriate numerical order. Hope that helps. Ed Timothy Driscoll wrote: > Hello, > > I am trying to force Chime 2.x to display a single bond between two atoms 2.2A > apart. Neither Chime nor RasMol will do this with the original CONECT records > in the pdb file. Adding a single CONECT record like this > > CONECT 1 2 > > forces RasMol (v2.7.1) to show a single bond, but not Chime. Adding two CONECT > records like this > > CONECT 1 2 > CONECT 2 1 > > forces Chime to show a double bond, though RasMol still shows only a single > bond. Strangely enough, in the original CONECT records for this structure, it > *appears* that atoms 1 and 2 should be bonded, though they do not display a > bond; for example, these records are already present: > > CONECT 2 3 1 > CONECT 1 2 4 5 6 > > How can I force Chime to show a *single* bond between these two atoms? And, > more abstractly, why doesn't it show one already? > > [I can send along the actual pdb file if anyone is interested.] > > TIA, > > Tim > _________________________________________ > timothy driscoll > molvisions.com - 3D molecular visualization > e: driscoll@molvisions.com > p: 508-864-6516 > f: 781-899-4108 > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: "Frances C. Bernstein" Subject: Re: Chime - 2 bonds or none? Date: Tue, 27 Feb 2001 09:19:03 -0500 (EST) To: RasMol List Hi, I cannot address the questions relative to Chime or Rasmol but I can provide an explanation of the correct format of CONECT records as they should appear in PDB-formatted entries. I have apppended excerpts from the PDB format document. It is important to note that there is no way to specify single bonds vs. double bonds. In addition if atoms m and n are connected (and this connectivity is not implicit from the residue names) there must be CONECT records for both atoms m and n. In addition, the CONECT records must be in ascending order of the first atom number and the numbers that follow the first on each CONECT record must be in ascending order. Thus the CONECT records that you gave > CONECT 2 3 1 > CONECT 1 2 4 5 6 should be CONECT 2 1 3 CONECT 1 2 4 5 6 Apparently a convention has arisen outside the PDB that a single CONECT record implies a single bond, two copies implies a double bond, etc. (I am not sure that I have presented this quite correctly.) I cannot address the use of such a format but only note that it is not standard PDB format and does not appear in entries that are prepared and distributed by the PDB. Please let me know if you have any questions about this. Frances C. Bernstein ---------------------------------------------------------------------- The CONECT records specify connectivity between atoms for which coordinates are supplied. The connectivity is described using the atom serial number as found in the entry. CONECT records are mandatory for HET groups (excluding water) and for other bonds not specified in the standard residue connectivity table which involve atoms in standard residues (see Appendix 4 for the list of standard residues). These records are generated by the PDB. Details * Intra-residue connectivity within non-standard (HET) residues (excluding water) is presented on the CONECT records. * Inter-residue connectivity of HET groups to standard groups (including water) or to other HET groups are represented on the CONECT records. * Disulfide bridges specified in the SSBOND records have corresponding CONECT records. * Hydrogen bonds and salt bridges have CONECT records. * No differentiation is made between donor and acceptor for hydrogen bonds. * No differentiation is made between atoms with excess negative or positive charge. * Atoms specified in the connectivity are presented by their serial numbers as found in the entry. * All atoms connected to the atom with serial number in columns 7 - 11 are listed in the remaining fields of the record. * If more than four fields are required for non-hydrogen and nonsalt-bridge bonds, a second CONECT record with the same atom serial number in columns 7 - 11 will be used. * These CONECT records occur in increasing order of the atom serial numbers they carry in columns 7 - 11. The target-atom serial numbers carried on these records also occur in increasing order. * The connectivity list given here is redundant in that each bond indicated is given twice, once with each of the two atoms involved specified in columns 7 - 11. * For nucleic acids, Watson-Crick hydrogen bonds between bases may be listed, but this is optional. * For hydrogen bonds, when the hydrogen atom is present in the coordinates, PDB generates a CONECT record between the hydrogen atom and its acceptor atom. * For NMR entries, CONECT records for all models are generated describing heterogen connectivity and others for LINK records. ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Frances C. Bernstein * *** fcb@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Tue, 27 Feb 2001, Timothy Driscoll wrote: > Hello, > > I am trying to force Chime 2.x to display a single bond between two atoms 2.2A > apart. Neither Chime nor RasMol will do this with the original CONECT records > in the pdb file. Adding a single CONECT record like this > > CONECT 1 2 > > forces RasMol (v2.7.1) to show a single bond, but not Chime. Adding two CONECT > records like this > > CONECT 1 2 > CONECT 2 1 > > forces Chime to show a double bond, though RasMol still shows only a single > bond. Strangely enough, in the original CONECT records for this structure, it > *appears* that atoms 1 and 2 should be bonded, though they do not display a > bond; for example, these records are already present: > > CONECT 2 3 1 > CONECT 1 2 4 5 6 > > > > How can I force Chime to show a *single* bond between these two atoms? And, > more abstractly, why doesn't it show one already? > > [I can send along the actual pdb file if anyone is interested.] > > > TIA, > > Tim > _________________________________________ > timothy driscoll > molvisions.com - 3D molecular visualization > e: driscoll@molvisions.com > p: 508-864-6516 > f: 781-899-4108 > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Robert Bateman Subject: kinemage users needed Date: Mon, 26 Feb 2001 14:31:59 -0600 To: rasmol@lists.umass.edu I would like to get in touch with individuals who have used kinemages in their teaching and/or research. I am looking for peer reviewers for an NSF grant project. Interested parties should email me offlist at robert.bateman@usm.edu. Thanks. Bob Bateman ___________________________________________ Robert C. Bateman, Jr. Associate Professor and Graduate Coordinator Department of Chemistry and Biochemistry University of Southern Mississippi Hattiesburg, MS 39406-5043 601-266-4707 (office), 6075 (fax), 5305 (lab), 5394 (secretary) Robert.Bateman@usm.edu http://ocean.otr.usm.edu/~rbateman ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: Problems running Protein Explorer on Macintosh iBook laptop Date: Tue, 27 Feb 2001 18:52:13 -0500 To: jmccray@morehouse.edu (Joseph McCray) Cc: mvisions@speakeasy.org, rasmol@lists.umass.edu Dear Joseph: I've only heard reports of the problem you report twice before out of the hundreds of Mac's on which PE has been run. In both cases the problem eventually went away but the Mac owners didn't know why for sure. I'm not very familiar with Macs and this problem has never come to my attention from a Windows computer. I'm copying this to Tim Driscoll in case he has any ideas -- he is a Mac expert. Perhaps it would be worthwhile reformatting one of the Macs in your lab and reinstalling the OS from the ground up. If that fixes it, at least you know what works. Sorry I can't be more help! Any chance you can move the session to a different computer lab? -Eric At 02/26/2001, you wrote: >Prof. Martz: > > I sent the following message to the rasmol e-mail list yesterday. > I am trying to load Protein Explorer onto Macintosh laptops for a >workshop. It will not run. The iBooks have OS9, Netscape 4.75, and Chime >2.6. When I try to run Protein Explorer, either online or from a >downloaded copy, I get a message saying that it cannot find the Java applet >"java40.jar" and suggesting that I check the Classpath (whatever that is ). >By clicking ok in this suggestion box I can get PE to start, but nothing >appears in the structure window. (By the way, the same error message >appears when I run Chime alone on this computer. However, in this case, if >I click ok, the structure comes up and appears to respond to the program >properly.) > Furthermore, I have reinstalled both Netscape 4.75 and Chime 2.6, >as well as PE, wwith the extensions turned off. This only made things >worse! Now Netscape shuts down when I try to run PE, saying an error of >type 2 has occurred. > Does anybody have any suggestions for solving this problem? Is >anybody running Protein Explorer 1.8 on a Mac iBook? Thanks for any help. > >Joseph > > I have only received one reply from the rasmol list. I had already >tried everything he suggested except rebuilding the desktop, which I tried. >PE still would not run. I hate to bother you personally, but there are >people coming from out of town this weekend to run a workshop on molecular >modeling and the organizers and I are getting a little desparate. Any >helpful suggestions you have would be greatly appreciated. Thank you. > >Joseph > >Dr. Joseph W. McCray, Jr. >Associate Professor of Biology >Department of Biology >Morehouse College >Tel.: (404) 681-2800 ext. 2320 >Fax: (404) 522-9564 > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Problems running Protein Explorer on Macintosh iBook laptop Date: Tue, 27 Feb 2001 18:50:36 -0500 To: Eric Martz Cc: Joseph McCray , rasmol@lists.umass.edu Hi Joseph, I experienced a similar problem with a new installation of NC 4.75 on a Mac (OS 9.[something]). It was months ago, so the details are fuzzy, but it also dealt with a "missing" jar. I downloaded the installer again from the Netscape site and performed the entire NC/Chime installation procedure anew, and the problem went away. So as big of a pain as it is, that's what I suggest. Note: you may want to upgrade to 4.76 if you are going to reinstall. I've run into only a few bugs that are apparently specific to 4.75, but it's always good to have the latest *working* version (I've never been able to even install Netscape 6 on my Mac). Hope that helps, Tim On 2/27/01 at 6:52 PM, emartz@microbio.umass.edu (Eric Martz) wrote: > Dear Joseph: > > I've only heard reports of the problem you report twice before out of the > hundreds of Mac's on which PE has been run. In both cases the problem > eventually went away but the Mac owners didn't know why for sure. > > I'm not very familiar with Macs and this problem has never come to my > attention from a Windows computer. I'm copying this to Tim Driscoll in case > he has any ideas -- he is a Mac expert. > > Perhaps it would be worthwhile reformatting one of the Macs in your lab and > reinstalling the OS from the ground up. If that fixes it, at least you know > what works. > > Sorry I can't be more help! Any chance you can move the session to a > different computer lab? > > -Eric > > At 02/26/2001, you wrote: > >Prof. Martz: > > > > I sent the following message to the rasmol e-mail list yesterday. > > I am trying to load Protein Explorer onto Macintosh laptops for a > >workshop. It will not run. The iBooks have OS9, Netscape 4.75, and Chime > >2.6. When I try to run Protein Explorer, either online or from a > >downloaded copy, I get a message saying that it cannot find the Java applet > >"java40.jar" and suggesting that I check the Classpath (whatever that is ). > >By clicking ok in this suggestion box I can get PE to start, but nothing > >appears in the structure window. (By the way, the same error message > >appears when I run Chime alone on this computer. However, in this case, if > >I click ok, the structure comes up and appears to respond to the program > >properly.) > > Furthermore, I have reinstalled both Netscape 4.75 and Chime 2.6, > >as well as PE, wwith the extensions turned off. This only made things > >worse! Now Netscape shuts down when I try to run PE, saying an error of > >type 2 has occurred. > > Does anybody have any suggestions for solving this problem? Is > >anybody running Protein Explorer 1.8 on a Mac iBook? Thanks for any help. > > > >Joseph > > > > I have only received one reply from the rasmol list. I had already > >tried everything he suggested except rebuilding the desktop, which I tried. > >PE still would not run. I hate to bother you personally, but there are > >people coming from out of town this weekend to run a workshop on molecular > >modeling and the organizers and I are getting a little desparate. Any > >helpful suggestions you have would be greatly appreciated. Thank you. > > > >Joseph > > > >Dr. Joseph W. McCray, Jr. > >Associate Professor of Biology > >Department of Biology > >Morehouse College > >Tel.: (404) 681-2800 ext. 2320 > >Fax: (404) 522-9564 > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > The Protein Explorer: http://proteinexplorer.org > World Index of Molecular Visualization Resources: http://molvisindex.org > PDB Lite molecule finder: http://pdblite.org > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > _________________________________________ timothy driscoll molvisions.com - 3D molecular visualization e: driscoll@molvisions.com p: 508-864-6516 f: 781-899-4108 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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 V5.00.2615.200 boundary="Boundary_(ID_8cEP5T4qK3htSRYUGSNt7w)" X-MSMail-priority: Normal References: <20010227084454-r01010600-5376dde6@216.254.100.238> ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: Chime - 2 bonds or none? Date: Wed, 28 Feb 2001 10:20:38 +0100 To: rasmol@lists.umass.edu, "Tamas E. Gunda" This is a multi-part message in MIME format. --Boundary_(ID_8cEP5T4qK3htSRYUGSNt7w) Hi, The problem with PDB files is, that although the PDB format definition, as written in the PDB documentation, is a very strict one (it is a good thing of course), there are some points where not. Therefore, as there are a number of programs using and generating this format, different variations may appear even in files describing the same structure. When developing my program Mol2Mol, I sweated quite a lot to take every varions into account I met in different pdb files. For example, at the very end of the files sometimes there is a closing TER, sometimes not, (END logically implies TER), sometimes both miss, sometimes TER appears between the last ATOM and first CONECT, etc: ATOM 274 1H NH2 B 10 9.105 2.951 20.225 ATOM 275 2H NH2 B 10 10.692 2.246 20.305 CONECT 1 2 4 6 7 CONECT 2 1 3 12 CONECT 4 1 5 8 9 TER END Different programs may therefore behave differently. The situation is even more complicated when HETATM and MODEL appear in the file, and the Chime-subvariant of pdb format (with double bonds) etc. As the CONECT records are redundant, every bonds are considered twice, (in the above example the 1-2 and 1-4 bonds ), when inputting the CONECT records, the programs skip automatically one of them. But it depends on the programmer, how is it organized: accept if the to-atom is higher than the from-atom or vice versa (i.e. 1 2 is read in but 2 1 not or vice versa). I promise I will make a rigorous test on the several pdb variations vs. reaction of Chime the next week-end, and I am going to report it soon. best regards Tamas PS: Tim, could send me the file in question? Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ----- Original Message ----- Sent: Tuesday, February 27, 2001 2:44 PM From: Timothy Driscoll Subject: Chime - 2 bonds or none? To: RasMol List > Hello, > > I am trying to force Chime 2.x to display a single bond between two atoms 2.2A > apart. Neither Chime nor RasMol will do this with the original CONECT records > in the pdb file. Adding a single CONECT record like this > > CONECT 1 2 > > forces RasMol (v2.7.1) to show a single bond, but not Chime. Adding two CONECT > records like this > > CONECT 1 2 > CONECT 2 1 > > forces Chime to show a double bond, though RasMol still shows only a single > bond. Strangely enough, in the original CONECT records for this structure, it > *appears* that atoms 1 and 2 should be bonded, though they do not display a > bond; for example, these records are already present: > > CONECT 2 3 1 > CONECT 1 2 4 5 6 > > > > How can I force Chime to show a *single* bond between these two atoms? And, > more abstractly, why doesn't it show one already? > > [I can send along the actual pdb file if anyone is interested.] > > > TIA, > > Tim > _________________________________________ > timothy driscoll > molvisions.com - 3D molecular visualization > e: driscoll@molvisions.com > p: 508-864-6516 > f: 781-899-4108 > --Boundary_(ID_8cEP5T4qK3htSRYUGSNt7w)
Hi,
 
The problem with PDB files is, that although the PDB format definition, as written in the PDB documentation, is a very strict one (it is a good thing of  course), there are some points where not. Therefore, as there are a number of programs using and generating this format, different variations may appear even in files describing the same structure. When developing my program Mol2Mol, I sweated quite a lot to take every varions into account I met in different pdb files.
 
 For example, at the very end of the files sometimes there is a closing TER, sometimes not, (END logically implies TER), sometimes both miss, sometimes TER appears between the last ATOM and first CONECT, etc:
 
ATOM    274 1H   NH2 B  10       9.105   2.951  20.225
ATOM    275 2H   NH2 B  10      10.692   2.246  20.305
CONECT    1    2    4    6    7
CONECT    2    1    3   12
CONECT    4    1    5    8    9
TER
END
 
Different programs may therefore behave differently. The situation is even more complicated when HETATM and MODEL appear in the file, and the Chime-subvariant of pdb format (with double bonds) etc.
 
As the CONECT records are redundant, every bonds are considered twice, (in the above example the 1-2 and 1-4 bonds ), when inputting the CONECT records, the programs skip automatically one of them. But it depends on the programmer, how is it organized: accept if the to-atom is higher than the from-atom or vice versa (i.e. 1 2 is read in but 2 1 not or vice versa).
 
I promise I will make a rigorous test on the several pdb variations vs. reaction of Chime the next week-end, and I am going to report it soon.
 
best regards
 
 
Tamas
 
PS: Tim, could send me the file in question?
 
 
Dr Tamas E. Gunda
Research Group for Antibiotics of the Hungarian Acad. Sci.
University of Debrecen, POBox 36
H-4010 Debrecen, Hungary
tel.: (+36-52) 512 900/2472
fax: (+36-52) 512 914
e-mail: tamasgunda@tigris.klte.hu
home-page: www.klte.hu/~gundat/gunda.htm
----- Original Message -----
From: Timothy Driscoll <mvisions@speakeasy.org>
To: RasMol List <rasmol@lists.umass.edu>
Sent: Tuesday, February 27, 2001 2:44 PM
Subject: Chime - 2 bonds or none?

> Hello,
>
> I am trying to force Chime 2.x to display a single bond between two atoms 2.2A
> apart.  Neither Chime nor RasMol will do this with the original CONECT records
> in the pdb file.  Adding a single CONECT record like this
>
> CONECT 1 2
>
> forces RasMol (v2.7.1) to show a single bond, but not Chime.  Adding two CONECT
> records like this
>
> CONECT 1 2
> CONECT 2 1
>
> forces Chime to show a double bond, though RasMol still shows only a single
> bond.  Strangely enough, in the original CONECT records for this structure, it
> *appears* that atoms 1 and 2 should be bonded, though they do not display a
> bond; for example, these records are already present:
>
> CONECT 2 3 1
> CONECT 1 2 4 5 6
>
>
>
> How can I force Chime to show a *single* bond between these two atoms?  And,
> more abstractly, why doesn't it show one already?
>
> [I can send along the actual pdb file if anyone is interested.]
>
>
> TIA,
>
> Tim
> _________________________________________
> timothy driscoll
> molvisions.com - 3D molecular visualization
> e: driscoll@molvisions.com
> p: 508-864-6516
> f: 781-899-4108
>
--Boundary_(ID_8cEP5T4qK3htSRYUGSNt7w)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Gordon Conference on Science Ed. and Visualization: International Date: Thu, 01 Mar 2001 09:18:48 -0500 To: rasmol@lists.umass.edu, pdb-l@rcsb.org Cc: lljones@bentley.unco.edu >>Date: Tue, 27 Feb 2001 >>From: "Loretta L. Jones" >>Subject: Gordon Conference on Science Ed. and Visualization: International >> >>The 2001 Gordon Research Conference on Science Education and >>Visualization: International. will be held on August 5-10, 2001, Mt. >>Holyoke College, South Hadley, Massachusetts. The conference >>will investigate the role of visualization of complex scientific >>phenomena in science education. The meeting will have a >>three-fold focus: to exchange information on advances in relevant >>technologies that support visualization, to consider how to represent >>complex phenomena for science students, and to enlighten this >>discussion with relevant results of cognitive science research. An >>application form and a preliminary program for the conference is >>posted on the web: >>http://www.grc.uri.edu/programs/2001/sciedu.htm >> >>Funding is available from the National Science Foundation for >>partial financial support of a limited number of participants in the >>following categories: faculty at four-year and two-year colleges, >>graduate students, and precollege teachers and administrators. To >>apply for support please send a brief electronic note to the >>conference chair, Loretta Jones (lljones@unco.edu), by 15 May >>2001. The note should include your complete mailing address, a >>justification for the request (describing your activities related to >>visualization in science education), indicate the resources you are >>able to provide, and give the amount requested (conference fees, >>meals, and lodging are $600). The amount awarded will depend on >>the number of participants funded and whether additional funding >>becomes available. >> >>Loretta L. Jones, Ph.D., D.A. >>Department of Chemistry and Biochemistry >>University of Northern Colorado >>501 20th Street, Greeley, CO 80639 >>Voice: 970/351-1443; FAX: 970/351-1269 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: New Tutorial Section Date: Thu, 01 Mar 2001 10:28:31 -0500 To: discuspv@usm.maine.edu Cc: rasmol@lists.umass.edu, pdb-l@rcsb.org Greetings, Deep Viewers! This morning I completed an elementary tutorial on homology modeling, and posted it as a new section of the Deep View Tutorial. http://www.usm.maine.edu/~rhodes/SPVTut/index.html Look for the Homology Modeling link in the lower part of the Contents frame on the left. A special feature of the new tutorial is an initial sequence search in the human genome. This exercise can serve you or your students as a very simple introduction to the vast maze of genome tools. In the modeling exercise, I emphasize means of evaluating homology models and searching for problems that might suggest limitations of the final product. This section has not yet been tested by students. I appreciate suggestions and corrections from users. Cheers! ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* ... the genetic variation found outside of Africa represents only a subset of that found within the African continent. From a genetic perspective, all humans are therefore Africans, either residing in Africa or in recent exile. Svante Paabo: "The Human Genome and Our View of Ourselves," Science, Volume 291, Number 5507, Issue of 16 Feb 2001, pp. 1219-1220. ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* Gale Rhodes Professor of Chemistry University of Southern Maine Portland, Maine, USA 207-780-4734 http://www.usm.maine.edu/~rhodes ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: David Crout Subject: Stereochemistry Date: Mon, 05 Mar 2001 13:36:04 +0000 To: rasmol@lists.umass.edu Can anyone tell me if they know of webs sites or software that deal with the stereochemistry of organic and inorganic (coordination) compounds? I am looking for sources that illustrate stereochemical principles, both static and dynamic (e.g. stereochemistru of standard reaction mechanisms), preferably interactive, and also quiz-type sources. I know of one or two commercial sources of software that seem very expensive for what they offer, so would welcome suggestions about alternatives. I have searched the Rasmol email history list but have not found anything relevant. David Crout -- Professor D.H.G. Crout Department of Chemistry University of Warwick Coventry CV4 7AL UK Tel: +44 (0)24 76523961 FAX: +44 (0)24 76524429 e-mail: msrky@csv.warwick.ac.uk ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: David Margulies Subject: lost it Date: Tue, 06 Mar 2001 08:14:32 -0500 To: "'rasmol@lists.umass.edu'" Eric and friends: PE has been going well until I tried to rig up the RCSB to launch PE directly. Now my PE either standalone or web based, can't find the plugin it seems (cracked icon and always busy). when I try to get the chime plug in to reinstall via MDl, it takes me to a dead web page. Any thoughts? Suggestions would be better. (This is all on a Mac G4 running netscape 4.7.5) D David H. Margulies, MD, PhD Chief, Molecular Biology Section Laboratory of Immunology NIAID, NIH Bldg. 10; Rm. 11N311 10 Center Dr. Bethesda, MD 20892-1892 ph: 301-496-6429 fax: 301-496-0222 e-mail: dhm@nih.gov ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <1A8D3CB9ED99D411AF5400D0B720F6544D1C96@atlas.niaid.nih.gov> ++++------+------+------+------+------+------+------+------+------+------+ From: Jeffrey Atkinson Subject: Re: lost it Date: Tue, 06 Mar 2001 08:30:34 -0500 To: rasmol@lists.umass.edu David; I had the same problem albeit after I had upgraded to Netscape 4.76 but on a G4. No amount of tinkering alleviated either the standalone or web absed access to PE. It sat there permanently busy doing nothing. The only fix was a complete reload of Chime and Netscape. Did the trick and really not to much effort. Jeffrey >Eric and friends: > PE has been going well until I tried to rig up the RCSB to launch PE >directly. Now my PE either standalone or web based, can't find the plugin >it seems (cracked icon and always busy). when I try to get the chime plug in >to reinstall via MDl, it takes me to a dead web page. Any thoughts? >Suggestions would be better. > > (This is all on a Mac G4 running netscape 4.7.5) > >D > > > >David H. Margulies, MD, PhD >Chief, Molecular Biology Section >Laboratory of Immunology >NIAID, NIH >Bldg. 10; Rm. 11N311 >10 Center Dr. >Bethesda, MD 20892-1892 -- Dr. Jeffrey Atkinson Associate Professor Department of Chemistry Brock University St. Catharines, Ontario Canada L2S 3A1 jatkin@spartan.ac.BrockU.ca http://chemiris.labs.brocku.ca/~chemweb/faculty/atkinson/ phone: 905 688-5550 ext 3967 fax: 905 682-9020 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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 f26FE1x09149 ++++------+------+------+------+------+------+------+------+------+------+ From: Jean Richelle Subject: hbonds and water molecules Date: Tue, 06 Mar 2001 16:13:02 +0100 To: rasmol@lists.umass.edu Hi, I have two questions: 1) is there some place where the "set hbonds chain on|off" feature is described ? 2) is it possible to calculate/display hbonds between water molecules, and between water molecules and peptidic or nucleic chains ? Best regards, Jean _____________________________________________________________________________ Jean Richelle Service de Conformation des Macromolécules Biologiques Tel: +32 02 650 3587 et de Bioinformatique - Université libre de Bruxelles FAX: +32 02 648 8954 av. F.D. Roosevelt 50 - CP160/16, B-1050 Bruxelles, Belgium _____________________________________________________________________________ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Timothy Driscoll Subject: Re: Chime - 2 bonds or none? Date: Tue, 06 Mar 2001 12:39:39 -0500 To: rasmol@lists.umass.edu A bit after the fact, but there is a very good page at Eric Martz's Molecular Visualization Freeware site regarding bonds, conect records, and more: http://www.umass.edu/microbio/rasmol/rasbonds.htm Tim On 2/27/01 at 8:06 AM, ed.nater@soils.umn.edu (Edward A. Nater) wrote: > Tim - > > What we found in our use of Chime is that the CONECT records must be stated in > numerical order. That is, the statement > > CONECT 1 2 > > will produce the appropriate bond (provided it hasn't been described before) > > but the statement > > CONECT 2 1 > > will not. Chime displays the bonds specified in the CONECT records until it runs > into a statement that specifies bonds out of order. At that point it will ignore > that particular bond and will proceed to calculate bonds on its own for some > period of time. We have yet to figure out what stops it, but eventually it will > begin to display bonds as specified until it runs into another record in the > wrong > numerical order. When it is calculating bonds on its own it will often display > ones that are not specified. (we're working with mineral models, so the default > covalent radii cause lots of erroneous bonds to be appear). > > Using the > > preloadscript="set connect save" > > command appears to force Chime to display the bonds specified in the CONECT > records as long as they are all in appropriate numerical order. > > Hope that helps. > > Ed > > > Timothy Driscoll wrote: > > > Hello, > > > > I am trying to force Chime 2.x to display a single bond between two atoms 2.2A > > apart. Neither Chime nor RasMol will do this with the original CONECT records > > in the pdb file. Adding a single CONECT record like this > > > > CONECT 1 2 > > > > forces RasMol (v2.7.1) to show a single bond, but not Chime. Adding two > CONECT > > records like this > > > > CONECT 1 2 > > CONECT 2 1 > > > > forces Chime to show a double bond, though RasMol still shows only a single > > bond. Strangely enough, in the original CONECT records for this structure, it > > *appears* that atoms 1 and 2 should be bonded, though they do not display a > > bond; for example, these records are already present: > > > > CONECT 2 3 1 > > CONECT 1 2 4 5 6 > > > > How can I force Chime to show a *single* bond between these two atoms? And, > > more abstractly, why doesn't it show one already? > > > > [I can send along the actual pdb file if anyone is interested.] > > > > TIA, > > > > Tim > > _________________________________________ > > timothy driscoll > > molvisions.com - 3D molecular visualization > > e: driscoll@molvisions.com > > p: 508-864-6516 > > f: 781-899-4108 > > > > > _________________________________________ timothy driscoll molvisions.com - 3D molecular visualization e: driscoll@molvisions.com p: 508-864-6516 f: 781-899-4108 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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 f2714gx18639 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: hbonds and water molecules Date: Tue, 06 Mar 2001 20:16:02 -0500 To: rasmol@lists.umass.edu At 03/06/2001, you wrote: >Hi, > >I have two questions: >1) is there some place where the "set hbonds chain on|off" feature is >described ? Like most RasMol and Chime features, this is described in Protein Explorer (http://www.proteinexplorer.org). In QuickViews, on the DISPLAY menu, select HBonds, and details appear automatically. >2) is it possible to calculate/display hbonds between water >molecules, and between water molecules and peptidic or nucleic chains >? Not directly in RasMol or Chime. I don't know of any free web site where all hbonds can be calculated but I wish I did! If you do locate the hbonds, they can be displayed using methods described at http://www.umass.edu/microbio/rasmol/rasbonds.htm What are the values used by RasMol and Chime for van der Waals radii in the spacefill rendering? How do RasMol and Chime determine which atoms in a PDB file are covalently bonded? How can arbitrary bonds be added or hidden? Why don't RasMol or Chime show most of the hydrogen bonds? > >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 >_____________________________________________________________________________ /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Re: hbonds and water molecules Date: Tue, 06 Mar 2001 20:28:44 -0500 To: rasmol@lists.umass.edu Deep View computes and displays all H-bonds, including those to solvent and ligands. Cheers! ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* ... the genetic variation found outside of Africa represents only a subset of that found within the African continent. From a genetic perspective, all humans are therefore Africans, either residing in Africa or in recent exile. Svante Paabo: "The Human Genome and Our View of Ourselves," Science, Volume 291, Number 5507, Issue of 16 Feb 2001, pp. 1219-1220. ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* Gale Rhodes Professor of Chemistry University of Southern Maine Portland, Maine, USA 207-780-4734 http://www.usm.maine.edu/~rhodes ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: When I say "all H-bonds", .... Date: Tue, 06 Mar 2001 20:49:32 -0500 To: rasmol@lists.umass.edu I mean all traditional X-H -- X H-bonds, in which X is an electronegative atom. Folks are beginning to realize that other kinds of H-bonds contribute to protein stability, including X--H-C, where C is a backbone alpha carbon, or X-H--phe, where phe is a face of an aromatic ring. And there are others. Nice little meeting report, "The Borders of Hydrogen Bonds" in the latest IUCR Newsletter (Vol 8, #4, 2000, p 19). Also see J. Mol. Biol. 305, 535, 2001, Steiner and Koellner. I don't know of any program that finds these. By the way, Deep View (Swiss-PdbViewer)'s H-bond criteria are adjustable in the Prefs: H-bonds dialog, and can be computed in models with or without hydrogens present. >From deep in the snow, Cheers! ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* ... the genetic variation found outside of Africa represents only a subset of that found within the African continent. From a genetic perspective, all humans are therefore Africans, either residing in Africa or in recent exile. Svante Paabo: "The Human Genome and Our View of Ourselves," Science, Volume 291, Number 5507, Issue of 16 Feb 2001, pp. 1219-1220. ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* Gale Rhodes Professor of Chemistry University of Southern Maine Portland, Maine, USA 207-780-4734 http://www.usm.maine.edu/~rhodes ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <200103070103.f2713a606051@chmls20.mediaone.net> X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id f27EcPx27503 ++++------+------+------+------+------+------+------+------+------+------+ From: Jean Richelle Subject: Re: hbonds and water molecules Date: Wed, 07 Mar 2001 15:37:21 +0100 To: rasmol@lists.umass.edu Think you for the answer. > >2) is it possible to calculate/display hbonds between water >>molecules, and between water molecules and peptidic or nucleic chains >>? > >Not directly in RasMol or Chime. >I don't know of any free web site where all hbonds can be calculated but I >wish I did! Let me add that I have a 2.6 variant, modified according to a suggestion by Roger Sayle, that calculate and display all the possible hbonds, i.e. internal to a chain and between chains, these "chains" being peptidic, nucleic or water ! As now, for version 2.7, it seems to exist a command to control the set of displayed hbonds, between or not between chain, I was wondering if another command could trigger the display of hbonds involving water. As I understand the answer is no ! 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-- References: <200103070103.f2713a606051@chmls20.mediaone.net> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: hbonds and water molecules Date: Wed, 07 Mar 2001 09:53:21 -0500 To: rasmol@lists.umass.edu At 03/06/2001, Gale Rhodes wrote: >Deep View computes and displays all H-bonds, including those to solvent and >ligands. Gale, can DeepView's hbond assignments be either 1. Put out as a text list of paired atom serial number's, or 2. Better yet, put out as CONECT records in the PDB file? (Then they can be displayed in Chime with 'set connect save') 3. Is it documented what algorithm DeepView uses? -Eric ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <200103070103.f2713a606051@chmls20.mediaone.net> ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Re: hbonds and water molecules Date: Wed, 07 Mar 2001 10:07:17 -0500 To: rasmol@lists.umass.edu >can DeepView's hbond assignments be either >1. Put out as a text list of paired atom serial number's, or no, not that I know of. >2. Better yet, put out as CONECT records in the PDB file? (Then they can be >displayed in Chime with 'set connect save') no. I don't think anyone uses CONECT records for noncovalent bonds. If they're in CONECT records, there would be no way to turn them off or distinguish them from covalent bonds. >3. Is it documented what algorithm DeepView uses? There's a manual coming soon, but I don't know its content on that subject. But just about as good, under Prefs:Hbonds you can see and change the geometric criteria Deep View uses to assign Hbonds (shown green) and weak Hbonds (shown gray). You can set criteria for both models with H absent (most X-ray models) or H-present (NMR, some very hi-res X-ray, and some theoretical). Hope this helps. Gale ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Gorga, Frank" Subject: RE: Stereochemistry Date: Wed, 07 Mar 2001 10:21:33 -0500 To: "'rasmol@lists.umass.edu'" David & list, May I, modestly ;-), suggest taking a look at my site "Isomers of Organic Compounds": http://webhost.bridgew.edu/fgorga/Stereochem/default.HTM This site concentrates on stereoisomers of organic compounds and thus does not do all you are interested in, but it is a start. List members may also be interested in my other sites: Introduction to Protein Structure (http://webhost.bridgew.edu/fgorga/proteins/default.htm) and The Ras Oncogene Product (http://webhost.bridgew.edu/fgorga/ras/default.htm). I just spent the last two days (snow-bound at home) updating these sites. The stereochemistry site was updated to give it a more modern look... I had not updated it since I put it together in 1996. Thus if you find a "bug" please let me know! All of the sites were updated to fix a problem when using Mac's to access them... my thanks to list member Tim Driscoll for pointing out both the problem and the solution. (Thanks Tim! Please let me know if the problem is fixed.) I would also publicly like to thank list member Gale Rhodes for pointing me towards Swiss PDB Viewer / Deep View and its ability to align two structures... I used this capability to prepare the Ras site. (Thanks Gale). As always, comments on any of my sites is greatly appreciated... peer review is an important method for improvement! --- Frank ----------------------------------------------------- Frank R. Gorga, Ph.D., Chair Department of Chemical Sciences Bridgewater State College Bridgewater, MA 02325 508-531-2827 / 508-531-1785 (fax) fgorga@bridgew.edu webhost.bridgew.edu/fgorga ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Steven Verhey Subject: RE: Stereochemistry Date: Wed, 07 Mar 2001 08:27:09 -0800 To: rasmol@lists.umass.edu Hi Frank, I've just taken a look at your oncogene product site, and I'm very impressed. It's brief enough to hold a beginning student's attention, but informative enough for more advanced students (or faculty!). If you don't mind I'd like to link to it for my advanced cell biology class. Thanks for all your work, and for sharing, Steve >>> FGORGA@bridgew.edu - 3/7/01 7:21 AM >>> David & list, May I, modestly ;-), suggest taking a look at my site "Isomers of Organic Compounds": http://webhost.bridgew.edu/fgorga/Stereochem/default.HTM This site concentrates on stereoisomers of organic compounds and thus does not do all you are interested in, but it is a start. List members may also be interested in my other sites: Introduction to Protein Structure (http://webhost.bridgew.edu/fgorga/proteins/default.htm) and The Ras Oncogene Product (http://webhost.bridgew.edu/fgorga/ras/default.htm). I just spent the last two days (snow-bound at home) updating these sites. The stereochemistry site was updated to give it a more modern look... I had not updated it since I put it together in 1996. Thus if you find a "bug" please let me know! All of the sites were updated to fix a problem when using Mac's to access them... my thanks to list member Tim Driscoll for pointing out both the problem and the solution. (Thanks Tim! Please let me know if the problem is fixed.) I would also publicly like to thank list member Gale Rhodes for pointing me towards Swiss PDB Viewer / Deep View and its ability to align two structures... I used this capability to prepare the Ras site. (Thanks Gale). As always, comments on any of my sites is greatly appreciated... peer review is an important method for improvement! --- Frank ----------------------------------------------------- Frank R. Gorga, Ph.D., Chair Department of Chemical Sciences Bridgewater State College Bridgewater, MA 02325 508-531-2827 / 508-531-1785 (fax) fgorga@bridgew.edu webhost.bridgew.edu/fgorga ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <200103070103.f2713a606051@chmls20.mediaone.net> X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id f28873x01135 ++++------+------+------+------+------+------+------+------+------+------+ From: Jean Richelle Subject: Re: hbonds and water molecules (correction) Date: Thu, 08 Mar 2001 09:06:21 +0100 To: rasmol@lists.umass.edu Sorry, I made a mistake in a previous message. >Let me add that I have a 2.6 variant, modified according to a >suggestion by Roger Sayle, that calculate and display all the >possible hbonds, i.e. internal to a chain and between chains, these >"chains" being peptidic, nucleic or water ! That modified version does not calculate (and display) hbonds involving water molecules. _____________________________________________________________________________ Jean Richelle Service de Conformation des Macromolécules Biologiques Tel: +32 02 650 3587 et de Bioinformatique - Université libre de Bruxelles FAX: +32 02 648 8954 av. F.D. Roosevelt 50 - CP160/16, B-1050 Bruxelles, Belgium _____________________________________________________________________________ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Tamas Gunda Subject: mol and pdb files in Chime Date: Thu, 08 Mar 2001 22:51:57 +0100 To: rasmol@lists.umass.edu Hi Chime Gurus, I came across an odd behaviour of Chime, when using the pdb or mol file of the same compound: the image displayed by Chime in the case of the pdb file looks to be rotated by 180 around the x axes. I embed here the two files (if reconstruction of the files proves to be difficult, I can send them as attachments). As the simplest way to try, drag and drop the files onto NS or IE with installed Chime 2.6 plugin, and see the result! Similar experiences by somebody else out there? Regards Dr Tamas E. Gunda Research for Antibiotics University of Debrecen H-4010 Debrecen, POBox 36 Hungary e-mail: tamasgunda@tigris.klte.hu http://dragon.klte.hu/~gundat gpen.mol file: ----cut here -------- Penicillin G MOL2MOL 03080121593D 41 43 0 0 0 0 0 0 0 0999 V2000 1.2578 -1.8240 0.6033 N 0 0 0 0 0 0 0 0 0 0.0632 -1.4609 1.2116 C 0 0 0 0 0 0 0 0 0 -0.6144 -1.9691 2.0835 O 0 0 0 0 0 0 0 0 0 1.1380 -0.8539 -0.4765 C 0 0 0 0 0 0 0 0 0 -0.2846 -0.5395 0.0506 C 0 0 0 0 0 0 0 0 0 2.5000 0.2713 -0.2899 S 0 0 0 0 0 0 0 0 0 3.4633 -1.2071 0.2372 C 0 0 0 0 0 0 0 0 0 4.7597 -0.7901 0.9583 C 0 0 0 0 0 0 0 0 0 3.8066 -1.9752 -1.0538 C 0 0 0 0 0 0 0 0 0 2.5771 -2.1006 1.1618 C 0 0 0 0 0 0 0 0 0 2.8608 -3.5790 1.0436 C 0 0 0 0 0 0 0 0 0 1.9344 -4.3726 0.8862 O 0 0 0 0 0 0 0 0 0 4.1166 -4.0243 1.1101 O 0 0 0 0 0 0 0 0 0 -0.6075 0.8471 0.3040 N 0 0 0 0 0 0 0 0 0 -1.8465 1.2882 0.1063 C 0 0 0 0 0 0 0 0 0 -2.7179 0.5169 -0.2920 O 0 0 0 0 0 0 0 0 0 -2.1832 2.7362 0.3709 C 0 0 0 0 0 0 0 0 0 -3.2951 3.1573 -0.5519 C 0 0 0 0 0 0 0 0 0 -3.5526 2.4273 -1.7112 C 0 0 0 0 0 0 0 0 0 -4.5824 2.8172 -2.5661 C 0 0 0 0 0 0 0 0 0 -5.3544 3.9372 -2.2615 C 0 0 0 0 0 0 0 0 0 -5.0970 4.6672 -1.1025 C 0 0 0 0 0 0 0 0 0 -4.0672 4.2774 -0.2476 C 0 0 0 0 0 0 0 0 0 1.3127 -1.1642 -1.5248 H 0 0 0 0 0 0 0 0 0 -1.1164 -0.8325 -0.6040 H 0 0 0 0 0 0 0 0 0 4.5943 -0.7776 1.9443 H 0 0 0 0 0 0 0 0 0 5.0271 0.1215 0.6459 H 0 0 0 0 0 0 0 0 0 5.4795 -1.4496 0.7415 H 0 0 0 0 0 0 0 0 0 4.6121 -2.5446 -0.8894 H 0 0 0 0 0 0 0 0 0 3.9968 -1.3178 -1.7829 H 0 0 0 0 0 0 0 0 0 3.0287 -2.5501 -1.3074 H 0 0 0 0 0 0 0 0 0 2.5883 -1.8026 2.2102 H 0 0 0 0 0 0 0 0 0 4.1146 -4.9799 1.0175 H 0 0 0 0 0 0 0 0 0 0.1009 1.4743 0.6278 H 0 0 0 0 0 0 0 0 0 -1.3711 3.2951 0.2038 H 0 0 0 0 0 0 0 0 0 -2.4745 2.8341 1.3225 H 0 0 0 0 0 0 0 0 0 -2.9519 1.5563 -1.9479 H 0 0 0 0 0 0 0 0 0 -4.7825 2.2495 -3.4675 H 0 0 0 0 0 0 0 0 0 -6.1551 4.2402 -2.9264 H 0 0 0 0 0 0 0 0 0 -5.6973 5.5379 -0.8656 H 0 0 0 0 0 0 0 0 0 -3.8666 4.8449 0.6541 H 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 4 1 0 0 0 0 1 10 1 0 0 0 0 2 3 2 0 0 0 0 2 5 1 0 0 0 0 4 5 1 0 0 0 0 4 6 1 0 0 0 0 4 24 1 0 0 0 0 5 14 1 0 0 0 0 5 25 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 7 10 1 0 0 0 0 8 26 1 0 0 0 0 8 27 1 0 0 0 0 8 28 1 0 0 0 0 9 29 1 0 0 0 0 9 30 1 0 0 0 0 9 31 1 0 0 0 0 10 11 1 0 0 0 0 10 32 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 13 33 1 0 0 0 0 14 15 1 0 0 0 0 14 34 1 0 0 0 0 15 16 2 0 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 17 35 1 0 0 0 0 17 36 1 0 0 0 0 18 19 2 0 0 0 0 18 23 1 0 0 0 0 19 20 1 0 0 0 0 19 37 1 0 0 0 0 20 21 2 0 0 0 0 20 38 1 0 0 0 0 21 22 1 0 0 0 0 21 39 1 0 0 0 0 22 23 2 0 0 0 0 22 40 1 0 0 0 0 23 41 1 0 0 0 0 M END -------cut here -------------------------- gpen.pdb file: --------cut here ------------------------ HEADER penicillin G COMPND penicillin G SOURCE GPEN.MOL SOURCE Created by Mol2Mol 4.0 test alfa 56 SOURCE 21:19:34, Thursday, Mar 08, 2001 REMARK This file contains 1-2-3 bond type info (RasMol/Chime pdb subtype) HETATM 1 N 1 1.258 -1.824 0.603 N HETATM 2 C 1 0.063 -1.461 1.212 C HETATM 3 O 1 -0.614 -1.969 2.083 O HETATM 4 C 1 1.138 -0.854 -0.477 C HETATM 5 C 1 -0.285 -0.539 0.051 C HETATM 6 S 1 2.500 0.271 -0.290 S HETATM 7 C 1 3.463 -1.207 0.237 C HETATM 8 C 1 4.760 -0.790 0.958 C HETATM 9 C 1 3.807 -1.975 -1.054 C HETATM 10 C 1 2.577 -2.101 1.162 C HETATM 11 C 1 2.861 -3.579 1.044 C HETATM 12 O 1 1.934 -4.373 0.886 O HETATM 13 O 1 4.117 -4.024 1.110 O HETATM 14 N 1 -0.608 0.847 0.304 N HETATM 15 C 1 -1.847 1.288 0.106 C HETATM 16 O 1 -2.718 0.517 -0.292 O HETATM 17 C 1 -2.183 2.736 0.371 C HETATM 18 C 1 -3.295 3.157 -0.552 C HETATM 19 C 1 -3.553 2.427 -1.711 C HETATM 20 C 1 -4.582 2.817 -2.566 C HETATM 21 C 1 -5.354 3.937 -2.261 C HETATM 22 C 1 -5.097 4.667 -1.102 C HETATM 23 C 1 -4.067 4.277 -0.248 C HETATM 24 H 1 1.313 -1.164 -1.525 H HETATM 25 H 1 -1.116 -0.832 -0.604 H HETATM 26 H 1 4.594 -0.778 1.944 H HETATM 27 H 1 5.027 0.122 0.646 H HETATM 28 H 1 5.479 -1.450 0.742 H HETATM 29 H 1 4.612 -2.545 -0.889 H HETATM 30 H 1 3.997 -1.318 -1.783 H HETATM 31 H 1 3.029 -2.550 -1.307 H HETATM 32 H 1 2.588 -1.803 2.210 H HETATM 33 H 1 4.115 -4.980 1.018 H HETATM 34 H 1 0.101 1.474 0.628 H HETATM 35 H 1 -1.371 3.295 0.204 H HETATM 36 H 1 -2.474 2.834 1.322 H HETATM 37 H 1 -2.952 1.556 -1.948 H HETATM 38 H 1 -4.782 2.250 -3.467 H HETATM 39 H 1 -6.155 4.240 -2.926 H HETATM 40 H 1 -5.697 5.538 -0.866 H HETATM 41 H 1 -3.867 4.845 0.654 H CONECT 1 2 4 10 CONECT 2 1 3 3 5 CONECT 3 2 2 CONECT 4 1 5 6 24 CONECT 5 2 4 14 25 CONECT 6 4 7 CONECT 7 6 8 9 10 CONECT 8 7 26 27 28 CONECT 9 7 29 30 31 CONECT 10 1 7 11 32 CONECT 11 10 12 12 13 CONECT 12 11 11 CONECT 13 11 33 CONECT 14 5 15 34 CONECT 15 14 16 16 16 CONECT 15 17 CONECT 16 15 15 15 CONECT 17 15 18 35 36 CONECT 18 17 19 23 CONECT 19 18 20 37 CONECT 20 19 21 38 CONECT 21 20 22 39 CONECT 22 21 23 40 CONECT 23 18 22 41 CONECT 24 4 CONECT 25 5 CONECT 26 8 CONECT 27 8 CONECT 28 8 CONECT 29 9 CONECT 30 9 CONECT 31 9 CONECT 32 10 CONECT 33 13 CONECT 34 14 CONECT 35 17 CONECT 36 17 CONECT 37 19 CONECT 38 20 CONECT 39 21 CONECT 40 22 CONECT 41 23 END ---------cut here ------------------------ MDL V3000 mol file format, looks also OK: --------- cut here ----------------- Penicillin G MOL2MOL 03080122463D 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 41 43 0 0 0 M V30 BEGIN ATOM M V30 1 N 1.2578 -1.8240 0.6033 0 M V30 2 C 0.0632 -1.4609 1.2116 0 M V30 3 O -0.6144 -1.9691 2.0835 0 M V30 4 C 1.1380 -0.8539 -0.4765 0 M V30 5 C -0.2846 -0.5395 0.0506 0 M V30 6 S 2.5000 0.2713 -0.2899 0 M V30 7 C 3.4633 -1.2071 0.2372 0 M V30 8 C 4.7597 -0.7901 0.9583 0 M V30 9 C 3.8066 -1.9752 -1.0538 0 M V30 10 C 2.5771 -2.1006 1.1618 0 M V30 11 C 2.8608 -3.5790 1.0436 0 M V30 12 O 1.9344 -4.3726 0.8862 0 M V30 13 O 4.1166 -4.0243 1.1101 0 M V30 14 N -0.6075 0.8471 0.3040 0 M V30 15 C -1.8465 1.2882 0.1063 0 M V30 16 O -2.7179 0.5169 -0.2920 0 M V30 17 C -2.1832 2.7362 0.3709 0 M V30 18 C -3.2951 3.1573 -0.5519 0 M V30 19 C -3.5526 2.4273 -1.7112 0 M V30 20 C -4.5824 2.8172 -2.5661 0 M V30 21 C -5.3544 3.9372 -2.2615 0 M V30 22 C -5.0970 4.6672 -1.1025 0 M V30 23 C -4.0672 4.2774 -0.2476 0 M V30 24 H 1.3127 -1.1642 -1.5248 0 M V30 25 H -1.1164 -0.8325 -0.6040 0 M V30 26 H 4.5943 -0.7776 1.9443 0 M V30 27 H 5.0271 0.1215 0.6459 0 M V30 28 H 5.4795 -1.4496 0.7415 0 M V30 29 H 4.6121 -2.5446 -0.8894 0 M V30 30 H 3.9968 -1.3178 -1.7829 0 M V30 31 H 3.0287 -2.5501 -1.3074 0 M V30 32 H 2.5883 -1.8026 2.2102 0 M V30 33 H 4.1146 -4.9799 1.0175 0 M V30 34 H 0.1009 1.4743 0.6278 0 M V30 35 H -1.3711 3.2951 0.2038 0 M V30 36 H -2.4745 2.8341 1.3225 0 M V30 37 H -2.9519 1.5563 -1.9479 0 M V30 38 H -4.7825 2.2495 -3.4675 0 M V30 39 H -6.1551 4.2402 -2.9264 0 M V30 40 H -5.6973 5.5379 -0.8656 0 M V30 41 H -3.8666 4.8449 0.6541 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 1 4 M V30 3 1 1 10 M V30 4 2 2 3 M V30 5 1 2 5 M V30 6 1 4 5 M V30 7 1 4 6 M V30 8 1 4 24 M V30 9 1 5 14 M V30 10 1 5 25 M V30 11 1 6 7 M V30 12 1 7 8 M V30 13 1 7 9 M V30 14 1 7 10 M V30 15 1 8 26 M V30 16 1 8 27 M V30 17 1 8 28 M V30 18 1 9 29 M V30 19 1 9 30 M V30 20 1 9 31 M V30 21 1 10 11 M V30 22 1 10 32 M V30 23 2 11 12 M V30 24 1 11 13 M V30 25 1 13 33 M V30 26 1 14 15 M V30 27 1 14 34 M V30 28 2 15 16 M V30 29 1 15 17 M V30 30 1 17 18 M V30 31 1 17 35 M V30 32 1 17 36 M V30 33 2 18 19 M V30 34 1 18 23 M V30 35 1 19 20 M V30 36 1 19 37 M V30 37 2 20 21 M V30 38 1 20 38 M V30 39 1 21 22 M V30 40 1 21 39 M V30 41 2 22 23 M V30 42 1 22 40 M V30 43 1 23 41 M V30 END BOND M V30 END CTAB M END ----------------------------- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Robert Dickey Subject: RE: mol and pdb files in Chime Date: Thu, 08 Mar 2001 15:54:07 -0800 To: "'rasmol@lists.umass.edu'" Please send the files as attachments. Thanks, Bob Dickey -----Original Message----- Sent: Thursday, March 08, 2001 1:52 PM From: Tamas Gunda [mailto:tamasgunda@tigris.klte.hu] Subject: mol and pdb files in Chime To: rasmol@lists.umass.edu Hi Chime Gurus, I came across an odd behaviour of Chime, when using the pdb or mol file of the same compound: the image displayed by Chime in the case of the pdb file looks to be rotated by 180 around the x axes. I embed here the two files (if reconstruction of the files proves to be difficult, I can send them as attachments). As the simplest way to try, drag and drop the files onto NS or IE with installed Chime 2.6 plugin, and see the result! Similar experiences by somebody else out there? Regards Dr Tamas E. Gunda Research for Antibiotics University of Debrecen H-4010 Debrecen, POBox 36 Hungary e-mail: tamasgunda@tigris.klte.hu http://dragon.klte.hu/~gundat gpen.mol file: ----cut here -------- Penicillin G MOL2MOL 03080121593D 41 43 0 0 0 0 0 0 0 0999 V2000 1.2578 -1.8240 0.6033 N 0 0 0 0 0 0 0 0 0 0.0632 -1.4609 1.2116 C 0 0 0 0 0 0 0 0 0 -0.6144 -1.9691 2.0835 O 0 0 0 0 0 0 0 0 0 1.1380 -0.8539 -0.4765 C 0 0 0 0 0 0 0 0 0 -0.2846 -0.5395 0.0506 C 0 0 0 0 0 0 0 0 0 2.5000 0.2713 -0.2899 S 0 0 0 0 0 0 0 0 0 3.4633 -1.2071 0.2372 C 0 0 0 0 0 0 0 0 0 4.7597 -0.7901 0.9583 C 0 0 0 0 0 0 0 0 0 3.8066 -1.9752 -1.0538 C 0 0 0 0 0 0 0 0 0 2.5771 -2.1006 1.1618 C 0 0 0 0 0 0 0 0 0 2.8608 -3.5790 1.0436 C 0 0 0 0 0 0 0 0 0 1.9344 -4.3726 0.8862 O 0 0 0 0 0 0 0 0 0 4.1166 -4.0243 1.1101 O 0 0 0 0 0 0 0 0 0 -0.6075 0.8471 0.3040 N 0 0 0 0 0 0 0 0 0 -1.8465 1.2882 0.1063 C 0 0 0 0 0 0 0 0 0 -2.7179 0.5169 -0.2920 O 0 0 0 0 0 0 0 0 0 -2.1832 2.7362 0.3709 C 0 0 0 0 0 0 0 0 0 -3.2951 3.1573 -0.5519 C 0 0 0 0 0 0 0 0 0 -3.5526 2.4273 -1.7112 C 0 0 0 0 0 0 0 0 0 -4.5824 2.8172 -2.5661 C 0 0 0 0 0 0 0 0 0 -5.3544 3.9372 -2.2615 C 0 0 0 0 0 0 0 0 0 -5.0970 4.6672 -1.1025 C 0 0 0 0 0 0 0 0 0 -4.0672 4.2774 -0.2476 C 0 0 0 0 0 0 0 0 0 1.3127 -1.1642 -1.5248 H 0 0 0 0 0 0 0 0 0 -1.1164 -0.8325 -0.6040 H 0 0 0 0 0 0 0 0 0 4.5943 -0.7776 1.9443 H 0 0 0 0 0 0 0 0 0 5.0271 0.1215 0.6459 H 0 0 0 0 0 0 0 0 0 5.4795 -1.4496 0.7415 H 0 0 0 0 0 0 0 0 0 4.6121 -2.5446 -0.8894 H 0 0 0 0 0 0 0 0 0 3.9968 -1.3178 -1.7829 H 0 0 0 0 0 0 0 0 0 3.0287 -2.5501 -1.3074 H 0 0 0 0 0 0 0 0 0 2.5883 -1.8026 2.2102 H 0 0 0 0 0 0 0 0 0 4.1146 -4.9799 1.0175 H 0 0 0 0 0 0 0 0 0 0.1009 1.4743 0.6278 H 0 0 0 0 0 0 0 0 0 -1.3711 3.2951 0.2038 H 0 0 0 0 0 0 0 0 0 -2.4745 2.8341 1.3225 H 0 0 0 0 0 0 0 0 0 -2.9519 1.5563 -1.9479 H 0 0 0 0 0 0 0 0 0 -4.7825 2.2495 -3.4675 H 0 0 0 0 0 0 0 0 0 -6.1551 4.2402 -2.9264 H 0 0 0 0 0 0 0 0 0 -5.6973 5.5379 -0.8656 H 0 0 0 0 0 0 0 0 0 -3.8666 4.8449 0.6541 H 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 4 1 0 0 0 0 1 10 1 0 0 0 0 2 3 2 0 0 0 0 2 5 1 0 0 0 0 4 5 1 0 0 0 0 4 6 1 0 0 0 0 4 24 1 0 0 0 0 5 14 1 0 0 0 0 5 25 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 7 10 1 0 0 0 0 8 26 1 0 0 0 0 8 27 1 0 0 0 0 8 28 1 0 0 0 0 9 29 1 0 0 0 0 9 30 1 0 0 0 0 9 31 1 0 0 0 0 10 11 1 0 0 0 0 10 32 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 13 33 1 0 0 0 0 14 15 1 0 0 0 0 14 34 1 0 0 0 0 15 16 2 0 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 17 35 1 0 0 0 0 17 36 1 0 0 0 0 18 19 2 0 0 0 0 18 23 1 0 0 0 0 19 20 1 0 0 0 0 19 37 1 0 0 0 0 20 21 2 0 0 0 0 20 38 1 0 0 0 0 21 22 1 0 0 0 0 21 39 1 0 0 0 0 22 23 2 0 0 0 0 22 40 1 0 0 0 0 23 41 1 0 0 0 0 M END -------cut here -------------------------- gpen.pdb file: --------cut here ------------------------ HEADER penicillin G COMPND penicillin G SOURCE GPEN.MOL SOURCE Created by Mol2Mol 4.0 test alfa 56 SOURCE 21:19:34, Thursday, Mar 08, 2001 REMARK This file contains 1-2-3 bond type info (RasMol/Chime pdb subtype) HETATM 1 N 1 1.258 -1.824 0.603 N HETATM 2 C 1 0.063 -1.461 1.212 C HETATM 3 O 1 -0.614 -1.969 2.083 O HETATM 4 C 1 1.138 -0.854 -0.477 C HETATM 5 C 1 -0.285 -0.539 0.051 C HETATM 6 S 1 2.500 0.271 -0.290 S HETATM 7 C 1 3.463 -1.207 0.237 C HETATM 8 C 1 4.760 -0.790 0.958 C HETATM 9 C 1 3.807 -1.975 -1.054 C HETATM 10 C 1 2.577 -2.101 1.162 C HETATM 11 C 1 2.861 -3.579 1.044 C HETATM 12 O 1 1.934 -4.373 0.886 O HETATM 13 O 1 4.117 -4.024 1.110 O HETATM 14 N 1 -0.608 0.847 0.304 N HETATM 15 C 1 -1.847 1.288 0.106 C HETATM 16 O 1 -2.718 0.517 -0.292 O HETATM 17 C 1 -2.183 2.736 0.371 C HETATM 18 C 1 -3.295 3.157 -0.552 C HETATM 19 C 1 -3.553 2.427 -1.711 C HETATM 20 C 1 -4.582 2.817 -2.566 C HETATM 21 C 1 -5.354 3.937 -2.261 C HETATM 22 C 1 -5.097 4.667 -1.102 C HETATM 23 C 1 -4.067 4.277 -0.248 C HETATM 24 H 1 1.313 -1.164 -1.525 H HETATM 25 H 1 -1.116 -0.832 -0.604 H HETATM 26 H 1 4.594 -0.778 1.944 H HETATM 27 H 1 5.027 0.122 0.646 H HETATM 28 H 1 5.479 -1.450 0.742 H HETATM 29 H 1 4.612 -2.545 -0.889 H HETATM 30 H 1 3.997 -1.318 -1.783 H HETATM 31 H 1 3.029 -2.550 -1.307 H HETATM 32 H 1 2.588 -1.803 2.210 H HETATM 33 H 1 4.115 -4.980 1.018 H HETATM 34 H 1 0.101 1.474 0.628 H HETATM 35 H 1 -1.371 3.295 0.204 H HETATM 36 H 1 -2.474 2.834 1.322 H HETATM 37 H 1 -2.952 1.556 -1.948 H HETATM 38 H 1 -4.782 2.250 -3.467 H HETATM 39 H 1 -6.155 4.240 -2.926 H HETATM 40 H 1 -5.697 5.538 -0.866 H HETATM 41 H 1 -3.867 4.845 0.654 H CONECT 1 2 4 10 CONECT 2 1 3 3 5 CONECT 3 2 2 CONECT 4 1 5 6 24 CONECT 5 2 4 14 25 CONECT 6 4 7 CONECT 7 6 8 9 10 CONECT 8 7 26 27 28 CONECT 9 7 29 30 31 CONECT 10 1 7 11 32 CONECT 11 10 12 12 13 CONECT 12 11 11 CONECT 13 11 33 CONECT 14 5 15 34 CONECT 15 14 16 16 16 CONECT 15 17 CONECT 16 15 15 15 CONECT 17 15 18 35 36 CONECT 18 17 19 23 CONECT 19 18 20 37 CONECT 20 19 21 38 CONECT 21 20 22 39 CONECT 22 21 23 40 CONECT 23 18 22 41 CONECT 24 4 CONECT 25 5 CONECT 26 8 CONECT 27 8 CONECT 28 8 CONECT 29 9 CONECT 30 9 CONECT 31 9 CONECT 32 10 CONECT 33 13 CONECT 34 14 CONECT 35 17 CONECT 36 17 CONECT 37 19 CONECT 38 20 CONECT 39 21 CONECT 40 22 CONECT 41 23 END ---------cut here ------------------------ MDL V3000 mol file format, looks also OK: --------- cut here ----------------- Penicillin G MOL2MOL 03080122463D 0 0 0 0 0 0 V3000 M V30 BEGIN CTAB M V30 COUNTS 41 43 0 0 0 M V30 BEGIN ATOM M V30 1 N 1.2578 -1.8240 0.6033 0 M V30 2 C 0.0632 -1.4609 1.2116 0 M V30 3 O -0.6144 -1.9691 2.0835 0 M V30 4 C 1.1380 -0.8539 -0.4765 0 M V30 5 C -0.2846 -0.5395 0.0506 0 M V30 6 S 2.5000 0.2713 -0.2899 0 M V30 7 C 3.4633 -1.2071 0.2372 0 M V30 8 C 4.7597 -0.7901 0.9583 0 M V30 9 C 3.8066 -1.9752 -1.0538 0 M V30 10 C 2.5771 -2.1006 1.1618 0 M V30 11 C 2.8608 -3.5790 1.0436 0 M V30 12 O 1.9344 -4.3726 0.8862 0 M V30 13 O 4.1166 -4.0243 1.1101 0 M V30 14 N -0.6075 0.8471 0.3040 0 M V30 15 C -1.8465 1.2882 0.1063 0 M V30 16 O -2.7179 0.5169 -0.2920 0 M V30 17 C -2.1832 2.7362 0.3709 0 M V30 18 C -3.2951 3.1573 -0.5519 0 M V30 19 C -3.5526 2.4273 -1.7112 0 M V30 20 C -4.5824 2.8172 -2.5661 0 M V30 21 C -5.3544 3.9372 -2.2615 0 M V30 22 C -5.0970 4.6672 -1.1025 0 M V30 23 C -4.0672 4.2774 -0.2476 0 M V30 24 H 1.3127 -1.1642 -1.5248 0 M V30 25 H -1.1164 -0.8325 -0.6040 0 M V30 26 H 4.5943 -0.7776 1.9443 0 M V30 27 H 5.0271 0.1215 0.6459 0 M V30 28 H 5.4795 -1.4496 0.7415 0 M V30 29 H 4.6121 -2.5446 -0.8894 0 M V30 30 H 3.9968 -1.3178 -1.7829 0 M V30 31 H 3.0287 -2.5501 -1.3074 0 M V30 32 H 2.5883 -1.8026 2.2102 0 M V30 33 H 4.1146 -4.9799 1.0175 0 M V30 34 H 0.1009 1.4743 0.6278 0 M V30 35 H -1.3711 3.2951 0.2038 0 M V30 36 H -2.4745 2.8341 1.3225 0 M V30 37 H -2.9519 1.5563 -1.9479 0 M V30 38 H -4.7825 2.2495 -3.4675 0 M V30 39 H -6.1551 4.2402 -2.9264 0 M V30 40 H -5.6973 5.5379 -0.8656 0 M V30 41 H -3.8666 4.8449 0.6541 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 1 4 M V30 3 1 1 10 M V30 4 2 2 3 M V30 5 1 2 5 M V30 6 1 4 5 M V30 7 1 4 6 M V30 8 1 4 24 M V30 9 1 5 14 M V30 10 1 5 25 M V30 11 1 6 7 M V30 12 1 7 8 M V30 13 1 7 9 M V30 14 1 7 10 M V30 15 1 8 26 M V30 16 1 8 27 M V30 17 1 8 28 M V30 18 1 9 29 M V30 19 1 9 30 M V30 20 1 9 31 M V30 21 1 10 11 M V30 22 1 10 32 M V30 23 2 11 12 M V30 24 1 11 13 M V30 25 1 13 33 M V30 26 1 14 15 M V30 27 1 14 34 M V30 28 2 15 16 M V30 29 1 15 17 M V30 30 1 17 18 M V30 31 1 17 35 M V30 32 1 17 36 M V30 33 2 18 19 M V30 34 1 18 23 M V30 35 1 19 20 M V30 36 1 19 37 M V30 37 2 20 21 M V30 38 1 20 38 M V30 39 1 21 22 M V30 40 1 21 39 M V30 41 2 22 23 M V30 42 1 22 40 M V30 43 1 23 41 M V30 END BOND M V30 END CTAB M END ----------------------------- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: NO ATTACHMENTS TO THE LIST PLEASE Date: Fri, 09 Mar 2001 16:14:36 -0500 To: rasmol@lists.umass.edu At 03/08/2001, you wrote: >Please send the files as attachments. > >Thanks, >Bob Dickey OK to send attachements to INDIVIDUALS who request them, but ... Please DO NOT send any attachments to the list, ever. Most of the 600 subscribers won't want the attachments. And it spreads viruses. Put the files on a server and give the URL to the list for downloading. We have attempted to block all attachments automatically but so far nobody has tested this. As most of you know, the PDB list now blocks all messages with attachments due to a recent spread of a virus in this manner. Thanks, -Eric ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Robert Dickey Subject: RE: NO ATTACHMENTS TO THE LIST PLEASE Date: Fri, 09 Mar 2001 14:03:14 -0800 To: "'rasmol@lists.umass.edu'" Quite right. I requested them individually in a subsequent message. Sorry for the confusion. Bob Dickey -----Original Message----- Sent: Friday, March 09, 2001 1:15 PM From: Eric Martz [mailto:emartz@microbio.umass.edu] Subject: NO ATTACHMENTS TO THE LIST PLEASE To: rasmol@lists.umass.edu At 03/08/2001, you wrote: >Please send the files as attachments. > >Thanks, >Bob Dickey OK to send attachements to INDIVIDUALS who request them, but ... Please DO NOT send any attachments to the list, ever. Most of the 600 subscribers won't want the attachments. And it spreads viruses. Put the files on a server and give the URL to the list for downloading. We have attempted to block all attachments automatically but so far nobody has tested this. As most of you know, the PDB list now blocks all messages with attachments due to a recent spread of a virus in this manner. Thanks, -Eric ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer 1.81 released with faster cable/DSL access. Date: Tue, 13 Mar 2001 13:21:57 -0500 To: rasmol@lists.umass.edu I have released version 1.81 beta of the Protein Explorer freeware (http://proteinexplorer.org). 1. A QuickTour document has been added. It offers beginners an overview of how to visualize the main structural features of a protein in about an hour (http://molvis.sdsc.edu/protexpl/qtour.htm). I presented this QuickTour at a satisfactory pace in a 50 minute class yesterday. 2. Also new is a troubleshooting guide for getting Chime and Protein Explorer to work in problematic instances; it covers both Windows and Macintosh (http://molvis.sdsc.edu/protexpl/troubles.htm). 3. Protein Explorer 1.8x Beta is newly mirrored at the San Diego Supercomputer Center, in addition to the primary site at the Univesity of Massachusetts. This was done because UMass has an extremely poor link to Internet cable and wireless, and there is no evidence that this will be fixed anytime soon. Loading Protein Explorer from UMass via cable modem or DSL is painfully slow. To access the San Diego mirror, go to http://proteinexplorer.org and click on the San Diego mirror link just below the FrontDoor title. I don't expect people with direct Internet connections to find the San Diego site to be faster, but I'll be interested in hearing your impressions. When you begin a Protein Explorer session, if the startup page takes more than 8 seconds to load, and if PE is coming from UMass, a small window will automatically pop up offering the San Diego mirror site as a faster alternative. (In my tests via cable modem or direct Internet connection, this page loads in 2-3 sec from San Diego, with the cache cleared.) If anyone has problems with this new feature, please let me know. Several minor improvements and clarifications were also made in this version -- click on What's New at the FrontDoor page for a list. The new version is downloadable for off-line use, or fastest possible responses when on-line. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: xyz file creation Date: Wed, 14 Mar 2001 12:48:47 -0500 To: RasMol List hello, does anyone know of any resources explaining how to generate xyz animation files? tia, tim _________________________________________ timothy driscoll molvisions.com - 3D molecular visualization 80 fiske ave, waltham, ma 02453 usa e: driscoll@molvisions.com p: 508.864.6516 (usa) 781.899.3873 (international) f: 781.899.4108 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: <20010314124847-r01010600-5382dc3b@216.254.100.238> ++++------+------+------+------+------+------+------+------+------+------+ From: Hens Borkent Subject: Re: xyz file creation Date: Thu, 15 Mar 2001 09:35:55 +0100 To: rasmol@lists.umass.edu timothy driscoll wrote: > > hello, > > does anyone know of any resources explaining how to generate xyz animation > files? > 1. We wrote scripts (perl, csh) that convert MOPAC output into multiple xyz-files. MOPAC is convenient for scanning variables, reaction coordinates, etc. The scripts also allow a selection from the very many structures resulting from a mopac IRC calculation, reversal of the order, and even interchanging the first two structures, as Chime does the same with m-xyz files. Contact us if interested. In fact we do a lot more, with data written to and from the second line of the xyz-files, but that's another matter. See http://www.cmbi.kun.nl/wetche/organic/ select the 'editor' and scroll to the bottom for a link to m-xyz examples. 2. m-xyz files of vibrations can easily be made in MOLDEN, that reads Gaussian or MOPAC frequency files and writes the animation to m-xyz when started with the command flag -w1. See http://www.cmbi.kun.nl/~schaft/molden/molden.html Hope this is useful. Hens Borkent -- ***** J.H. (Hens) Borkent, CMBI, *CMBI * P.O. Box 9010, 6500 GL Nijmegen, The Netherlands * / * Tel 0031 24 36 52137 Fax 0031 24 36 52977 * CMBI* http://www.cmbi.kun.nl/ ***** Centre for Molecular and Biomolecular Informatics ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <20010314124847-r01010600-5382dc3b@216.254.100.238> ++++------+------+------+------+------+------+------+------+------+------+ From: Me Subject: Re: xyz file creation Date: Thu, 15 Mar 2001 07:42:25 -0800 To: rasmol@lists.umass.edu At 09:35 AM 3/15/01 +0100, you wrote: >timothy driscoll wrote: > > > > hello, > > > > does anyone know of any resources explaining how to generate xyz animation > > files? > > There's quite a few ways to do it - see for example http://world.std.com/~wware/xyz2rgb.html I used Re_view quite a bit myself with good results - the author provides a free version for educational use, and it doesn't require Spartan or other mol modeling suites. OTOH if you have access to Spartan it is an excellent modelling program and there are ancillary programs such as Vibread (eg http://www.chem.umass.edu/~nermmw/Spectra/1.htm ) that will convert the thermal data into xyz animation files. I had a lot of fun using povray to convert these into molecular movies - these can be mpeg formatted for web apps...cheers! ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer 1.85 released with Animations Date: Fri, 16 Mar 2001 20:11:50 -0500 To: rasmol@lists.umass.edu Cc: coon@codon.nih.gov, Klein@helix.nih.gov I have just released version 1.85 beta of the Protein Explorer freeware (http://proteinexplorer.org). The ability to display animations of conformational changes of proteins has been greatly enhanced. At the FrontDoor, click on the animated image of an EF Hand binding Calcium for a full explanation with examples. Animations (ensembles of models in PDB files, demarcated as NMR models) can now be played faster, and without crashing Netscape. The animation can be rendered in a variety of ways (backbone, smoothed trace, cartoon, wireframe) and various color schemes applied, all from convenience buttons. Animations are now displayed in a separate new window. These windows can be saved as HTML files, and the animation replayed in Netscape (or even in Internet Explorer) without running Protein Explorer. Multiple animations can be run simultaneously. Animations can be zoomed, centered, be toggled into/out of stereo, or have the background toggled between white and black, all while running. A script of Chime commands is generated for each animation. The script is displayed in a window, where it can be edited. Thus, the display and color scheme can be customized. Examples are provided. Included in the page of examples (accessed by clicking on the animated EF Hand on the FrontDoor) are several morphs. After selecting one and waiting for Protein Explorer to complete its startup, you simply press a button labeled "Animate" (just one click): 1. EF hand binding calcium, sidechains displayable. (From recoverin.) 2. Recoverin expelling N-terminal myristic acid upon binding calcium. 3. Calmodulin binding peptide. These were previously available in the Protein Morpher. New morphs have been added: 4. Serotonin N-Acetyl transferase binding inhibitory substrate analog. A loop moves out of the substrate binding pocket to accomodate substrate. (Thanks to Steve Coon and Dave Klein at NIH for getting me interested in this one.) 5. Staphylococcal accessory transcriptional regulator A (SARA) binding DNA, with large conformational changes, as described in January's Nature by Schumacher et al. (http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&lis t_uids=11196648&dopt=Abstract) Thanks to the Morph Server of Werner Krebs and Mark Gerstein at Yale, where examples #1 and #4 were done including all sidechains. -Eric Martz /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <3A1036E0.1556B6FB@jmu.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Ian Musgrave & Peta O'Donohue" Subject: Re: Can I target more than one chime with the same button? Date: Tue, 20 Mar 2001 13:47:56 -1100 To: rasmol@lists.umass.edu G'Day All This is a thread from many moons ago. Has anyone got this method to work? I have tired to use it in in this simple page http://home.mira.net/~reynella/chime/adr_tut.htm but the first chime plug-in only responds. Any ideas? I'd rather not have to go to JAVA to fix this up. At 08:23 13/11/00, Tim wrote: >on 11.13.00 1:45 PM, Cindy Klevickis at klevicca@jmu.edu wrote: > > Here is the web page I'm working on: > > http://www.isat.jmu.edu/users/klevicca/shoebox/glucose.html > > > > I have six water molecules that I want to highlight all at once. They are > > each separate chimes but I want > > them all to respond to the same button. Has anyone done this before? > >I believe that if you name all of your plugins the same name (the ones that >hold the water molecules), you can send one script to them all using >TARGET="name_of_plugins" in the button's embed tag. I don't know if you >want to do this, b/c you will lose the ability to access each plugin >separately, but there it is anyway. Cheers! Ian Ian Musgrave PhD, Senior Lecturer Dept Clin Expt Pharmacology, Adelaide University, South Australia 5005 Email ian.musgrave@adelaide.edu.au phone +61 8 8303 3905 Fax +61 8 8224 0685 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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 "Ian Musgrave & Peta O'Donohue" ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: RE: Can I target more than one chime with the same button Date: Tue, 20 Mar 2001 09:25:00 -0500 To: rasmol@lists.umass.edu, Ian I have been trying to teach myself javasript so I took on your project as a "homework" assignment for myself. You can do this with javacript and button callback. I downloaded your page and made these changes: On the buttons, I removed the target and script tags and replaced them with a ButtonCallback=functionname tag. This executes the javascipt function when the button is pushed. There is a separate function for each button. Each button is given a name to match the function and I made the buttons radio buttons. I then renamed the chime plugins to have their own names, adr, nor, and ace. Between the head and body of the HTML text I added Javascript. There are five functions, one refering to each of the five button names. They all work the same and use these commands: function reset(nameofbutton,executeYet) { commands="script commands here unique to each button" document.adr.executeScript(commands); document.nor.executeScript(commands); document.ace.executeScript(commands); } I also made a few other minor changes in formatting. I posted the results at http://www.gvsu.edu/carlsont/adr_tut2.htm There is also a way to get the rotation of the molecules using the mouse to act on all three images but I can't recall how to do that. Perhaps someone else can help. There may be other (and better) ways to do it, but this works. It would be nice to have a single toggle button for the rotation, but I'm not sure how to use toggle buttons with ButtonCallback yet. todd Todd Carlson Dept of Chemistry Grand Valley State University. ______________________________ Reply Separator _________________________________ Author: "Ian Musgrave & Peta O'Donohue" at OFFICE ++++------+------+------+------+------+------+------+------+------+------+ Subject: Re: Can I target more than one chime with the same button? Date: 03/20/2001 7:47 PM G'Day All This is a thread from many moons ago. Has anyone got this method to work? I have tired to use it in in this simple page http://home.mira.net/~reynella/chime/adr_tut.htm but the first chime plug-in only responds. Any ideas? I'd rather not have to go to JAVA to fix this up. At 08:23 13/11/00, Tim wrote: >on 11.13.00 1:45 PM, Cindy Klevickis at klevicca@jmu.edu wrote: > > Here is the web page I'm working on: > > http://www.isat.jmu.edu/users/klevicca/shoebox/glucose.html > > > > I have six water molecules that I want to highlight all at once. They are > > each separate chimes but I want > > them all to respond to the same button. Has anyone done this before? > >I believe that if you name all of your plugins the same name (the ones that >hold the water molecules), you can send one script to them all using >TARGET="name_of_plugins" in the button's embed tag. I don't know if you >want to do this, b/c you will lose the ability to access each plugin >separately, but there it is anyway. Cheers! Ian Ian Musgrave PhD, Senior Lecturer Dept Clin Expt Pharmacology, Adelaide University, South Australia 5005 Email ian.musgrave@adelaide.edu.au phone +61 8 8303 3905 Fax +61 8 8224 0685 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: Mike Porter Subject: RE: Can I target more than one chime with the same button Date: Tue, 20 Mar 2001 14:51:32 +0000 To: rasmol@lists.umass.edu In response to Todd's question on getting multiple molecules to rotate in chime, using the mouse to act on more than one image, I have found a simple way is to set up a loop of "sendmouse" statements... in other words, the embed tag for structure "a" contains the lines name="a" target="b" sendmouse=true structure "b" has the lines name="b" target="c" sendmouse=true and structure "c" has the lines name="c" target="a" sendmouse=true If you set it up like this, using the mouse on any one of the structures should affect all three of them. Hope this helps, Mike At 14:25 20/03/01, you wrote: > > There is also a way to get the rotation of the molecules using the >mouse to > act on all three images but I can't recall how to do that. Perhaps >someone > else can help. >________________________________________________________ Dr M J Porter Lecturer in Organic Chemistry Department of Chemistry Email: m.j.porter@ucl.ac.uk UCL (University College London) Tel: +44 20 7679 4710 20 Gordon Street Fax: +44 20 7679 7463 London WC1H 0AJ, UK http://www.chem.ucl.ac.uk/people/porter/index.html ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RE: Can I target more than one chime with the same button Date: Tue, 20 Mar 2001 10:08:12 -0500 To: rasmol@lists.umass.edu At 03/20/2001, Carlson, Todd wrote: > There is also a way to get the rotation of the molecules using the mouse to > act on all three images but I can't recall how to do that. Perhaps someone > else can help. One way to find out is to start up Protein Comparator, press the Synch button (thereby displaying the relevant commands in the message window), and view the source of the Chime frame. Suppose you have two Chime's named chime1 and chime2: The embed tag that invokes chime1 must include sendmouse=true target="chime2" (and vice versa). This can be done in a chain among any number of Chimes. Rotations, zooms and any other mouse-contolled operations in one chime will propagate to the other chime. Rotations or zooms induced by commands will not propagate. The command 'send mouse [on|off]' can be used after Chime is invoked. It must be sent separately to each Chime unless you want a unidirectional result. This sendmouse feature is implemented only in Chime for Windows, not Macintosh. It works in Netscape; I don't know about IE. If you want to see it in Macs in a future Chime version, be sure to convey your wishes to webmaster@mdlchime.com To detect macs and behave accordingly: function client_mac() { if (navigator.appVersion.toLowerCase().indexOf("mac") != -1 return true; else return false; } /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Carlson, Todd" Subject: RE: Can I target more than one chime with the same button Date: Tue, 20 Mar 2001 10:12:00 -0500 To: rasmol@lists.umass.edu, Mike Porter Thanks Mike. I knew about the sendmouse command, but I forgot to use the target tag with it. Todd ______________________________ Reply Separator _________________________________ Author: "Mike Porter" at OFFICE ++++------+------+------+------+------+------+------+------+------+------+ Subject: RE: Can I target more than one chime with the same button Date: 03/20/2001 9:51 AM In response to Todd's question on getting multiple molecules to rotate in chime, using the mouse to act on more than one image, I have found a simple way is to set up a loop of "sendmouse" statements... in other words, the embed tag for structure "a" contains the lines name="a" target="b" sendmouse=true structure "b" has the lines name="b" target="c" sendmouse=true and structure "c" has the lines name="c" target="a" sendmouse=true If you set it up like this, using the mouse on any one of the structures should affect all three of them. Hope this helps, Mike At 14:25 20/03/01, you wrote: > > There is also a way to get the rotation of the molecules using the >mouse to > act on all three images but I can't recall how to do that. Perhaps >someone > else can help. >________________________________________________________ Dr M J Porter Lecturer in Organic Chemistry Department of Chemistry Email: m.j.porter@ucl.ac.uk UCL (University College London) Tel: +44 20 7679 4710 20 Gordon Street Fax: +44 20 7679 7463 London WC1H 0AJ, UK http://www.chem.ucl.ac.uk/people/porter/index.html ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: "Ian Musgrave & Peta O'Donohue" Subject: RE: Can I target more than one chime with the same button Date: Wed, 21 Mar 2001 10:23:30 -1100 To: "Carlson, Todd" , rasmol@lists.umass.edu G'Day All At 03:25 20/03/01, Carlson, Todd wrote: > Ian > > I have been trying to teach myself javasript so I took on your project > as a > "homework" assignment for myself. You can do this with javacript and > button callback. I downloaded your page and made these changes: [snip] > I posted the results at http://www.gvsu.edu/carlsont/adr_tut2.htm Fantastic! This was just what I needed! Many thanks (except now it looks like I need to learn Javascript :-( I'll look over the code and go back to the chime manual to learn more, thanks! Cheers! Ian Ian Musgrave PhD, Senior Lecturer Dept Clin Expt Pharmacology, Adelaide University, South Australia 5005 Email ian.musgrave@adelaide.edu.au phone +61 8 8303 3905 Fax +61 8 8224 0685 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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 vs. Windows Me Date: Sun, 25 Mar 2001 08:08:05 -0500 To: rasmol@lists.umass.edu Cc: tking@bio.umass.edu Has anyone tried Chime and/or Protein Explorer with Netscape under Windows Me? Do they work? Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: 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: Kelcy Newell Subject: Re: Chime vs. Windows Me Date: Sun, 25 Mar 2001 11:38:17 -0800 (PST) To: rasmol@lists.umass.edu Chime seems to work fine on all ME operating systems I've dealt with. kelcy --- Eric Martz wrote: > Has anyone tried Chime and/or Protein Explorer with > Netscape under Windows > Me? Do they work? > Thanks, -Eric > > /* - - - - - - - - - - - - - - - - - - - - - - - - - > - - > The Protein Explorer: http://proteinexplorer.org > World Index of Molecular Visualization Resources: > http://molvisindex.org > PDB Lite molecule finder: http://pdblite.org > Molecular Visualization EMail List: > > 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 > - - - - - - - - - - - - - - - - - - - - - - - - - - > - */ > > > __________________________________________________ Do You Yahoo!? Get email at your own domain with Yahoo! Mail. http://personal.mail.yahoo.com/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime works on Windows ME Date: Mon, 26 Mar 2001 08:31:22 -0500 To: rasmol@lists.umass.edu I now have reports from three people that Chime and Protein Explorer work well on Windows ME. -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: Eric Martz Subject: Chime and PE work in OS-X classic environment. Date: Mon, 26 Mar 2001 14:38:59 -0500 To: rasmol@lists.umass.edu >Date: Mon, 26 Mar 2001 11:18:44 -0500 >To: Eric Martz >From: Steve Johnston > >Hi Eric > >I have succesfuly tested Protein Explorer in Mac OS X. It runs out of the classic >environment and has no problems at a quick glance. > >--------------------------------------------------------------------------- ----- > >Steven C. Johnston Ph.D. (617) 258-6109 Office >Biocomputing Applications Specialist (617) 258-5062 Fax >Whitehead Institute for Biomedical Research stevej@wi.mit.edu >Nine Cambridge Center http://web.wi.mit.edu/proteins >Cambridge, MA 02142-1479 > >--------------------------------------------------------------------------- ----- > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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 f322irx28001 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Lipid Bilayers and the Gramicidin Channel in Chime Date: Sun, 01 Apr 2001 22:44:48 -0400 To: rasmol@lists.umass.edu, edmolvis@lists.umass.edu Lipid bilayers and the gramicidin channel are now available in a Chime presentation, thanks to Angel Herráez of the University of Alcalá, Spain. Angel adapted the content from my 1997 RasMol "Movie" Script, thereby fulfilling a goal that has been waiting for a long time. He also made a Spanish translation. http://molvis.sdsc.edu/bilayers This Chime presentation shows cholesterol, phosphatidyl choline, and then illustrates the assembly of a hydrated crystalline bilayer model. Results of two molecular dynamics simulations (by Helmut Heller et al.) are shown, resulting in gel- and fluid-like conformations. Then the gramicidin channel is shown in a hydrated bilayer of phosphatidyl ethanolamine (modeled by Serge Crouzy et al.). Links are provided for further exploration of these models in Protein Explorer. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <200104020244.f322i1x27981@marlin.bio.umass.edu> X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id f32Dd4x04963 ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: Re: Lipid Bilayers and the Gramicidin Channel in Chime Date: Mon, 02 Apr 2001 09:37:58 -0400 To: rasmol@lists.umass.edu Fabulous job and resource. Thank you, Angel and Eric, for this great presentation. Frieda >Lipid bilayers and the gramicidin channel are now available in a Chime >presentation, thanks to Angel Herráez of the University of Alcalá, Spain. >Angel adapted the content from my 1997 RasMol "Movie" Script, thereby >fulfilling a goal that has been waiting for a long time. He also made a >Spanish translation. http://molvis.sdsc.edu/bilayers > >This Chime presentation shows cholesterol, phosphatidyl choline, and then >illustrates the assembly of a hydrated crystalline bilayer model. Results >of two molecular dynamics simulations (by Helmut Heller et al.) are shown, >resulting in gel- and fluid-like conformations. Then the gramicidin channel >is shown in a hydrated bilayer of phosphatidyl ethanolamine (modeled by >Serge Crouzy et al.). Links are provided for further exploration of these >models in Protein Explorer. -- Frieda Reichsman, Ph.D. 30 South Whitney Street Molecules In Motion Amherst MA 01002 USA Interactive Molecular Structures Phone: (413) 253-2405 http://www.MoleculesInMotion.com Fax: (612) 397-9975 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- emartz@microbio.umass.edu Content-disposition: inline X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id f32GGbx13385 ++++------+------+------+------+------+------+------+------+------+------+ From: Steven Verhey Subject: Re: Lipid Bilayers and the Gramicidin Channel in Chime Date: Mon, 02 Apr 2001 09:06:10 -0700 To: edmolvis@lists.umass.edu, rasmol@lists.umass.edu, This new adaptation really does look very interesting and useful, but, FWIW, my Netscape crashes fairly reliably when I try to resize the frames during the bilayer presentation. I'm running Netscape 4.7 on a Mac G3 with OS 8.6. This business with text in frames and models in other frames is something that I've always been concerned with. If I can see any of the relevant text, I have this desire to be able to see all of it AND all of the molecule being described. Sometimes it's hard to do that on my 1024 x 768 (16" diag.) monitor. Another option that works for me is to see none of the text and all of the molecules, or vice versa. One thing I've tried is either to have text and models in completely separate windows, so that students toggle back and forth, or to use as small a frame as possible for buttons, as large a frame as possible for models, and a separate window for descriptive text. From a learning standpoint, it might actually be a good thing for students to have to hold in their minds the text while they look at the models. I note that the opening window for PE acknowledges a problem with window resizing, and also that 1024 x 768 is supposed to be the ideal size monitor for PE. My problem is with frame resizing, and, also, unfortunately I get a javascript error when I try to load one of the bilayer-associated models in PE ("JavaScript error: Type 'javascript:' into Location for details). Thanks for all your work on this stuff, everyone -- I apologize if my computer is unusually intolerant. Steve Steven Verhey, Ph.D Assistant Professor Department of Biology Central Washington University Ellensburg, WA 98926 509.963.3431 office 509.963.2730 fax verheys@cwu.edu >>> emartz@microbio.umass.edu - 4/1/01 7:44 PM >>> Lipid bilayers and the gramicidin channel are now available in a Chime presentation, thanks to Angel Herráez of the University of Alcalá, Spain. Angel adapted the content from my 1997 RasMol "Movie" Script, thereby fulfilling a goal that has been waiting for a long time. He also made a Spanish translation. http://molvis.sdsc.edu/bilayers This Chime presentation shows cholesterol, phosphatidyl choline, and then illustrates the assembly of a hydrated crystalline bilayer model. Results of two molecular dynamics simulations (by Helmut Heller et al.) are shown, resulting in gel- and fluid-like conformations. Then the gramicidin channel is shown in a hydrated bilayer of phosphatidyl ethanolamine (modeled by Serge Crouzy et al.). Links are provided for further exploration of these models in Protein Explorer. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Lipid Bilayers and the Gramicidin Channel in Chime Date: Mon, 02 Apr 2001 12:50:46 -0400 To: rasmol@lists.umass.edu hi Steve, 1. there is a known issue with Mac Communicator related to window/frame resizing. apparently, resizing initiates a partial or corrupted reload of the document contents such that js functions and style sheets are lost. I believe NC is somehow ignoring elements in the HEAD tag during a resizing reload, though that might not be completely accurate. in any case, the easy client-side fix is to resize a blank NC window, quit and restart the program so that new size is now considered default, and then run the presentation. the server-side fix for this is to disallow frame/window resizing completely for Mac users, which comes with its own set of troubles ;-) 2. I've played with many combinations of text, buttons, and 3d structure trying to create the most intuitive format. possibly the best solution is to minimize buttons, drop the text into an audio clip, and use most of the screen for the structure. of course, that requires expertise and software for audio editing, and synching audio to a chime animation is problematic (is it even possible?). the problem with using child windows to display text, imho, is that as soon as you grab the molecule to move it around, the text windows disappear behind the structure window. one way to get around this is to use signed scripts; a real pain. another is to use layers to pop text into sight. the advantage of layers over child windows is that layers can remain in the foreground, floating over other elements on the page (though *not* over a plug-in, unfortunately). another advantage is that layers are very accessible via javascript, including appearance, position, content, etc. one example of Chime tutorials that use text in layers is on the Web at . hth, tim On 04.02.01 at 9:06 AM, Steven.Verhey@cwu.EDU (Steven Verhey) wrote: > > > This new adaptation really does look very interesting and useful, but, FWIW, my > Netscape crashes fairly reliably when I try to resize the frames during the > bilayer presentation. I'm running Netscape 4.7 on a Mac G3 with OS 8.6. > > This business with text in frames and models in other frames is something that > I've always been concerned with. If I can see any of the relevant text, I have > this desire to be able to see all of it AND all of the molecule being > described. Sometimes it's hard to do that on my 1024 x 768 (16" diag.) monitor. > Another option that works for me is to see none of the text and all of the > molecules, or vice versa. One thing I've tried is either to have text and > models in completely separate windows, so that students toggle back and forth, > or to use as small a frame as possible for buttons, as large a frame as possible > for models, and a separate window for descriptive text. From a learning > standpoint, it might actually be a good thing for students to have to hold in > their minds the text while they look at the models. > > I note that the opening window for PE acknowledges a problem with window > resizing, and also that 1024 x 768 is supposed to be the ideal size monitor for > PE. My problem is with frame resizing, and, also, unfortunately I get a > javascript error when I try to load one of the bilayer-associated models in PE > ("JavaScript error: Type 'javascript:' into Location for details). > > Thanks for all your work on this stuff, everyone -- I apologize if my computer > is unusually intolerant. > > Steve > > > Steven Verhey, Ph.D > Assistant Professor > Department of Biology > Central Washington University > Ellensburg, WA 98926 > 509.963.3431 office > 509.963.2730 fax > verheys@cwu.edu > _________________________________________ 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 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- emartz@microbio.umass.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Karl Oberholser Subject: Re: Lipid Bilayers and the Gramicidin Channel in Chime Date: Mon, 02 Apr 2001 12:53:54 -0400 To: edmolvis@lists.umass.edu, rasmol@lists.umass.edu, This is a MIME message. If you are reading this text, you may want to consider changing to a mail reader or gateway that understands how to properly handle MIME multipart messages. --Boundary_(ID_oUmfOLfch5ECixM0JColDw) Content-disposition: inline I want to add my thanks for a job well done. I have been wanting to add = something like this to our Molecular Science Lab at http://www.messiah.edu/= molscilab/.=20 THANK YOU! Karl M. Oberholser, Ph.D. Phone: Professor of Chemistry Voice: 717-766-0512 Natural Sciences Dept. Fax: 717-691-6002 Messiah College e-mail: oberhols@messiah.edu P.O. Box 3030 =20 One College Avenue Grantham, Pa 17027 =20 >>> emartz@microbio.umass.edu 04/01/01 10:44PM >>> Lipid bilayers and the gramicidin channel are now available in a Chime presentation, thanks to Angel Herr=E1ez of the University of Alcal=E1, = Spain. Angel adapted the content from my 1997 RasMol "Movie" Script, thereby fulfilling a goal that has been waiting for a long time. He also made a Spanish translation. http://molvis.sdsc.edu/bilayers=20 This Chime presentation shows cholesterol, phosphatidyl choline, and then illustrates the assembly of a hydrated crystalline bilayer model. Results of two molecular dynamics simulations (by Helmut Heller et al.) are shown, resulting in gel- and fluid-like conformations. Then the gramicidin = channel is shown in a hydrated bilayer of phosphatidyl ethanolamine (modeled by Serge Crouzy et al.). Links are provided for further exploration of these models in Protein Explorer. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org=20 World Index of Molecular Visualization Resources: http://molvisindex.org=20= PDB Lite molecule finder: http://pdblite.org=20 Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm=20 Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz=20 - - - - - - - - - - - - - - - - - - - - - - - - - - - */ --Boundary_(ID_oUmfOLfch5ECixM0JColDw) Content-disposition: attachment; filename="Karl Oberholser.vcf" BEGIN:VCARD VERSION:2.1 X-GWTYPE:USER FN:Oberholser, Karl EMAIL;WORK;PREF;NGW:Oberhols@messiah.edu X-GWUSERID:Oberhols ORG:;Faculty - Natural Sciences N:Oberholser;Karl END:VCARD --Boundary_(ID_oUmfOLfch5ECixM0JColDw)-- emartz@microbio.umass.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Karl Oberholser Subject: Re: Lipid Bilayers and the Gramicidin Channel in Chime Date: Mon, 02 Apr 2001 12:53:54 -0400 To: edmolvis@lists.umass.edu, rasmol@lists.umass.edu, This is a MIME message. If you are reading this text, you may want to consider changing to a mail reader or gateway that understands how to properly handle MIME multipart messages. --Boundary_(ID_aJWO5gqU3O3WaPLTRMsNfA) Content-disposition: inline I want to add my thanks for a job well done. I have been wanting to add = something like this to our Molecular Science Lab at http://www.messiah.edu/= molscilab/.=20 THANK YOU! Karl M. Oberholser, Ph.D. Phone: Professor of Chemistry Voice: 717-766-0512 Natural Sciences Dept. Fax: 717-691-6002 Messiah College e-mail: oberhols@messiah.edu P.O. Box 3030 =20 One College Avenue Grantham, Pa 17027 =20 >>> emartz@microbio.umass.edu 04/01/01 10:44PM >>> Lipid bilayers and the gramicidin channel are now available in a Chime presentation, thanks to Angel Herr=E1ez of the University of Alcal=E1, = Spain. Angel adapted the content from my 1997 RasMol "Movie" Script, thereby fulfilling a goal that has been waiting for a long time. He also made a Spanish translation. http://molvis.sdsc.edu/bilayers=20 This Chime presentation shows cholesterol, phosphatidyl choline, and then illustrates the assembly of a hydrated crystalline bilayer model. Results of two molecular dynamics simulations (by Helmut Heller et al.) are shown, resulting in gel- and fluid-like conformations. Then the gramicidin = channel is shown in a hydrated bilayer of phosphatidyl ethanolamine (modeled by Serge Crouzy et al.). Links are provided for further exploration of these models in Protein Explorer. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org=20 World Index of Molecular Visualization Resources: http://molvisindex.org=20= PDB Lite molecule finder: http://pdblite.org=20 Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm=20 Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz=20 - - - - - - - - - - - - - - - - - - - - - - - - - - - */ --Boundary_(ID_aJWO5gqU3O3WaPLTRMsNfA) Content-disposition: attachment; filename="Karl Oberholser.vcf" BEGIN:VCARD VERSION:2.1 X-GWTYPE:USER FN:Oberholser, Karl EMAIL;WORK;PREF;NGW:Oberhols@messiah.edu X-GWUSERID:Oberhols ORG:;Faculty - Natural Sciences N:Oberholser;Karl END:VCARD --Boundary_(ID_aJWO5gqU3O3WaPLTRMsNfA)-- X-pair-Authenticated: 209.139.22.189 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Euro compliance Date: Thu, 05 Apr 2001 19:11:10 -0400 To: rasmol@lists.umass.edu In response to a question by "Sinead O'Rourke" (by way of George Drake) forwarded by Eric martz, the following has been added to: http://www.OpenRasMol.org/FAQ.html#euro Is RasMol "Euro compliant"? IT managers in the "euro-zone" need to assure themselves that all software they use will support the Euro by January 1, 2002. RasMol does not deal with currency, and therefore is effectively "Euro compliant". However, most existing versions of RasMol use the Latin-1 (ANSI), Macintosh, or MS Windows OEM characters sets, without explicit support for the Euro symbol, which might cause RasMol to be rejected in testing for "Euro compliance" against standards intended for financial software. If this proves to be a nuisance, please contact EuroCompliance@OpenRasMol.org ===================================================== **** 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 ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: dank@hq.lindsayelec.com (Dan Kolis) Subject: Euro compliance ! Date: Thu, 05 Apr 2001 19:46:48 -0400 To: rasmol@lists.umass.edu Moments ago this idea popped up... >Is RasMol "Euro compliant"? Hmmm, if nessessary I suppose I could make a molecule in PDB format which LOOKS like this apparently earth shaking symbol. It could feature only atoms discovered by Europeans. I always think "no institution can possibly think thing X"; where X is dumber than a thing previously thought. I'm always wrong. I don't know. Its close. I remember hearing a story about storm doors and Y2K compliance paperwork... Its even weirder to visualize any enforcement regime which tries to make people stop using software for such an arcane reason. Well, we pay for these polititians to dream up this stuff. And, unfortunately, we get what we pay for; (on both sides of the pond). Dan ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Andrew Coulson Subject: Re: Euro compliance ! Date: Fri, 06 Apr 2001 09:25:00 +0100 To: rasmol@lists.umass.edu Surely this idea started circulating 4 days ago? -- well, 5, now, on this side of the pond. Andrew Coulson At 07:46 PM 5/4/01 -0400, you wrote: >Moments ago this idea popped up... > > >Is RasMol "Euro compliant"? > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: a call for help to anyone serving pdb files Date: Fri, 06 Apr 2001 09:23:25 -0400 To: RasMol List hello, I am having trouble setting my server to deliver pdb and spt files as anything but text/html. according to my settings, any file with the extension .pdb should return with the MIME type chemical/x-pdb. then my browser should fire Chime and display the structure. it seems simple to me except that it doesn't work - test pdb files are delivered as text/html. for an example, compare (a single atom; this file happens to be gzipped but I get the same result with the uncompressed file) and if you also view info on both the above pages, you'll see that the first MIME is text/html, whereas the second is chemical/x-pdb. can anyone suggest anything that might help? at this point, I'll try just about anything. here's what I've gone through already, in chronological order: reading the instructions (snicker) restarting the server deleting and redefining the pdb MIME type definition testing preinstalled MIMEs - for example, pdf works fine defining specific file type and creator for pdb (instead of the wildcard *) deleting all MIME types that return text/html reinstalling the server software three times pleading on various techie lists for help (silence) meditation (more silence) praying to various pantheons (deafening silence) the vulcan mind probe the vulcan death grip I hesitate to sacrifice my first-born child; she's too cute - I'll switch to NT first ;-) my server is a Mac G4, running OS 9.1 and AppleShare IP 6.3.3. please 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 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Alex Brown Subject: Re: a call for help to anyone serving pdb files Date: Fri, 06 Apr 2001 14:47:00 +0100 To: rasmol@lists.umass.edu >hello, > >I am having trouble setting my server to deliver pdb and spt files as >anything >but text/html. according to my settings, any file with the extension .pdb >should return with the MIME type chemical/x-pdb. then my browser should fire >Chime and display the structure. it seems simple to me except that it >doesn't >work - test pdb files are delivered as text/html. for an example, compare > > >(a single atom; this file happens to be gzipped but I get the same result >with >the uncompressed file) > >and > > > >if you also view info on both the above pages, you'll see that the first >MIME is >text/html, whereas the second is chemical/x-pdb. > >can anyone suggest anything that might help? at this point, I'll try just >about >anything. here's what I've gone through already, in chronological order: > >reading the instructions (snicker) >restarting the server >deleting and redefining the pdb MIME type definition >testing preinstalled MIMEs - for example, pdf works fine >defining specific file type and creator for pdb (instead of the wildcard *) >deleting all MIME types that return text/html >reinstalling the server software three times >pleading on various techie lists for help (silence) >meditation (more silence) >praying to various pantheons (deafening silence) >the vulcan mind probe >the vulcan death grip > >I hesitate to sacrifice my first-born child; she's too cute - I'll switch >to NT >first ;-) > >my server is a Mac G4, running OS 9.1 and AppleShare IP 6.3.3. please help? > > >thanks, > >tim I notice you didn't try "Banging your Head on the Wall(tm)" (any other hard object should do the trick). On a more serious note - it may be that you need to configure your browser. This may be different, depending on which you use, but in general you need to set the "File Helpers" or "Protocol Helpers" in your preferences. For example, and file with the .pdb you would set the "File Helper" as something like RasMol, or "Protocol Helper" as Chime (but only in Netscape, Chime doesn't work in IE :-( ). The MIME-tag chemical/x-pbd is sent by the server and your browser needs to be able to interpret that tag. Hope this helps. You might have already tried it. My first-born used to be cute, too. But that was several years ago. Now he's a teenager, sacrifice seems a viable option..... :-). Cheers, Alex. ===================================================================== | Alex Brown ||e-mail: abrown@nimr.mrc.ac.uk | | MRC-T, || : abrown@hgmp.mrc.ac.uk | | 1-3 Burtonhole Lane, ||tel.: +44 (0)20 8 906 3811 x 6137 | | Mill Hill, London NW7 1AD. UK.||fax.: +44 (0)20 8 906 1395 | ===================================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: a call for help to anyone serving pdb files Date: Fri, 06 Apr 2001 09:56:17 -0400 To: rasmol@lists.umass.edu On 04.06.01 at 2:47 PM, abrown@nimr.mrc.ac.uk (Alex Brown) wrote: > > I notice you didn't try "Banging your Head on the Wall(tm)" (any other > hard > object should do the trick). > huh? what? I couldn't hear you over the loud ringing in my head. > On a more serious note - it may be that you need to configure your > browser. > This may be different, depending on which you use, but in general you need > to set the "File Helpers" or "Protocol Helpers" in your preferences. For > example, and file with the .pdb you would set the "File Helper" as > something > like RasMol, or "Protocol Helper" as Chime (but only in Netscape, Chime > doesn't > work in IE :-( ). The MIME-tag chemical/x-pbd is sent by the server and > your browser needs to be able to interpret that tag. > yes, this is true - but my browser is configured properly (lots of other Chime-enabled sites work fine). I've also tried various browser versions on three different computers, with the same frustrating results. > My first-born used to be cute, too. But that was several years ago. Now > he's a teenager, sacrifice seems a viable option..... :-). > I don't know - would sacrificing *your* first-born help *me*? maybe we should talk ;-) thanks, though! 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 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: a call for help to anyone serving pdb files Date: Fri, 06 Apr 2001 10:38:38 -0400 To: "Williams, Dewey" Cc: RasMol List On 04.06.01 at 10:23 AM, williams@email.uncc.edu (Williams, Dewey) wrote: > When I tried the links, the umass link worked fine, showing the molecule in > Chime. The MolVision link shows text, as you indicated. > this is what I see as well. > One person already pointed out that the browser must be setup to properly > render MIME files with the appropriate program. I think Chime does this on > installation, but you must manually enter the information for RasMol. Also, > the server must be configured to send the proper MIME code when a file is > requested. Since you could not view the UMass site, I think the problem is > with your browser, however. > except that I do see the structure at the umass site. I know my client-side browser is set up properly. it's just my own server (molvisions.com) that doesn't seem to send pdb files with the proper mime, as you noticed, and that's what I can't figure out. someone please correct me if I'm wrong, but setting mime types on the Appleshare IP server is *reportedly* as simple as configuring your client-side browser - just add the extension and file mapping to the mime list and restart the server. but that doesn't solve this problem. my current thought is that another mime type is taking precedence over the pdb setting, but I don't know how to resolve that conflict (I've already removed all mimes that return text/html, to no avail!). thanks for checking it out, though. regards, tim > > -----Original Message----- > > From: timothy driscoll [mailto:driscoll@molvisions.com] > > Sent: Friday, April 06, 2001 8:23 AM > > To: RasMol List > > Subject: a call for help to anyone serving pdb files > > > > > > hello, > > > > I am having trouble setting my server to deliver pdb and spt files as > > anything > > but text/html. according to my settings, any file with the extension .pdb > > should return with the MIME type chemical/x-pdb. then my browser should > > fire > > Chime and display the structure. it seems simple to me except that it > > doesn't > > work - test pdb files are delivered as text/html. for an example, compare > > > > > > (a single atom; this file happens to be gzipped but I get the same result > > with > > the uncompressed file) > > > > and > > > > > > > > if you also view info on both the above pages, you'll see that the first > > MIME is > > text/html, whereas the second is chemical/x-pdb. > > > > can anyone suggest anything that might help? at this point, I'll try just > > about > > anything. here's what I've gone through already, in chronological order: > > > > reading the instructions (snicker) > > restarting the server > > deleting and redefining the pdb MIME type definition > > testing preinstalled MIMEs - for example, pdf works fine > > defining specific file type and creator for pdb (instead of the wildcard *) > > deleting all MIME types that return text/html > > reinstalling the server software three times > > pleading on various techie lists for help (silence) > > meditation (more silence) > > praying to various pantheons (deafening silence) > > the vulcan mind probe > > the vulcan death grip > > > > I hesitate to sacrifice my first-born child; she's too cute - I'll switch to > > NT > > first ;-) > > > > my server is a Mac G4, running OS 9.1 and AppleShare IP 6.3.3. please 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 _________________________________________ 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 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: MIME type issue resolved! Date: Fri, 06 Apr 2001 15:05:39 -0400 To: RasMol List thanks to all of the kind souls who sent in suggestions for my pdb MIME type trouble. the problem has been fixed! now I can serve all sorts of neat MIME types like pdb, spt, mol, xyz, cat, dog, cow, etc. (yes, if I wanted to serve etc files, I could - whatever they might be). for interested folks, the changes I was making through my server software gui were not registering in the MIME type preferences file - in other words, my own server was ignoring me. boy, that's cold. after many contortions and an expensive service call to Apple, we figured out how to fix that. it's some consolation that the Apple tech had never seen this behavior, either. maybe I should've charged him a consulting fee? ;-) now, on to perfecting that vulcan mind probe. oh, I know what you're thinking... tim original message: > hello, > > I am having trouble setting my server to deliver pdb and spt files as anything > but text/html. according to my settings, any file with the extension .pdb > should return with the MIME type chemical/x-pdb. then my browser should fire > Chime and display the structure. it seems simple to me except that it doesn't > work - test pdb files are delivered as text/html. for an example, compare > > > (a single atom; this file happens to be gzipped but I get the same result with > the uncompressed file) > > and > > > > if you also view info on both the above pages, you'll see that the first MIME is > text/html, whereas the second is chemical/x-pdb. > > can anyone suggest anything that might help? at this point, I'll try just about > anything. here's what I've gone through already, in chronological order: > > reading the instructions (snicker) > restarting the server > deleting and redefining the pdb MIME type definition > testing preinstalled MIMEs - for example, pdf works fine > defining specific file type and creator for pdb (instead of the wildcard *) > deleting all MIME types that return text/html > reinstalling the server software three times > pleading on various techie lists for help (silence) > meditation (more silence) > praying to various pantheons (deafening silence) > the vulcan mind probe > the vulcan death grip > > I hesitate to sacrifice my first-born child; she's too cute - I'll switch to NT > first ;-) > > my server is a Mac G4, running OS 9.1 and AppleShare IP 6.3.3. please help? > _________________________________________ 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 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric C Niederhoffer Subject: NC 4.75 with Chime 2.0a and 2.6 Date: Mon, 09 Apr 2001 14:11:15 -0500 To: RasMol email list On 2/22/01 at 1:09 PM, emartz@microbio.umass.edu (Eric Martz) wrote: > > >Date: Thu, 22 Feb 2001 08:19:44 +1300 > >From: John Tweedie > >Subject: Open Page command in Communicator 4.76 with Chime 2.6 > >Sender: owner-rasmol@lists.umass.edu > >X-Sender: JTweedie@pop3.massey.ac.nz > >To: rasmol@lists.umass.edu > >Reply-to: rasmol@lists.umass.edu > > > >I am running Navigator 4.76 on a Beige G3 (266 mH) under system 9.1. At > >the same time I set these up I also installed Chime 2.6. All seemed to be > >OK until I tried to open some of my Chime material using the "Open Page" > >command in Navigator. The page loaded OK but I received a broken PlugIn > >icon and the "Click here to get the Plug-In message". > > > > > >Accessing the same Chime scripts on a PowerBook 1400c system 8.5, Navigator > >4.0 and Chime 2.0a using "Open Page" works fine. This is accessing the > >same scripts from a Zip disk. > > > >The setup on the G3 works fine with the scripts accessed by normal links or > >by using the Open Location command in Navigator. > > > >Any ideas? I am sure it is something simple but I could not find anything > >relevant with a quick scan of the Chime FAQ's at UMass or MDL. and a search > >of my accumulated posts through this list. > > > >Thanks > > > >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 > > > > I am not running Chime 2.6 yet, but on my network 2.0a works fine in all versions of NC between 4.5 and 4.76 (Mac G4 and Powerbook G3, both under system 9.04 and, recently, 9.1). I use Open:Page all the time to view local files. Assuming your embed tags follow strict syntax, check About:Plug-ins to make sure spt is mapped to Chime. (BTW, although omitting the TYPE attribute from the EMBED tag will work, sometimes it doesn't, so I suggest including it.) No matter what, my gut reaction is to suggest that you delete all old Chime files, restart with extensions off (Shift-Restart) and reinstall Chime. Also, don't install multiple copies during the same installation (the installer will ask you if you want to Continue or Quit once you've installed the plug-in; choose quit). Always quit the installer and re-run it to install Chime again. I've had faulty installations trying to do more than one at once. HTH, Tim _________________________________________ timothy driscoll molvisions.com - 3D molecular visualization e: driscoll@molvisions.com p: 508-864-6516 f: 781-899-4108 John and Tim: I have noticed that NC 4.75 with Chime 2.6 plug-in installed, fails to launch when accessing my local files. Access of my Chime site is fine over the internet when using either Chime 2.0a or 2.6. http://www.siu.edu/departments/biochem/chime_rasmol/instruct.htm When I try to open local files from my hard drive, I get the broken icon for the Chime 2.6 plug-in. Everything works when I remove Chime 2.6 from the NC browser plug-in folder and install Chime 2.0a instead. I work on a beige G3 (OS 8.1) at work and a G3 pismo powerbook (OS 9.0.4) at home. The Chime 2.0a installer appears not to be available from MDL Chime site anymore. Eric Niederhoffer Eric C Niederhoffer, PhD Associate Professor Biochemistry & Molecular Biology, MC 4413 1245 Lincoln Drive, Rm 211 Southern Illinois University School of Medicine Carbondale, IL 62901-4413 eniederhoffer@siumed.edu 618.453.6467 (office) 618.453.6440 (fax) http://www.siu.edu/departments/biochem/faculty/Niederhoffer.html ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Fergus Doherty Subject: Ball and stick in Chime Date: Thu, 12 Apr 2001 12:24:17 +0100 To: rasmol@lists.umass.edu Hell all, Is it possible to include a command in a RasMol script for Chime to display in ball and stick? I've tried various combinatiopns of "ball" and "stick" to no avail. I suppose the question is: what is the RasMol command line command for ball and stick? Thanks fergus -- _____________________________________________________________________ Fergus Doherty PhD, School of BioMedical Sciences, D Floor, University Medical School, Queen's Medical Centre, Nottingham NG7 2UH mailto:Fergus.Doherty@nottingham.ac.uk Tel: 0115 970 9366 FAX: 0115 970 9969 URL: http://www.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html Teaching URL: http://www.nottingham.ac.uk/~mbzmail/students/student.html ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Cindy Klevickis Subject: Re: Ball and stick in Chime Date: Thu, 12 Apr 2001 08:13:13 -0400 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_d4WSvubmO/9eHJs9fhlATQ) For ball and stick, sometimes "ball&stick" works. But, what always works is spacefill 0.4; wireframe 40. Cindy Klevickis Fergus Doherty wrote: > Hell all, > > Is it possible to include a command in a RasMol script for Chime to > display in ball and stick? I've tried various combinatiopns of > "ball" and "stick" to no avail. > > I suppose the question is: what is the RasMol command line command > for ball and stick? > > Thanks > > fergus > -- > > _____________________________________________________________________ > Fergus Doherty PhD, > School of BioMedical Sciences, > D Floor, > University Medical School, > Queen's Medical Centre, > Nottingham NG7 2UH > > mailto:Fergus.Doherty@nottingham.ac.uk > Tel: 0115 970 9366 > FAX: 0115 970 9969 > URL: http://www.nottingham.ac.uk/~mbzmail/biochem/people/fjd.html > Teaching URL: http://www.nottingham.ac.uk/~mbzmail/students/student.html > --Boundary_(ID_d4WSvubmO/9eHJs9fhlATQ) Content-description: Card for Cindy Klevickis Content-disposition: attachment; filename=klevicca.vcf begin:vcard n:Klevickis;Cindy tel;home:office phone: 540-568-2726 tel;work:James Madison University x-mozilla-html:FALSE adr:;;;;;; version:2.1 email;internet:klevicca@jmu.edu x-mozilla-cpt:;-22192 fn:Cindy Klevickis end:vcard --Boundary_(ID_d4WSvubmO/9eHJs9fhlATQ)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Ball and stick in Chime Date: Thu, 12 Apr 2001 13:20:56 -0400 To: rasmol@lists.umass.edu At 04/12/2001, Fergus Doherty wrote: >Is it possible to include a command in a RasMol script for Chime to >display in ball and stick? I've tried various combinatiopns of >"ball" and "stick" to no avail. > >I suppose the question is: what is the RasMol command line command >for ball and stick? In Protein Explorer's QuickViews menu system, DISPLAY Ball & Stick does it for you, AND shows you the commands it sends to Chime (wireframe 0.15, spacefill 0.45). This is a good way to learn RasMol commands. Remember, all RasMol commands are understood and work in Protein Explorer so the transition from RasMol is easy. Warning: once you start using Protein Explorer's command alias feature (short abbreviations for common commands, e.g. "bs" for Ball and Stick, user configurable with a text editor), you may not want to go back to RasMol. [Click on "Aliases" below the message box to see the list of aliases that come with Protein Explorer, and instructions on how to change the aliases.] /* - - - - - - - - - - - - - - - - - - - - - - - - - - - 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-pair-Authenticated: 12.79.128.161 X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id f3HKwrx07576 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: RasMol 2.7.2.1 with French and Italian Date: Tue, 17 Apr 2001 16:57:56 -0400 To: rasmol@lists.umass.edu, pdb-l@rcsb.org Testers are needed for RasMol_2.7.2.1. This version combines the multilingual features released with RasMol 2.7.1.1 in January 2001 with the features in RasMol 2.7.2 (support for multiple molecules and bond rotation), and with some of the improvements to RasMol from RasTop 1.3 (back-clipping, glassy surfaces). RasMol_2.7.2.1 can be found at http://www.bernstein-plus-sons.com/software/RasMol_2.7.2.1. This version supports messages and menus in English, French, Italian and Spanish. In addition to the Spanish translation of the RasMol manual, we now have an Italian translation of the RasMol Help file. We are indebted to those who have worked so hard to make RasMol available in multiple languages: Author Item Language Margaret Wong 2.6 Manual Spanish José Miguel Fernández Fernández 2.7.1 Manual Spanish Fernando Gabriel Ranea 2.7.1 menus and messages Spanish Jean-Pierre Demailly 2.7.1 menus and messages French Giuseppe Martini, Giovanni Paolella, A. Davassi, M. Masullo, C. Liotto 2.7.1 menus and messages Italian 2.7.1 help file Contributions of translations into other languages would be appreciated. We have used a combination of automated translation (using babelfish.altavista.com) and dictionaries to update the contributed translations for recent changes. We make no claim to personal fluency in any of the languages involved. We apologize to the original contributors for the errors that may have been introduced. Suggestion for improvements would be appreciated. In addition to the language upgrades, the mouse logic from RasMol 2.7.2 has been extensively reworked and other bugs have been fixed, but, once again, in order to allow for release of new language capabilities, we have left several bug fixes and improvements behind in order to have a reasonably stable and timely release. The most important changes not yet ready for release are: Automatic sensing of pixel bit depth; Corrections to colors in exported images; Selection of alternative help files depending on the language selected; Determination of the default language from the environment; and Crashes generated in drawing very large images. Our apologies for any inconvenience caused by this reordering of priorities. -- 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 ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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 2.7.2.1 with French and Italian Date: Tue, 17 Apr 2001 19:04:05 -0400 (EDT) To: rasmol@lists.umass.edu, pdb-l@rcsb.org My apologies, the URL given in the prior message should have been: http://www.bernstein-plus-sons.com/software/RasMol_2.7.2.1 without a terminal period. Sorry for any inconvenience. -- HJB ===================================================== **** 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 Tue, 17 Apr 2001, Herbert J. Bernstein wrote: > Testers are needed for RasMol_2.7.2.1. This version combines the > multilingual features released with RasMol 2.7.1.1 in January 2001 > with the features in RasMol 2.7.2 (support for multiple molecules > and bond rotation), and with some of the improvements to RasMol from > RasTop 1.3 (back-clipping, glassy surfaces). > > RasMol_2.7.2.1 can be found at > http://www.bernstein-plus-sons.com/software/RasMol_2.7.2.1. > > This version supports messages and menus in English, French, Italian > and Spanish. In addition to the Spanish translation of the RasMol > manual, we now have an Italian translation of the RasMol Help file. > > We are indebted to those who have worked so hard to make RasMol available > in multiple languages: ... ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: RasTop 1.3.1 release Date: Tue, 27 Mar 2001 12:14:30 -0800 To: rasmol@lists.umass.edu, pdb-l@rcsb.org RasTop offers a user friendly graphical interface to the program RasMol under Windows platforms. The 1.3.1 version is now available on the openrasmol site (www.openrasmol.org), as usual graciously distributed by Herbert Bernstein. This a minor update which corrects some of the major bugs reported since the release of the initial 1.3 version. In particular the software is now supported under Windows 2000 and seems stable under Windows ME. Thanks for your continuous bug reports and suggestions which were decisive in the making of this new version. Thinking about a potential future version, I thought this could be an opportunity for some of you to practice their talents at programming and help us to make a better and better state-of-the-art open source molecular visualization software. I gave up to understand Roger Sayle's code to render shadows. Nevertheless the code is still buggy (under Windows) and some help is clearly needed here. Many of you would love to see nice surface rendering in rasmol. A good start would be to finish the code to create continuous dot surface (Connolly's surface). I'll be very happy to help any of you to identify entries in the software to plug your work, just contact us! - Philippe --------------------------- *** RasTop *** --------------------------- Philippe Valadon P.O. Box 13014, La Jolla, CA 92039, USA. valadon@ix.netcom.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-Authentication-warning: taurus.ci.uc.pt: pferrand owned process doing -bs ++++------+------+------+------+------+------+------+------+------+------+ From: Paulo Ferrand Almeida Subject: Linux RedHat7.1 Date: Mon, 23 Apr 2001 15:53:14 +0100 (WET DST) To: rasmol@lists.umass.edu Is there any problem with the compilation of rasmol under RedHat 7.1? Any info welcome. -Paulo **************************** Paulo Ferrand Almeida, Ph.D. Universidade de Coimbra Departamento de Quimica Largo D. Dinis 3004-535 Coimbra Portugal e-mail: pferrand@ci.uc.pt http://www.qui.uc.pt/~pferrand/ FAX: +351 239 827703 Tel: +351 239 852080 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Francisco Blanco Subject: Re: Linux RedHat7.1 Date: Mon, 23 Apr 2001 16:24:32 +0200 To: rasmol@lists.umass.edu I tried to do it under RedHat7.0, unsuccessfully. The error message said that a file called something like "termio.h" was not found, I did not see it in the untared files. When I downloaded the linux binary (http://www.bernstein-plus-sons.com/software/rasmol/) it worked fine. paco ------------------------------------------------------------------------ Francisco Blanco phone: 34 915616800ext2406 Instituto de Estructura de la Materia, CSIC fax: 34 915645557 Serrano 121, 28006 Madrid, Spain paco@malika.iem.csic.es On Mon, 23 Apr 2001, Paulo Ferrand Almeida wrote: > Is there any problem with the compilation of rasmol under RedHat 7.1? > > Any info welcome. > -Paulo > **************************** > Paulo Ferrand Almeida, Ph.D. > Universidade de Coimbra > Departamento de Quimica > Largo D. Dinis > 3004-535 Coimbra > Portugal > e-mail: pferrand@ci.uc.pt > http://www.qui.uc.pt/~pferrand/ > FAX: +351 239 827703 > Tel: +351 239 852080 > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: Linux RedHat7.1 Date: Mon, 23 Apr 2001 10:47:30 -0600 (MDT) To: rasmol@lists.umass.edu > I tried to do it under RedHat7.0, unsuccessfully. The error message said > that a file called something like "termio.h" was not found, I did not see > it in the untared files. When I downloaded the linux binary > (http://www.bernstein-plus-sons.com/software/rasmol/) > it worked fine. I'm continually amazed by how long old versions of software can linger on the internet. Between versions 4.x and 5.x, RedHat Linux switched from libc5 to glibc, and the the BSD "termio.h" header was removed. The RasMol source code was immediately updated to use the more common SYSV interface "termios.h" instead. Hence the program has been fixed in all versions of RasMol, and its derivatives, since about 1996. My continued apologies to anyone using versions of RasMol more than 5 years old. [The recent versions, since 1991, can even read PDB files]. Roger -- Roger Sayle, E-mail: roger@metaphorics.com Bioinformatics Group, Metaphorics, WWW: http://www.metaphorics.com/ Office 104, 441 Greg Avenue, Tel: (+1) 505-954-3281 Santa Fe, New Mexico, 87501. Fax: (+1) 505-989-1200 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Markus Winter Subject: pdb movies in PowerPoint presentation? Date: Fri, 04 May 2001 16:14:05 +1200 To: rasmol@lists.umass.edu Hi all, we want to incorporate animated models of protein structures into our powerpoint presentations - what is the best way to achieve this? Please reply directly to my e-mail address too (m.winter@auckland.ac.nz ... I don't seem to get all the mails from the mailing list - nothing in the past week at all) ... Best Regards Markus -- Dr. Markus Winter 1st Floor, Room 15 The Liggins Institute University of Auckland 2-6 Park Road Grafton Auckland New Zealand Tel: 0064 (0)9 373 7599 (wait for message then type extension) 3960 Fax: 0064 (0)9 373 7492 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Henry Brzeski Subject: RE: pdb movies in PowerPoint presentation? Date: Fri, 04 May 2001 09:22:21 +0100 To: rasmol@lists.umass.edu Cc: m.winter@auckland.ac.nz Markus I have seen people start a web browser from PowerPoint and that is one way to do it (ie run PowerPoint and then run a browser and then rum chime - but it is not very elegant). However, I don't know of any way of embedding Chime in a PowerPoint slide directly. If anybody does know about this then I would also like to hear how to do it and would be grateful if they could copy their reply to the list as well as responding directly to Markus (maybe there are others out there who would also like to know how to do this). h Henry Brzeski Department of Biosciences University of Hertfordshire College Lane Hatfield Hertfordshire AL10 9AB Tel: 01707 284554 Fax: 01707 285046 > we want to incorporate animated models of protein structures into our > powerpoint presentations - what is the best way to achieve this? > > Please reply directly to my e-mail address too > (m.winter@auckland.ac.nz ... > I don't seem to get all the mails from the mailing list - nothing in the > past week at all) ... > > Best Regards > > Markus > > -- > > Dr. Markus Winter > 1st Floor, Room 15 > The Liggins Institute > University of Auckland > 2-6 Park Road > Grafton > Auckland > New Zealand > Tel: 0064 (0)9 373 7599 (wait for message then type extension) 3960 > Fax: 0064 (0)9 373 7492 > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: <200105040413.QAA03651@mailhost.auckland.ac.nz> ++++------+------+------+------+------+------+------+------+------+------+ From: Dr Nicholas Keep Subject: Re: pdb movies in PowerPoint presentation? Date: Fri, 04 May 2001 09:26:24 +0100 To: rasmol@lists.umass.edu, m.winter@auckland.ac.nz I have incoporated movies into powerpoint as mpeg generated using molscript and makemovie on an SGI. The mpeg files run in a powerpoint slide but are somewhat lossy. These are movies and not a manipulatable viewer like rasmol/CHIME would be. Does anyone have a better solution. I generate a set of 1 degree rotations of the image using molscript and render using the following script. #! /bin/csh -f set q=0 echo $q while ( $q < 360 ) @ q++ echo $q cat head.in >temp echo "by rotation y "$q".0" >>temp cat tail.in >>temp if ($q < 10 ) then molscript -r ++++------+------+------+------+------+------+------+------+------+------+ From: Kurt Giles Subject: Re: pdb movies in PowerPoint presentation? Date: Fri, 04 May 2001 09:55:56 +0100 To: rasmol@lists.umass.edu Cc: m.winter@auckland.ac.nz > I have seen people start a web browser from PowerPoint and that is one way > to do it (ie run PowerPoint and then run a browser and then rum chime - but > it is not very elegant). Launching the browser through a hyperlink in PowerPoint is cumbersome. I set up a full screen browser, with tools bars minimised, running the chime presentation (with buttons linked to scripts) in the background. I then just use Alt-Tab to toggle between the browser and the Powerpoint - effectively switching between them in a fraction of a second. If you ensure the backgrounds of you Chime and Powerpoint presentations are the same it can appear to be an integrated presentation. Kurt -- Dr Kurt Giles kurt.giles@psy.ox.ac.uk Course Coordinator, Graduate Centre for Biosciences Departments of Experimental Psychology and Zoology South Parks Road, Oxford OX1 3UD Phone: +44-1865-271342 Fax: +44-1865-310447 http://epwww.psych.ox.ac.uk/bioscience/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: <200105040413.QAA03651@mailhost.auckland.ac.nz> ++++------+------+------+------+------+------+------+------+------+------+ From: Jordi Oliver Subject: Re: pdb movies in PowerPoint presentation? Date: Fri, 04 May 2001 10:49:24 +0200 To: rasmol@lists.umass.edu Markus There are the possibility to insert a WebLab ActiveX Control 4.0. This ActiveX Control let to insert both structure files (pdb, msv, etc.) and button scripts. You may obtain it from MSI web page: http://www.msi.com. With the install program there are a powerpoint presentation sample. Best regards, Jordi ----------------------------------------------------- Jordi Oliver Oliver Lab. Biochemistry and Molecular Biology University of Balearic Island Cra. Valldemossa km 7,5 Palma de Mallorca 07071 Spain ------------------------------------------------------ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: pdb movies in PowerPoint presentation? Date: Fri, 04 May 2001 07:16:12 -0400 To: rasmol@lists.umass.edu On 05.04.01 at 4:14 PM, m.winter@auckland.ac.nz (Markus Winter) wrote: > Hi all, > > we want to incorporate animated models of protein structures into our > powerpoint presentations - what is the best way to achieve this? > > Please reply directly to my e-mail address too (m.winter@auckland.ac.nz ... > I don't seem to get all the mails from the mailing list - nothing in the > past week at all) ... > > Best Regards > > Markus > hi markus, powerpoint has an option to save as html - assuming that it works reasonably well, you could run your entire presentation in a browser. that would make it totally seamless, and easier to post on the web, too. I've never tried this option of powerpoint, but I would count on an additional "fixing" step in there to clean up the html. ;-) 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 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Michael Sternberg Subject: focus patch Date: Fri, 04 May 2001 21:17:36 +0200 (MET DST) To: rasmol@lists.umass.edu Hello Rasmol users and developers, I have developed a patch to Rasmol to allow perspective rendering, plus some enhancements for the boundbox and vectps output. Details and files, including binaries (currently for linux; Tru64 coming) are all given at: http://www.phys.upb.de/~stern/rasmol/patch/ Note that this addresses primarily users of rasmol under Unix, Win and Mac, not its variants. For historical and pragmatic reasons, this is a patch against the 2.6.4 release of Roger Sayle. It has served well for some time in my group, and I finally got together to make a public release. I added a few features only recently. Please consider this patch as a beta version. It works fine for most circumstances, but may crash for some extreme cases (large zooms, small focus). I am open for comments and suggestions. With best regards, -- Michael Sternberg, Dipl. Phys. | Uni-GH Paderborn http://www.phys.uni-paderborn.de/~stern/ | FB6 Theoretische Physik phone: +49-(0)5251-60-2329 fax: -3435 | 33098 Paderborn, Germany "Who disturrrbs me at this time?" << Zaphod Beeblebrox IV >> <*> ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: pdb movies in PowerPoint presentation? Date: Fri, 04 May 2001 16:20:02 -0400 To: m.winter@auckland.ac.nz Cc: rasmol@lists.umass.edu At 05/04/2001, you wrote: >we want to incorporate animated models of protein structures into our >powerpoint presentations - what is the best way to achieve this? > >Please reply directly to my e-mail address too (m.winter@auckland.ac.nz ... >I don't seem to get all the mails from the mailing list - nothing in the >past week at all) ... > >Dr. Markus Winter >1st Floor, Room 15 >The Liggins Institute >University of Auckland >2-6 Park Road >Grafton >Auckland >New Zealand Animated GIF's can be constructed for direct inclusion in Powerpoint. See instructions at http://www.umass.edu/microbio/rasmol/rotating.htm (bottom of page). Alternatively, if you make an NMR ensemble of models, Protein Explorer can play the movie. It creates a separate window, and the html of this window can be saved to play back later in Netscape or Internet Explorer without running Protein Explorer. You have to switch from Powerpoint to the browser window (e.g. using Alt-Tab on Windows does this instantly if you already have the browser window open). The advantage is you can rotate and zoom the movie. For details, click on the animated EF Hand GIF at the upper left of the Protein Explorer frontdoor (www.proteinexplorer.org). By the way, the Molecular Visualization Freeware EMail List (aka RasMol list) has just exceeded 600 subscribers. And you probably do get all messages, Markus -- the message previous to yours was sent April 23. You can check the history anytime at http://www.umass.edu/microbio/rasmol/raslist.htm -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: <20010504071613-r01010600-3e741f63@192.168.1.3> ++++------+------+------+------+------+------+------+------+------+------+ From: Christopher Harendza Subject: Re: pdb movies in PowerPoint presentation? Date: Sun, 06 May 2001 20:57:23 -0400 To: rasmol@lists.umass.edu Hi, I am a novice here, but since there has been some exchange on placement of pdb files into Microsoft Powerpoint, I thought I'd ask the same about inserting pdb files into Macromedia's Authorware program (I am using the academic 3.5 - which is a few years old). I would appreciate any feedback from folks who have some experience with this. Thank you, Christopher Harendza http://www.mc3.edu/gen/faculty/charend/charend.htm timothy driscoll wrote: > On 05.04.01 at 4:14 PM, m.winter@auckland.ac.nz (Markus Winter) wrote: > > > Hi all, > > > > we want to incorporate animated models of protein structures into our > > powerpoint presentations - what is the best way to achieve this? ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_+HonNV3g0ZHcqVq4GkBUhA)" X-MIMETrack: Serialize by Router on BOSmail01/M/US/Vpharm(Release 5.0.7 |March 21, 2001) at 05/08/2001 10:45:32 AM, Serialize complete at 05/08/2001 10:45:32 AM ++++------+------+------+------+------+------+------+------+------+------+ From: Darin_Takemoto@vpharm.com Subject: More than one file in Chime? Date: Tue, 08 May 2001 10:45:31 -0400 To: rasmol@lists.umass.edu This is a multipart message in MIME format. --Boundary_(ID_+HonNV3g0ZHcqVq4GkBUhA) This is probably a FAQ, but since I didn't find the answer in the FAQ, here goes. Can you use more than one source pdb file in one Chime? I know I could concatenate the files, but I'd like to avoid that in this case. Darin Takemoto darin_takemoto@vpharm.com --Boundary_(ID_+HonNV3g0ZHcqVq4GkBUhA)
This is probably a FAQ, but since I didn't find the answer in the FAQ, here goes.
Can you use more than one source pdb file in one Chime?  I know I could
concatenate the files, but I'd like to avoid that in this case.

Darin Takemoto
darin_takemoto@vpharm.com --Boundary_(ID_+HonNV3g0ZHcqVq4GkBUhA)-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: More than one file in Chime? Date: Tue, 08 May 2001 10:51:55 -0400 To: rasmol@lists.umass.edu On 05.08.01 at 10:45 AM, Darin_Takemoto@vpharm.com wrote: > This is probably a FAQ, but since I didn't find the answer in the FAQ, > here goes. > Can you use more than one source pdb file in one Chime? I know I could > concatenate the files, but I'd like to avoid that in this case. > > Darin Takemoto > darin_takemoto@vpharm.com chime only loads a single file at a time; however, putting multiple structures into one file works well (separated by MODEL/ENDMDL) as long as they are aligned. you can use Swiss PDB Viewer (DeepView) to align them. 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 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: More than one file in Chime? Date: Tue, 08 May 2001 12:05:03 -0400 To: rasmol@lists.umass.edu Cc: shindyal@sdsc.edu At 05/08/2001, you wrote:

This is probably a FAQ, but since I didn't find the answer in the FAQ, here goes.
Can you use more than one source pdb file in one Chime? =A0I know I could
concatenate the files, but I'd lik= e to avoid that in this case.

Darin Takemoto
darin_takemoto@vpharm.com

Adding to Tim's (correct) response, software that does support loading and independently manipulating multiple PDB files includes:

-Swiss PDB Viewer (DeepView)

-Berkeley RasMol

-WebLab Viewer

For more on how to put multiple aligned molecules into one PDB file for independent rendering and coloring (but not independent movement) in Chime, click on the animated EF Hand at the FrontDoor to Protein Explorer. See also on the FrontDoor the CE alignment site (in the section under 'finding your molecule') -- for single protein chains, it does an intelligent job of alignment and hands the result back to you from the website (but loses hetero atoms).

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

Eric Martz, Professor (Immunology), Dept Microbiology
U Mass, Amherst MA US  413-545-2325/FAX 413-545-2532
            = ;  http://www.umass.edu/molvis/martz
- - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en,es-ES ++++------+------+------+------+------+------+------+------+------+------+ From: shalpine@earthlink.net Subject: IEEE Multimedia article on Molecular Visualization Date: Tue, 08 May 2001 13:34:31 -0700 To: rasmol@lists.umass.edu The article, "Molecular Visualization: A Microcosm of the E-Revolution," was published in the April-June issue of IEEE MultiMedia: . Last Fall I attended IEEE Multimedia's national meeting and discovered that few, if any, of the attendees were familiar with molecular visualization software and the associated Internet community. I was subsequently asked to write on the topic. Therefore, the target audience is primarily non-chemist engineers and multimedia developers. (It has already sparked some interest within the animation community here in LA.) I am very grateful to the RasMol List members that helped me with contacts and additional information for the article. Thanks again! Susana Susana Maria Halpine Artist-Biochemist 8640 Gulana Ave., J-1016 Playa del Rey, CA 90293 (310) 306-8399 shalpine@earthlink.net http://home.earthlink.net/~shalpine ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en,es-ES ++++------+------+------+------+------+------+------+------+------+------+ From: shalpine@earthlink.net Subject: PDF Reader for IEEE Multimedia, Molecular Visualization Date: Tue, 08 May 2001 17:07:29 -0700 To: rasmol@lists.umass.edu P.S. The PDF file requires Adobe Acrobat 4.0 to view text and full color images. To download the latest free version of Adobe Acrobat Reader visit: http://www.adobe.com/products/acrobat/readstep2.html ***** The article, "Molecular Visualization: A Microcosm of the E-Revolution," was published in the April-June issue of IEEE MultiMedia: . Last Fall I attended IEEE Multimedia's national meeting and discovered that few, if any, of the attendees were familiar with molecular visualization software and the associated Internet community. I was subsequently asked to write on the topic. Therefore, the target audience is primarily non-chemist engineers and multimedia developers. (It has already sparked some interest within the animation community here in LA.) I am very grateful to the RasMol List members that helped me with contacts and additional information for the article. Thanks again! Susana Susana Maria Halpine Artist-Biochemist 8640 Gulana Ave., J-1016 Playa del Rey, CA 90293 (310) 306-8399 shalpine@earthlink.net http://home.earthlink.net/~shalpine ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: "James W. Caras" Subject: chime and AOL Date: Mon, 14 May 2001 15:27:32 -0500 To: rasmol@lists.umass.edu Hi everyone- I have been working on a number of Chime-based structure tutorials for a website, and have run into some compatibility issues that maybe someone knows something about. It seems very clear that Explorer will not handle scripted buttons or the LiveConnect interface with the plug-in. Requiring Netscape I can live with. Netscape 6 appears to be laughable in many respects (not just including Chime support), so I guess I will require the use of the older Netscape 4. If I am wrong on any of this please let me know. What troubles me is that people who have taken a look at the tutorials who are using AOL (even if they are running Netscape 4 and chime 2) seem to have problems with some (but not all) of the tutorials. The AOL users have reported "Error occurred in Plug-Ins" (what you might expect from IE), and that Chime will begin to execute a button-called script file and stall (with ldkfjks.spt executing... in the status bar of the browser). Unfortunately, many college students (my audience) use AOL and I want to avoid these problems, for it will appear to them that they have taken the time to get Netscape 4 and Chime 2, and things still are not working. I do not think requiring an exorcism of AOL from their computer would be well received. It appears AOL not only screwed up Netscape (with v. 6), but is even reaching back into successful Netscape browsers and messing them up as well. If you can help with any of these questions, or have come to any conclusions from experiences with similar problems, I would greatly appreciate your assistance. Jamie -- _______________________________ Dr. James Caras The Institute for Cellular and Molecular Biology The University of Texas at Austin MBB 3.122 2500 Speedway Austin, TX 78712 caras@mail.utexas.edu (512) 471-0416 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Favorite PDB files Date: Thu, 24 May 2001 17:22:20 -0400 To: rasmol@lists.umass.edu I'd like to invite subscribers to this list to share their favorite PDB files, or particularly interesting newly published results (regardless of whether you're the author). This will help keep us all better informed. Here are a few I like. The links will launch them into Protein Explorer (PE). Ribosome, complete, with 3 tRNA's and mRNA. Too many chains to fit in a single PDB file (1gix + 1giy), so here are the backbones only as two models in a single file: http://molvis.sdsc.edu/protexpl/pe.htm?id=../pdb/1gix1giy.pdb&nmr=1& (This link forces PE to go to the NMR Models page so as to show both models initially. Note that the QuickViews menus are limited to model 1 only.) Calcineurin (ser/thr phosphatase) catalytic and regulatory domains bound to FK-binding protein and FK506. Iron and zinc and phosphate in active site. 4 calciums in regulatory domain with N-terminal myristate. Catalytic domain sticks long alpha helix finger into groove in regulatory domain. http://molvis.sdsc.edu/protexpl/pe.htm?id=1tco Lipid bilayer with gramicidin (not in the PDB; theoretical model courtesy Crouzy et al, Biophys J 67:1370, 1994). http://molvis.sdsc.edu/protexpl/pe.htm?id=../pdb/bilagram.pdb& Be sure to show only water to see it penetrating the channel! (With the QuickViews menus: SELECT Solvent, DISPLAY Only.) Virus capsid with circumscribed icosahedron, simplified model of SV40 where each of 360 VP1 chains is represented by a single atom. http://molvis.sdsc.edu/pdb/sv40_360.spt (This shows a script in bare Chime because support for a single script like this is not yet completed in PE.) A tutorial about capsid assembly is at http://www.umass.edu/microbio/chime/pipe Morph of an EF hand binding calcium (courtesy the Gerstein & Krebs morph server at Yale). http://molvis.sdsc.edu/protexpl/pe.htm?id=../shared/rv_mgef2.pdb&nmr=1& This link forces PE to start at the page where Animation is the first button. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TRANSMEMBRANE MOLECULES Please share others you know about! Be sure to inspect the hydrophobic surfaces: with the QuickViews menus: DISPLAY Spacefill, COLOR Polarity2. Alpha hemolysin, heptamer "mushroom". http://molvis.sdsc.edu/protexpl/pe.htm?id=7ahl Calcium transporting ATPase, transmembrane + 3 soluble domains. http://molvis.sdsc.edu/protexpl/pe.htm?id=1eul Potassium channel http://molvis.sdsc.edu/protexpl/pe.htm?id=1bl8 Note how the Trp's all sit at the lipid-water interface. (Enter command 's trp; sf') Bacteriorhodopsin http://molvis.sdsc.edu/protexpl/pe.htm?id=1c8r -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en,pdf References: <200105242116.f4OLGX328926@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Ilan Samish Subject: Re: Favorite PDB files Date: Fri, 25 May 2001 10:45:28 +0300 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_w0Qq9dOh4T8ttTUqrii9nw) Dear Eric, How are you? Enjoyed browsing through your favorite PDB files. Perhaps you would like to add a representative of the photosynthetic 'green clan': 1fe1 - Photosystem II reaction center (RC) (2000). 1c51 - Photosystem I RC (1999); first deposited as 2pps (1997). 1prc - Bacterial RC; Rhodopseudomonas viridis; 1st high resolution membrane crystal; Nobel winning; (1988). Hope to see you at the Protein Society conference (if not in Israel, at least in the states...), Best regards, Ilan ps Am currently teaching protein structure-function at the Open-University and next year will teach protein bioinformatics in a postgraduate bioinformatics 'retraining' course at the Open University. Of course, will give a full workshop on your great PE software. --Boundary_(ID_w0Qq9dOh4T8ttTUqrii9nw) Content-description: Card for Ilan Samish Content-disposition: attachment; filename=ilan.samish.vcf begin:vcard n:; tel;fax:08-9344181 tel;home:08-9300723 tel;work:08-9344300 x-mozilla-html:FALSE org:Weizmann Institute of Science;Plant Sciences Department adr:;;;Rehovot;;76100;Israel version:2.1 email;internet:Ilan.Samish@weizmann.ac.il title:Ilan Samish end:vcard --Boundary_(ID_w0Qq9dOh4T8ttTUqrii9nw)-- X-Accept-Language: en References: <200105242116.f4OLGX328926@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Cindy Klevickis Subject: Re: Favorite PDB files Date: Fri, 25 May 2001 15:14:18 -0400 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_7WXipIML1kUqq5nz3ePZXQ) boundary="Boundary_(ID_4aHEzDNQLubJfEhU6zNfkA)" --Boundary_(ID_4aHEzDNQLubJfEhU6zNfkA) Hello to all, My favorite pdb files are the ones my students create themselves by using rulers and gumdrop models. Here is a "lesson plan" that one of my students, Leila Kessler, wrote for this activity. http://www.isat.jmu.edu/users/klevicca/Shoebox/lesson2.doc Some students used Chemistry model kits for their pdb files. Some built random shapes using toothpicks and gum drops. Some used toys and made models of toy trucks or houses. Cindy Klevickis Eric Martz wrote: > I'd like to invite subscribers to this list to share their favorite PDB > files, or particularly interesting newly published results (regardless of > whether you're the author). This will help keep us all better informed. Here > are a few I like. The links will launch them into Protein Explorer (PE). > > Ribosome, complete, with 3 tRNA's and mRNA. Too many chains to fit in a > single PDB file (1gix + 1giy), so here are the backbones only as two models > in a single file: > http://molvis.sdsc.edu/protexpl/pe.htm?id=../pdb/1gix1giy.pdb&nmr=1& > (This link forces PE to go to the NMR Models page so as to show both models > initially. Note that the QuickViews menus are limited to model 1 only.) > > Calcineurin (ser/thr phosphatase) catalytic and regulatory domains bound to > FK-binding protein and FK506. Iron and zinc > and phosphate in active site. 4 calciums in regulatory domain with > N-terminal myristate. Catalytic domain sticks long alpha helix finger into > groove in regulatory domain. > > http://molvis.sdsc.edu/protexpl/pe.htm?id=1tco > > Lipid bilayer with gramicidin (not in the PDB; theoretical model courtesy > Crouzy et al, Biophys J 67:1370, 1994). > > http://molvis.sdsc.edu/protexpl/pe.htm?id=../pdb/bilagram.pdb& > Be sure to show only water to see it penetrating the channel! (With the > QuickViews menus: SELECT Solvent, DISPLAY Only.) > > Virus capsid with circumscribed icosahedron, simplified model of SV40 where > each of 360 VP1 chains is represented by a single atom. > > http://molvis.sdsc.edu/pdb/sv40_360.spt (This shows a script in bare Chime > because support for a single > script like this is not yet completed in PE.) A tutorial about capsid > assembly is at http://www.umass.edu/microbio/chime/pipe > > Morph of an EF hand binding calcium (courtesy the Gerstein & Krebs morph > server at Yale). > > http://molvis.sdsc.edu/protexpl/pe.htm?id=../shared/rv_mgef2.pdb&nmr=1& > This link forces PE to start at the page where Animation is the first button. > > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > TRANSMEMBRANE MOLECULES > Please share others you know about! Be sure to inspect the hydrophobic > surfaces: with the QuickViews menus: DISPLAY Spacefill, COLOR Polarity2. > > Alpha hemolysin, heptamer "mushroom". > > http://molvis.sdsc.edu/protexpl/pe.htm?id=7ahl > > Calcium transporting ATPase, transmembrane + 3 soluble domains. > > http://molvis.sdsc.edu/protexpl/pe.htm?id=1eul > > Potassium channel > > http://molvis.sdsc.edu/protexpl/pe.htm?id=1bl8 > Note how the Trp's all sit at the lipid-water interface. (Enter command 's > trp; sf') > > Bacteriorhodopsin > > http://molvis.sdsc.edu/protexpl/pe.htm?id=1c8r > > -Eric > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > The Protein Explorer: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > PDB Lite molecule finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > --Boundary_(ID_4aHEzDNQLubJfEhU6zNfkA) Hello to all,

My favorite pdb files are the ones my students create themselves by using rulers and gumdrop models.  Here is a "lesson plan" that one of my students, Leila Kessler, wrote for this activity.

http://www.isat.jmu.edu/users/klevicca/Shoebox/lesson2.doc

Some students used Chemistry model kits for their pdb files.  Some built random shapes using toothpicks and gum drops.  Some used toys and made models of toy trucks or houses.

Cindy Klevickis

Eric Martz wrote:

I'd like to invite subscribers to this list to share their favorite PDB
files, or particularly interesting newly published results (regardless of
whether you're the author). This will help keep us all better informed. Here
are a few I like. The links will launch them into Protein Explorer (PE).

Ribosome, complete, with 3 tRNA's and mRNA. Too many chains to fit in a
single PDB file (1gix + 1giy), so here are the backbones only as two models
in a single file:
http://molvis.sdsc.edu/protexpl/pe.htm?id=../pdb/1gix1giy.pdb&nmr=1&
(This link forces PE to go to the NMR Models page so as to show both models
initially. Note that the QuickViews menus are limited to model 1 only.)

Calcineurin (ser/thr phosphatase) catalytic and regulatory domains bound to
FK-binding protein and FK506. Iron and zinc
and phosphate in active site. 4 calciums in regulatory domain with
N-terminal myristate. Catalytic domain sticks long alpha helix finger into
groove in regulatory domain.

http://molvis.sdsc.edu/protexpl/pe.htm?id=1tco

Lipid bilayer with gramicidin (not in the PDB; theoretical model courtesy
Crouzy et al, Biophys J 67:1370, 1994).

http://molvis.sdsc.edu/protexpl/pe.htm?id=../pdb/bilagram.pdb&
Be sure to show only water to see it penetrating the channel! (With the
QuickViews menus: SELECT Solvent, DISPLAY Only.)

Virus capsid with circumscribed icosahedron, simplified model of SV40 where
each of 360 VP1 chains is represented by a single atom.

http://molvis.sdsc.edu/pdb/sv40_360.spt (This shows a script in bare Chime
because support for a single
script like this is not yet completed in PE.) A tutorial about capsid
assembly is at http://www.umass.edu/microbio/chime/pipe

Morph of an EF hand binding calcium (courtesy the Gerstein & Krebs morph
server at Yale).

http://molvis.sdsc.edu/protexpl/pe.htm?id=../shared/rv_mgef2.pdb&nmr=1&
This link forces PE to start at the page where Animation is the first button.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
TRANSMEMBRANE MOLECULES
Please share others you know about! Be sure to inspect the hydrophobic
surfaces: with the QuickViews menus: DISPLAY Spacefill, COLOR Polarity2.

Alpha hemolysin, heptamer "mushroom".

http://molvis.sdsc.edu/protexpl/pe.htm?id=7ahl

Calcium transporting ATPase, transmembrane + 3 soluble domains.

http://molvis.sdsc.edu/protexpl/pe.htm?id=1eul

Potassium channel

http://molvis.sdsc.edu/protexpl/pe.htm?id=1bl8
Note how the Trp's all sit at the lipid-water interface. (Enter command 's
trp; sf')

Bacteriorhodopsin

http://molvis.sdsc.edu/protexpl/pe.htm?id=1c8r

-Eric

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

Eric Martz, Professor (Immunology), Dept Microbiology
U Mass, Amherst MA US  413-545-2325/FAX 413-545-2532
              http://www.umass.edu/molvis/martz
- - - - - - - - - - - - - - - - - - - - - - - - - - - */ --Boundary_(ID_4aHEzDNQLubJfEhU6zNfkA)-- --Boundary_(ID_7WXipIML1kUqq5nz3ePZXQ) Content-description: Card for Cindy Klevickis Content-disposition: attachment; filename=klevicca.vcf begin:vcard n:Klevickis;Cindy tel;work:540-568-2726 x-mozilla-html:FALSE adr:;;;;;; version:2.1 email;internet:klevicca@jmu.edu fn:Cindy Klevickis end:vcard --Boundary_(ID_7WXipIML1kUqq5nz3ePZXQ)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Want Teaching Experiences with Protein Explorer Date: Sat, 26 May 2001 13:42:54 -0400 To: rasmol@lists.umass.edu I have drafted an article describing Protein Explorer intended for the journal Biochemistry and Molecular Biology Education (BAMBEd, http://www.elsevier.com/locate/bambed). The section of this article subtitled "Teaching with PE" needs strengthening with teaching experiences. It mentions PE's built-in QuickTours, the Form for Recording Observations, the new Index & Glossary, the larger Tutorials included in PE, and the option to make class-specific web pages with hyperlinks that display specific molecules in PE. But for historical reasons, I do not teach in any introductory level biology, chemistry, or biochemistry courses, and therefore have no personal experiences using Protein Explorer in such courses. Do you have experience with specific PE-based class assignments or exercises? Information about the effectiveness of such exercises, and/or student reactions to the use of PE? Such information would strengthen this article, either as a separate note under your authorship, or mentioned in my article with URL's to your class syllabus and on-line assignments. Experiences and on-line assignments would be most valuable in a form that could be adapted readily by other educators. Please contact me if you have such experiences and are willing to describe them to me or for publication in BAMBEd. Sincerely, -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-- boundary="Boundary_(ID_tUoTO3W6Qz29ArSmRLC4dg)" References: <200105242116.f4OLGX328926@marlin.bio.umass.edu> <3B0EAF09.373D3AF9@jmu.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: Re: Favorite PDB files Date: Sat, 26 May 2001 13:51:49 -0400 To: rasmol@lists.umass.edu --Boundary_(ID_tUoTO3W6Qz29ArSmRLC4dg) At 3:14 PM -0400 5/25/01, Cindy Klevickis wrote: >Hello to all, > >My favorite pdb files are the ones my students create themselves by >using rulers and gumdrop models. Here is a "lesson plan" that one >of my students, Leila Kessler, wrote for this activity. > >http://www.isat.jmu.edu/users/klevicca/Shoebox/lesson2.doc > >Some students used Chemistry model kits for their pdb files. Some >built random shapes using toothpicks and gum drops. Some used toys >and made models of toy trucks or houses. > >Cindy Klevickis What a cool way to use RasMol! Thanks for contributing this-- it has all kinds of different teaching applications, IMO. Would any of your students' PDB files be accessible online? (I'd sure like to see that toy truck!) -Frieda -- Frieda Reichsman, Ph.D. 30 South Whitney Street Molecules In Motion Amherst MA 01002 USA Interactive Molecular Structures Phone: (413) 253-2405 http://www.MoleculesInMotion.com Fax: (612) 397-9975 --Boundary_(ID_tUoTO3W6Qz29ArSmRLC4dg) Re: Favorite PDB files

At 3:14 PM -0400 5/25/01, Cindy Klevickis wrote:
Hello to all,
My favorite pdb files are the ones my students create themselves by using rulers and gumdrop models.  Here is a "lesson plan" that one of my students, Leila Kessler, wrote for this activity.
http://www.isat.jmu.edu/users/klevicca/Shoebox/lesson2.doc
Some students used Chemistry model kits for their pdb files.  Some built random shapes using toothpicks and gum drops.  Some used toys and made models of toy trucks or houses.
Cindy Klevickis


What a cool way to use RasMol! Thanks for contributing this-- it has all kinds of different teaching applications, IMO. Would any of your students' PDB files be accessible online? (I'd sure like to see that toy truck!)

-Frieda
--
Frieda Reichsman, Ph.D.                          30 South Whitney Street
Molecules In Motion                                 Amherst MA 01002   USA
Interactive Molecular Structures              Phone: (413) 253-2405
http://www.MoleculesInMotion.com        Fax: (612) 397-9975
--Boundary_(ID_tUoTO3W6Qz29ArSmRLC4dg)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: concatenated XYZ files Date: Sat, 26 May 2001 14:38:09 -0400 To: "Gebauer, Peter A." Cc: rasmol@lists.umass.edu Dear Peter: XYZ files are good for small organic molecules, but not for proteins. I have documented some methods for NMR files for proteins (click on the animated EF Hand at the upper left of the FrontDoor page at http://proteinexplorer.org), but since I don't work with micromolecules, I have not documented XYZ methods. I'm copying this to the Molecular Visualization Freeware/"RasMol" email list so others can help you with XYZ. For examples of XYZ, see http://www.umass.edu/microbio/chime/ir-spect/index.htm This is a downloadable resource so you can examine the actual XYZ file contents. At 05/25/2001, you wrote: >Professor Martz - Your web pages have been my best resources for learning >about RasMol and Chime, so I'd like to begin by thanking you for putting >them together. I've reached the point where I'd like to do some animations >in Chime. Can you tell me how to generate the concatenated XYZ files that >are needed for that or is there a good source of information about them >somewhere? (I apologize if there is something I've missed in your web >pages.) > >Thank you very much. > >Peter Gebauer >Chemistry Department >Monmouth College (IL) > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Eric C Niederhoffer Subject: Re: Want Teaching Experiences with Protein Explorer Date: Tue, 29 May 2001 10:26:35 -0500 To: rasmol@lists.umass.edu > >Do you have experience with specific PE-based class assignments or >exercises? Information about the effectiveness of such exercises, and/or >student reactions to the use of PE? Such information would strengthen this >article, either as a separate note under your authorship, or mentioned in >my article with URL's to your class syllabus and on-line assignments. >Experiences and on-line assignments would be most valuable in a form that >could be adapted readily by other educators. > >Please contact me if you have such experiences and are willing to describe >them to me or for publication in BAMBEd. > >Sincerely, -Eric Eric: I used PE as a teaching and visual-aid tool for two courses that I taught during my Fulbright Scholar activities in Trujillo, Peru from August through December 2000. You are more than welcome to use any of the information contained on the web site and associated links. http://www.siu.edu/departments/biochem/fulbright_2000/fulbright_2000.html PE was introduced and used for classroom activities beginning with lecture 9 of "Molecular Aspects of Metalloproteins" (course 1) and during most of "Role of Metal Ions in Microbial Gene Regulation" (course 2). You should find links to the pdf files of course notes (my comments and reflections) from the main course pages. Let me know if you would like more information. Eric Eric C Niederhoffer, PhD Associate Professor Biochemistry & Molecular Biology, MC 4413 1245 Lincoln Drive, Rm 211 Southern Illinois University School of Medicine Carbondale, IL 62901-4413 eniederhoffer@siumed.edu 618.453.6467 (office) 618.453.6440 (fax) http://www.siu.edu/departments/biochem/faculty/Niederhoffer.html ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Originating-IP: [142.150.224.190] X-OriginalArrivalTime: 30 May 2001 21:50:23.0936 (UTC) FILETIME=[87AF0C00:01C0E952] ++++------+------+------+------+------+------+------+------+------+------+ From: Baagi Mmereki Subject: New member Date: Wed, 30 May 2001 21:50:23 +0000 To: rasmol@lists.umass.edu Hi everyone! My name is Baagi Mmereki. I am a graduate student at the University of Toronto in Environmental chemistry. I am currently looking at ab initio calculations of small water complexes and wish to view my molecules in 3-D. I managed to download the PC/win 95 version of rasmol but could not proceed from there as to how to imput my XYZ gaussian output so that it can be viewed in 3-D. I vaguely remeber using it at Georgetown when we had our XYZ typed in word and saved as a either text or something.....PLEASE HELP ME WITH HOW I SHOULD PROCEED. Thank you Baagi T. Mmereki Chemistry Department University of Toronto Toronto ON Canada M5S 3H6 (416) 978 8596 *************************************************************** **The Ground of liberty is to be gained by inches. We must be * **contended to secure what we can from time to time and ******* **eternally press forward for what is yet to get. It takes **** **time to persuade men to do even what is for their own good*** *************************************************************** _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at 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-- sa.umich.edu> References: <200106051540.f55Fe6306316@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Javascript to warn students using IE for Chime projects Date: Tue, 05 Jun 2001 14:07:57 -0400 To: Karen A Ocorr Cc: rasmol@lists.umass.edu Karen Ocorr (U Mich) told me she had problems with a Chime project in her course, namely, students were using IE rather than Netscape. If your Chime projects don't work in IE (mine don't!), you can easily insert javascript into your class web page that will inform students who are using IE that they must switch to Netscape. To see an example in action, visit http://molvis.sdsc.edu/bilayers/ BOTH in IE and in Netscape. In the body of your html page, insert everything below. If your page background is white, rather than black, change color='#00ff00' to color='green'. The 'noscript' block guards against the unlikely possibility that java or javascript are disabled in the browser. In that case, the second message about the browser won't appear at all since it requires that javascript be enabled -- instead, a red message appears explaining how to enable them appears instead. (You can easily test this by disabling javascript in Netscape and visiting the above URL.) At the URL above, there are a couple of minor problems with the code which I have fixed below. If you have any problems using this, send me the URL of the page in questions and I'll try to tell you how to fix it. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: Javascript to warn students using IE for Chime projects Date: Tue, 05 Jun 2001 14:39:04 -0400 To: rasmol@lists.umass.edu Cc: Karen A Ocorr On 06.05.01 at 2:07 PM, emartz@microbio.umass.edu (Eric Martz) wrote: > Karen Ocorr (U Mich) told me she had problems with a Chime project in her > course, namely, students were using IE rather than Netscape. > > If your Chime projects don't work in IE (mine don't!), you can easily > insert javascript into your class web page that will inform students who > are using IE that they must switch to Netscape. To see an example in > action, visit > > > http://molvis.sdsc.edu/bilayers/ > > BOTH in IE and in Netscape. > > In the body of your html page, insert everything below. If your page > background is white, rather than black, change color='#00ff00' to > color='green'. The 'noscript' block guards against the unlikely > possibility that java or javascript are disabled in the browser. In that > case, the second message about the browser won't appear at all since it > requires that javascript be enabled -- instead, a red message appears > explaining how to enable them appears instead. (You can easily test this by > disabling javascript in Netscape and visiting the above URL.) At the URL > above, there are a couple of minor problems with the code which I have > fixed below. If you have any problems using this, send me the URL of the > page in questions and I'll try to tell you how to fix it. > alternatively, you can use redirection. for example, put the following code in the head of your opening page: then make an alternate start page (in this example, "indexalt.html") for non-netscape visitors, including appropriate content. my two cents! 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 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Sophie Siedlberg Subject: Still stuck on Mol to PDB porting. Date: Wed, 06 Jun 2001 19:21:47 +0100 To: rasmol@lists.umass.edu Hi I have been using the ACD Chemsketch package to generate small peptide chains, and they are then saved as Mol files. However I find it very difficult to port to PDB from the MDL Mol file formats and then see the residues as separate entities whan using the "shapeley" colour scheme. (Rasmol or Chime) I know that it has a lot to do with the way the residues are declared in the PDBs that come from the Protein Data Bank. Can anyone suggest a way of porting from Mol to PDB so I can display all the options that are avaliable. Is there a freeware package that can do this. I am limited to windows 3x and 9x and have been trying to write my own porting application for this, but seem to come across dead ends. Advice on this would be really appreciated. (I use turbo pascal and Delphi pascal) Oh my favourite PDBs are: The viral capsid that Eric Martz suggested. I find that really fascinating. and also the PDB entries for Oxytocin. (1xy1 and 1xy2). And I like them more for aesthetic reasons than anything else. Wether that is a good or a bad thing I dont know! All the best :-) Sophia Siedlberg Orlania Biosystems. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 X-MSMail-priority: Normal References: <000501c0eeb5$a5af6340$129a883e@default> ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: Still stuck on Mol to PDB porting. Date: Thu, 07 Jun 2001 10:15:12 +0200 To: rasmol@lists.umass.edu Hi, I think that the most straightforward and easiest solution would be to use a modelling program which supports the automatic building of peptides, for example HyperChem (not to mention Sybyl or Insight or other "big" applications). It is not freeware, but even an older or lite version would suite well. Small peptides with default helix or sheet conformations can be built in seconds. To convert an MDL mol file to pdb is not difficult, if only the bare structure is concerned, a lot of simpler programs can do it, (I use Mol2Mol for every kind of conversions) but to add the residue info (what you probably want) needs an amino-acid library with sophisticated structure deciphering algorithms etc, features that programs just like HyperChem possess. Maybe freewares also can be found somewhere out there, you'll see from the answers. Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ----- Original Message ----- Sent: Wednesday, June 06, 2001 8:21 PM From: "Sophie Siedlberg" Subject: Still stuck on Mol to PDB porting. To: > Hi > > I have been using the ACD Chemsketch package to generate small peptide > chains, and they are then saved as Mol files. However I find it very > difficult to port to PDB from the MDL Mol file formats and then see the > residues as separate entities whan using the "shapeley" colour scheme. > (Rasmol or Chime) I know that it has a lot to do with the way the residues > are declared in the PDBs that come from the Protein Data Bank. Can anyone > suggest a way of porting from Mol to PDB so I can display all the options > that are avaliable. Is there a freeware package that can do this. I am > limited to windows 3x and 9x and have been trying to write my own porting > application for this, but seem to come across dead ends. Advice on this > would be really appreciated. (I use turbo pascal and Delphi pascal) > > Oh my favourite PDBs are: > > The viral capsid that Eric Martz suggested. I find that really fascinating. > and also the PDB entries for Oxytocin. (1xy1 and 1xy2). And I like them more > for aesthetic reasons than anything else. Wether that is a good or a bad > thing I dont know! > > All the best :-) > > Sophia Siedlberg > > Orlania Biosystems. > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Importance: Normal X-MSMail-priority: Normal X-Apparently-From: ++++------+------+------+------+------+------+------+------+------+------+ From: experimentalsciences Subject: Extension problem Date: Sun, 10 Jun 2001 10:53:23 +0200 To: rasmol@lists.umass.edu Dear List, Forgive me if this issue has already been discussed, but I'm new to the list. I use both Chime and WebLabViewer Lite 4.0 to view molecules. A problem I've noticed lately following some operating system upgrading on M$Windows98 is that .CHM and .MSI molecule file extensions are now ambiguous. .CHM is now the default extension for HTML help files, and .MSI is now a new lightweight installation protocol enabling a slim download of c.50kb instead of 1.5Mb for a small installation program. Is there any response to the extension ambiguity? One theoretical work-around would be to change the molecule extensions, and reprogram the viewers to seek the new extensions. Can Windows be configured to do this without awaiting a new release of Chime or WebLabVeiwer? Best wishes Keith Wilkinson List Owner for Chemists' Net www.chemclub.com/teachers eGroups Chemists' Net page http://www.egroups.co.uk/group/Chemistry-Teachers --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.260 / Virus Database: 131 - Release Date: 06/06/01 _________________________________________________________ Do You Yahoo!? Get your free @yahoo.com address at http://mail.yahoo.com ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Homology Modeling for Beginners Date: Sun, 10 Jun 2001 12:49:39 -0400 To: rasmol@lists.umass.edu, discuspv@USM.MAINE.EDU Cc: drbevan@vt.edu, vriend@cmbi.kun.nl I have taken a first stab at gathering web resources about homology modeling at http://www.umass.edu/molvis/workshop/homolmod.htm This is intended to complement Gale Rhodes' excellent tutorial using DeepView and SWISS-MODEL, http://www.usm.maine.edu/~rhodes/SPVTut/index.html Gale's tutorial, while indispensible for researchers doing their first homology modeling, is primarily a "how to" tutorial aimed at students. I have not written a tutorial, but have attempted to give researchers who are novices in homology modeling an overview of available freeware, web resources, and of the limitations of homology models. I myself am a complete novice at homology modeling. I will appreciate your comments, suggestions, and pointing out important omissions. One thing I did not find on the web is an estimate of the percentage of protein sequences for which templates with >30% sequence identity currently exist -- can someone please direct me to that information? -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: "Frieda S. Reichsman" Subject: long DNA/protein pdb files? Date: Sun, 10 Jun 2001 21:54:01 -0400 To: rasmol@lists.umass.edu Hi All, I am interested in finding pdb files of particularly long stretches of double-stranded DNA, preferably with protein bound as well. The DNA sequence and identity of the protein are unimportant, but I am hoping for a length of DNA in the 15-20 base pair range at least. Does anyone know of such a file or files? Thanks, Frieda -- Frieda Reichsman, Ph.D. 30 South Whitney Street Molecules In Motion Amherst MA 01002 USA Interactive Molecular Structures Phone: (413) 253-2405 http://www.MoleculesInMotion.com Fax: (612) 397-9975 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: German/Germany, de-DE, en References: ++++------+------+------+------+------+------+------+------+------+------+ From: jr Subject: Re: long DNA/protein pdb files? Date: Mon, 11 Jun 2001 08:15:12 +0200 To: rasmol@lists.umass.edu You may be interested in our Helix and bending analysis of nucleic acid double helix structures pages http://www.imb-jena.de/Piet/html/ where you may have a look at those with more than 12 bp e.g. [234]KBD, 1SAA and on All double helix structures there are the structures with the NUCLEOSOME CORE PARTICLE including 146 bp DNA e.g. 1AOI, 1EQZ, 1F66 Regards, Jan "Frieda S. Reichsman" wrote: > Hi All, > > I am interested in finding pdb files of particularly long stretches > of double-stranded DNA, preferably with protein bound as well. The > DNA sequence and identity of the protein are unimportant, but I am > hoping for a length of DNA in the 15-20 base pair range at least. > Does anyone know of such a file or files? > > Thanks, > > Frieda > -- > Frieda Reichsman, Ph.D. 30 South Whitney Street > Molecules In Motion Amherst MA 01002 USA > Interactive Molecular Structures Phone: (413) 253-2405 > http://www.MoleculesInMotion.com Fax: (612) 397-9975 > -- Snail to:Jan Reichert, IMB, D-07708 Jena, POB 100813. Voice:+49 3641 6562-05 (Fax:+49 3641 6562-10) :/i mailto:jr@imb-jena.de http://www.imb-jena.de/~jr/index.shtml ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (X11; U; Linux 2.2.19 i686; en-US; rv:0.9) Gecko/20010505 X-Accept-Language: es-AR, es, en, hr References: <3B2461F0.A5859BCA@imb-jena.de> ++++------+------+------+------+------+------+------+------+------+------+ From: davinci Subject: Re: long DNA/protein pdb files? Date: Mon, 11 Jun 2001 05:01:40 -0300 To: rasmol@lists.umass.edu Hi!, I have visited your page but I can't access to the linked pages. Regards, jr wrote: >You may be interested in our Helix and bending analysis of nucleic acid >double helix structures pages > >http://www.imb-jena.de/Piet/html/ > >where you may have a look at those with more than 12 bp >e.g. [234]KBD, 1SAA >and on All double helix structures there are the structures with the >NUCLEOSOME CORE PARTICLE including 146 bp DNA >e.g. 1AOI, 1EQZ, 1F66 >Regards, Jan > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: Extension problem Date: Mon, 11 Jun 2001 10:33:52 +0200 To: experimentalsciences@yahoo.de, rasmol@lists.umass.edu If two extensions interfere, the most simple way to reprogram Windows, or start not the associated program: 1 - In Explorer or My computer shift-leftclick on the file; 2 - Select Open with....; 3 - From the dialog select the appropriate program; 4 - At the bottom of the dialog select the "Always use this program..." check box, if you want so; 5 - OK This assumes that the program with installed according to Windows' taste and appears in the above dialog. Omit step 4 if you want leave the original file association. Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ----- Original Message ----- Sent: Sunday, June 10, 2001 10:53 AM From: "experimentalsciences" Subject: Extension problem To: > Dear List, > > Forgive me if this issue has already been discussed, but I'm new to the > list. I use both Chime and WebLabViewer Lite 4.0 to view molecules. A > problem I've noticed lately following some operating system upgrading on > M$Windows98 is that .CHM and .MSI molecule file extensions are now > ambiguous. > > .CHM is now the default extension for HTML help files, and > .MSI is now a new lightweight installation protocol enabling a slim download > of c.50kb instead of 1.5Mb for a small installation program. > > Is there any response to the extension ambiguity? One theoretical > work-around would be to change the molecule extensions, and reprogram the > viewers to seek the new extensions. Can Windows be configured to do this > without awaiting a new release of Chime or WebLabVeiwer? > > Best wishes > > Keith Wilkinson > List Owner for Chemists' Net > www.chemclub.com/teachers > eGroups Chemists' Net page > http://www.egroups.co.uk/group/Chemistry-Teachers > --- > Outgoing mail is certified Virus Free. > Checked by AVG anti-virus system (http://www.grisoft.com). > Version: 6.0.260 / Virus Database: 131 - Release Date: 06/06/01 > > > > _________________________________________________________ > > Do You Yahoo!? > > Get your free @yahoo.com address at http://mail.yahoo.com > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <3B2461F0.A5859BCA@imb-jena.de> ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: Re: long DNA/protein pdb files? Date: Mon, 11 Jun 2001 07:30:14 -0400 To: rasmol@lists.umass.edu Thank you everyone for the great suggestions, links and files!! I now have plenty of choices. I had no idea the Image Library of Macromolecules had such an extensive sorting interface. What a great resource! Thanks! Frieda -- Frieda Reichsman, Ph.D. 30 South Whitney Street Molecules In Motion Amherst MA 01002 USA Interactive Molecular Structures (413) 253-2405 http://www.MoleculesInMotion.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-- Originator-info: login-token=Mulberry:01sa2z1yga40fDGztd+C7jNEQNLgQ84SweIuE85y0=; token_authority=postmaster@andrew.cmu.edu Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: wm0p Subject: Re: long DNA/protein pdb files? Date: Mon, 11 Jun 2001 09:05:56 -0400 To: rasmol@lists.umass.edu --On Mon, Jun 11, 2001 7:30 AM -0400 Frieda Reichsman wrote: > Thank you everyone for the great suggestions, links and > files!! I now have plenty of choices. I had no idea the > Image Library of Macromolecules had such an extensive > sorting interface. What a great resource! Thanks! > > Frieda, You may also be interested in "making" a DNA (or RNA) of any length or any sequence. The only constraint is that standard B-form (or A-form) PDB files are generated. Look at the Pittsburgh Supercomputer page: http://www.psc.edu/general/help/webtools.html and click on: "Generate PDB display from text input." -Will McClure ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Hannah Wexler Subject: Re: Homology Modeling for Beginners Date: Mon, 11 Jun 2001 09:57:00 -0700 To: rasmol@lists.umass.edu Dear Dr. Martz-- Thank you for the informative page on homology modelling. I am modelling an OmpA (outer membrane protein A) found in an anaerobic bacterium which has only 11% identity with its aerobic counterpart. I first did the model on 3D pssm. i just used one of the pages you suggested,--ModBase- and am trying to paste one of the alignment sin the protein explorer msa3d-- which i can't find on that page. How do I get to it? Also, do you know of any modelling program that would work on PC that would draw aromatics as rings? Molscript apparently does but it is not written for PC. I need something fairly simple as I am very new to this. One more question--I loaded a PDB file into protein explorer and get back a model--all gray. I assume I have to enter commands but I can't figure that out. Is there any appropriate tutorial to explain that? Thanks so much. Hana Hana Wexler, PhD. Director, Wadsworth Anaerobe Lab VA West Los Angeles At 12:49 PM 6/10/01 -0400, you wrote: >I have taken a first stab at gathering web resources about homology >modeling at http://www.umass.edu/molvis/workshop/homolmod.htm > >This is intended to complement Gale Rhodes' excellent tutorial using >DeepView and SWISS-MODEL, > >http://www.usm.maine.edu/~rhodes/SPVTut/index.html > >Gale's tutorial, while indispensible for researchers doing their first >homology modeling, is primarily a "how to" tutorial aimed at students. I >have not written a tutorial, but have attempted to give researchers who are >novices in homology modeling an overview of available freeware, web >resources, and of the limitations of homology models. > >I myself am a complete novice at homology modeling. I will appreciate your >comments, suggestions, and pointing out important omissions. > >One thing I did not find on the web is an estimate of the percentage of >protein sequences for which templates with >30% sequence identity currently >exist -- can someone please direct me to that information? > >-Eric >/* - - - - - - - - - - - - - - - - - - - - - - - - - - - >The Protein Explorer: http://proteinexplorer.org >Workshops: http://www.umass.edu/molvis/workshop >World Index of Molecular Visualization Resources: http://molvisindex.org >PDB Lite molecule finder: http://pdblite.org >Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > >Eric Martz, Professor (Immunology), Dept Microbiology >U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz >- - - - - - - - - - - - - - - - - - - - - - - - - - - */ > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en,pdf References: <5.0.0.25.2.20010611095117.009f2a20@pop.bol.ucla.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Ilan Samish Subject: Re: Homology Modeling for Beginners Date: Mon, 11 Jun 2001 23:23:22 +0300 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_SGClxFsnQCcwBC+CDAXbYw) Shalom Hannah, First, if you have trouble with colors with the Protein Explorer, begin with the great tutorial: http://molvis.sdsc.edu/protexpl/pe_tut.htm Second, searching for new software, you can visit the structural biology software database: http://www.ks.uiuc.edu/Development/biosoftdb/ Third, I am not an expert to threading and have no idea what is the aim of your research, i.e. whether you need a confident model or just to locate an active site. In both cases, and in the first in particular, 11% identity is too low for regular homology modeling. This requires threading techniques, intensive multiple alignment and perhaps carefull molecular-dynamics, in addition to the regular minimization, (and above all, hopefully, additional biological information). Unfortunately, most of this can be (still) done much better with expensive software found (still) only on Silicon Graphics platform e.g. Insight (of Accelrys) or Tripos. Just as an example, Miri Eiesenstein at the weizmann succeeded with such a project (12% identity): JMB 1998 Apr 3;277(3):509-12. Last, for your question on aromatics, all programs should draw them correctly. If you didn't succeed with PE and Swiss PDB viewer and want an easy, but capable program for visualisation, try WebLab (1 month free trial, then it costs ~$300), or many others linked from the KS database. Hope this helps as a first strart, Best regards, Ilan Hannah Wexler wrote: > Dear Dr. Martz-- > > Thank you for the informative page on homology modelling. I am modelling > an OmpA (outer membrane protein A) found in an anaerobic bacterium which > has only 11% identity with its aerobic counterpart. I first did the model > on 3D pssm. i just used one of the pages you suggested,--ModBase- and am > trying to paste one of the alignment sin the protein explorer msa3d-- which > i can't find on that page. How do I get to it? > > Also, do you know of any modelling program that would work on PC that would > draw aromatics as rings? Molscript apparently does but it is not written > for PC. I need something fairly simple as I am very new to this. > > One more question--I loaded a PDB file into protein explorer and get back a > model--all gray. I assume I have to enter commands but I can't figure that > out. Is there any appropriate tutorial to explain that? > > Thanks so much. > > Hana > > Hana Wexler, PhD. > Director, Wadsworth Anaerobe Lab > VA West Los Angeles > > At 12:49 PM 6/10/01 -0400, you wrote: > >I have taken a first stab at gathering web resources about homology > >modeling at http://www.umass.edu/molvis/workshop/homolmod.htm > > > >This is intended to complement Gale Rhodes' excellent tutorial using > >DeepView and SWISS-MODEL, > > > >http://www.usm.maine.edu/~rhodes/SPVTut/index.html > > > >Gale's tutorial, while indispensible for researchers doing their first > >homology modeling, is primarily a "how to" tutorial aimed at students. I > >have not written a tutorial, but have attempted to give researchers who are > >novices in homology modeling an overview of available freeware, web > >resources, and of the limitations of homology models. > > > >I myself am a complete novice at homology modeling. I will appreciate your > >comments, suggestions, and pointing out important omissions. > > > >One thing I did not find on the web is an estimate of the percentage of > >protein sequences for which templates with >30% sequence identity currently > >exist -- can someone please direct me to that information? > > > >-Eric > >/* - - - - - - - - - - - - - - - - - - - - - - - - - - - > >The Protein Explorer: http://proteinexplorer.org > >Workshops: http://www.umass.edu/molvis/workshop > >World Index of Molecular Visualization Resources: http://molvisindex.org > >PDB Lite molecule finder: http://pdblite.org > >Molecular Visualization EMail List: > > http://www.umass.edu/microbio/rasmol/raslist.htm > > > >Eric Martz, Professor (Immunology), Dept Microbiology > >U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > > http://www.umass.edu/molvis/martz > >- - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > > --Boundary_(ID_SGClxFsnQCcwBC+CDAXbYw) Content-description: Card for Ilan Samish Content-disposition: attachment; filename=ilan.samish.vcf begin:vcard n:; tel;fax:08-9344181 tel;home:08-9300723 tel;work:08-9344300 x-mozilla-html:FALSE org:Weizmann Institute of Science;Plant Sciences Department adr:;;;Rehovot;;76100;Israel version:2.1 email;internet:Ilan.Samish@weizmann.ac.il title:Ilan Samish end:vcard --Boundary_(ID_SGClxFsnQCcwBC+CDAXbYw)-- References: <200106101642.f5AGgM303539@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Homology Modeling for Beginners Date: Tue, 12 Jun 2001 19:30:04 -0400 To: rasmol@lists.umass.edu At 06/11/2001, Hana Wexler wrote: >Dear Dr. Martz-- > >Thank you for the informative page on homology modelling. I am modelling >an OmpA (outer membrane protein A) found in an anaerobic bacterium which >has only 11% identity with its aerobic counterpart. I first did the model >on 3D pssm. i just used one of the pages you suggested,--ModBase- and am >trying to paste one of the alignment sin the protein explorer msa3d-- which >i can't find on that page. How do I get to it? Go to http://proteinexplorer.org Click on the small yellow and green molecule at the upper left, labeled "Color by multiple sequence alignment". > >One more question--I loaded a PDB file into protein explorer and get back a >model--all gray. I assume I have to enter commands but I can't figure that >out. Is there any appropriate tutorial to explain that? The main purpose of Protein Explorer is that you DO NOT HAVE TO LEARN ANY COMMANDS! An all-gray model is a typical first view in Protein Explorer when there is only one protein chain with no ligands and no water. The best place for beginners to start with Protein Explorer is the QuickTour. I have made it even more visible at the FrontDoor (main) page at http://proteinexplorer.org -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: request for lipid micelle structure Date: Thu, 14 Jun 2001 11:56:19 -0400 To: RasMol List hello, can anyone point me towards an atomic coordinate file for a lipid micelle? I've had no luck at the rcsb or the world index of molvis resources. 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 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- RasMol List ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: lipid micelles Date: Thu, 14 Jun 2001 13:38:40 -0400 To: Eric C Niederhoffer , On 06.14.01 at 12:10 PM, eniederhoffer@siumed.edu (Eric C Niederhoffer) wrote: > Tim: > > I think you asked for pdb files of micelle structures. Here is one > site that I found from a google search. > > http://indigo1.biop.ox.ac.uk/tieleman/download.html > > Eric > Eric C Niederhoffer, PhD > Associate Professor > Biochemistry & Molecular Biology, MC 4413 > 1245 Lincoln Drive, Rm 211 > Southern Illinois University School of Medicine > Carbondale, IL 62901-4413 > > eniederhoffer@siumed.edu > 618.453.6467 (office) > 618.453.6440 (fax) > > http://www.siu.edu/departments/biochem/faculty/Niederhoffer.html > thanks, eric! this site does indeed have several micelle pdbs. I didn't think to try searching with google. 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 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id f5EM7S325752 ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: World Index and List Stats Date: Thu, 14 Jun 2001 18:14:08 -0400 To: rasmol@lists.umass.edu At 06/11/2001, Will McClure wrote: > You may also be interested in "making" a DNA (or RNA) of >any length or any sequence. The only constraint is that >standard B-form (or A-form) PDB files are generated. Look >at the Pittsburgh Supercomputer page: >http://www.psc.edu/general/help/webtools.html >and click on: >"Generate PDB display from text input." Thanks, Will, that is a great resource! (Although most of the hydrogens are missing ...) I have indexed it at molvisindex.org under sources of PDB files. By the way, the World Index of Molecular Visualization Resources (molvisindex.org) now has: - Under Biochemistry Tutorials in Chime: Over 80 sites by over 40 authors. The subject index for this section has nearly 600 topics and molecules! - Under Molecules: Sources of PDB Files, there are now 23 sites with over 100 cross-indexing subject terms. Remember, anyone can enter a new resource URL, description, and subject terms and it will appear in the title, author, and subject indices as soon as it is approved (usually within 24 hours). Anyone can also improve an existing entry or submit comments on a resource to be included in the description. You just fill out a form -- no password is required. Other (less populated) categories are -Biochemistry Structure Visualization Tutorials (not in Chime) -Organic Chemistry Structure Visualization Tutorials (with or without Chime) -Inorganic/Crystal Structure Visualization Tutorials (with or without Chime) -K-12 Molecular Visualization Tutorials (with or without Chime) -How to create new tutorials with Chime -Deep View / Swiss-PDBViewer Resources -Galleries of Molecular Images (static - no plugins required) -EMail Lists and Newsgroups on Molecular Visualization -Deutsch? ¿Español? Francais? etc. -Free Molecular Visualization and Modeling Software -Commerical Software for Molecular Visualization and Modeling Finally, our MolVis Freeware email list now has over 600 subscribers. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <0GF2000603527F@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Craig T. Martin" Subject: Re: RASMOL digest 195 Date: Mon, 18 Jun 2001 13:03:42 -0400 To: rasmol@lists.umass.edu >Date: Sun, 10 Jun 2001 10:53:23 +0200 >From: experimentalsciences >Subject: Extension problem >To: rasmol@lists.umass.edu >Forgive me if this issue has already been discussed, but I'm new to the >list. I use both Chime and WebLabViewer Lite 4.0 to view molecules. A >problem I've noticed lately following some operating system upgrading on >M$Windows98 is that .CHM and .MSI molecule file extensions are now >ambiguous. > >.CHM is now the default extension for HTML help files, and >.MSI is now a new lightweight installation protocol enabling a slim download >of c.50kb instead of 1.5Mb for a small installation program. > >Is there any response to the extension ambiguity? There is also the problem that many Palm database files have a .pdb extension. I would not suggest that CHIME be modified, since any new extension will simply have problems with some other file extension, now or in the future... This is a problem with no clean solution - except to use a Mac. -- Craig Martin *** Chemistry *** X5-3299 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <0GF2000603527F@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Craig T. Martin" Subject: Re: RASMOL digest 195 - long DNA protein files Date: Mon, 18 Jun 2001 13:16:53 -0400 To: rasmol@lists.umass.edu Cc: "Frieda S. Reichsman" Frieda, I know that your problem was answered, but I thought that I would add two more useful bits. The Nucleic Acids Database lets you search on all sorts of criteria http://ndbserver.rutgers.edu/NDB/ndb.html A program called NAMOT will let you generate all sorts of theoretical structures, including putting bends and kinks in DNA, playing with twist, etc. It runs on only on Unix, but is easy to use (assuming you know some DNA fundamentals) and is publicly available. You could generate PDB files much longer than any crystal structure solved to date (although, I'll guess that Will McClure's program will allow that as well). http://namot.lanl.gov:80/ >Date: Sun, 10 Jun 2001 21:54:01 -0400 >From: "Frieda S. Reichsman" >Subject: long DNA/protein pdb files? >To: rasmol@lists.umass.edu > >Hi All, > >I am interested in finding pdb files of particularly long stretches >of double-stranded DNA, preferably with protein bound as well. The >DNA sequence and identity of the protein are unimportant, but I am >hoping for a length of DNA in the 15-20 base pair range at least. >Does anyone know of such a file or files? > >Thanks, > >Frieda -- Craig T. Martin Associate Professor Department of Chemistry 701 Lederle Graduate Research Tower University of Massachusetts 710 North Pleasant St. Amherst, MA 01003-9336 413-545-3299 Voice 413-545-4490 FAX CMartin@Chem.UMass.edu http://www.chem.umass.edu/~cmartin/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: <5.0.0.25.2.20010611095117.009f2a20@pop.bol.ucla.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Tamas E. Gunda" Subject: Re: draw aromatics as rings + ruth.jpg attached Date: Tue, 19 Jun 2001 14:31:12 +0200 To: rasmol@lists.umass.edu, hwexler@ucla.edu This is a multi-part message in MIME format. --Boundary_(ID_hle0plF8ppdkAc8hFrpeaQ) Dear Hana, > > Also, do you know of any modelling program that would work on PC that would > draw aromatics as rings? Molscript apparently does but it is not written > for PC. I need something fairly simple as I am very new to this. > In modelling programs for PC? Usually dotted lines are used for aromatics, as it is simple to draw, as it is a built-in feature in programming environments. The drawing of aromatic circles means technically the drawing of rotated ellipses, the calculation of its points is time etc consuming. In the case of a modeling program the calculation of structure, energies etc is of first priority, this kind of visualization is not so important. Anyway, Mol2Mol can calculate and generate POV-Ray input files with aromatic rings, if visualization is important, as seen in the attached image (if Eric forgives me for the attachment.... or see at http://www.klte.hu/~gundat/povraya.htm) Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm ----- Original Message ----- Sent: Monday, June 11, 2001 6:57 PM From: "Hannah Wexler" Subject: Re: Homology Modeling for Beginners To: > > Also, do you know of any modelling program that would work on PC that would > draw aromatics as rings? Molscript apparently does but it is not written > for PC. 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Gunda) wrote: > Dear Hana, > > > > Also, do you know of any modelling program that would work on PC that would > > draw aromatics as rings? Molscript apparently does but it is not written > > for PC. I need something fairly simple as I am very new to this. > > > In modelling programs for PC? Usually dotted lines are used for > aromatics, as it is simple to draw, as it is a built-in feature in > programming environments. The drawing of aromatic circles means > technically the drawing of rotated ellipses, the calculation of its > points is time etc consuming. In the case of a modeling program the > calculation of structure, energies etc is of first priority, this kind > of visualization is not so important. Anyway, Mol2Mol can calculate > and generate POV-Ray input files with aromatic rings, if visualization > is important, as seen in the attached image (if Eric forgives me for > the attachment.... or see at http://www.klte.hu/~gundat/povraya.htm) > > > Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian > Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary > tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: > tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm > WebLab ViewerPro lets you add "aromatic" bonds (dotted lines, as Tamas suggests), though AFAIK it won't calculate aromaticity for 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 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: <200105242116.f4OLGX328926@marlin.bio.umass.edu> <3B0EAF09.373D3AF9@jmu.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Cindy Klevickis Subject: Re: Favorite PDB files Date: Sat, 23 Jun 2001 10:33:02 -0400 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_YNdncP58JirzmvD679HtIw) boundary="Boundary_(ID_Ge9rIPE1br29s8KISXYQig)" --Boundary_(ID_Ge9rIPE1br29s8KISXYQig) Thanks for your interest. I found a few of these files and have attached them. One is a toy skateboard and one is a Lego model of a plane. I can't find the truck.pdb file. But, the skateboard is very cute. Cindy Klevickis Frieda Reichsman wrote: > At 3:14 PM -0400 5/25/01, Cindy Klevickis wrote: > >> Hello to all, > >> My favorite pdb files are the ones my students create themselves by >> using rulers and gumdrop models. Here is a "lesson plan" that one >> of my students, Leila Kessler, wrote for this activity. > >> http://www.isat.jmu.edu/users/klevicca/Shoebox/lesson2.doc > >> Some students used Chemistry model kits for their pdb files. Some >> built random shapes using toothpicks and gum drops. Some used toys >> and made models of toy trucks or houses. > >> Cindy Klevickis > > What a cool way to use RasMol! Thanks for contributing this-- it has > all kinds of different teaching applications, IMO. Would any of your > students' PDB files be accessible online? (I'd sure like to see that > toy truck!) -Frieda-- > Frieda Reichsman, Ph.D. 30 South Whitney Street > Molecules In Motion Amherst MA 01002 USA > Interactive Molecular Structures Phone: (413) 253-2405 > http://www.MoleculesInMotion.com Fax: (612) 397-9975 --Boundary_(ID_Ge9rIPE1br29s8KISXYQig) Thanks for your interest.  I found a few of these files and have attached them.  One is a toy skateboard and one is a Lego model of a plane.  I can't find the truck.pdb file.  But, the skateboard is very cute.

Cindy Klevickis

Frieda Reichsman wrote:

At 3:14 PM -0400 5/25/01, Cindy Klevickis wrote:
Hello to all,
My favorite pdb files are the ones my students create themselves by using rulers and gumdrop models.  Here is a "lesson plan" that one of my students, Leila Kessler, wrote for this activity.
http://www.isat.jmu.edu/users/klevicca/Shoebox/lesson2.doc
Some students used Chemistry model kits for their pdb files.  Some built random shapes using toothpicks and gum drops.  Some used toys and made models of toy trucks or houses.
Cindy Klevickis
  What a cool way to use RasMol! Thanks for contributing this-- it has all kinds of different teaching applications, IMO. Would any of your students' PDB files be accessible online? (I'd sure like to see that toy truck!) -Frieda--
Frieda Reichsman, Ph.D.      30 South Whitney Street
Molecules In Motion             Amherst MA 01002   USA
Interactive Molecular Structures      Phone: (413) 253-2405
http://www.MoleculesInMotion.com        Fax: (612) 397-9975
--Boundary_(ID_Ge9rIPE1br29s8KISXYQig)-- --Boundary_(ID_YNdncP58JirzmvD679HtIw) Content-disposition: inline; filename=skateboard.pdb COMPND skateboard.pdb HETATM 1 S 2.000 1.000 2.000 HETATM 2 S 1.000 1.500 2.500 HETATM 3 S 0.500 2.500 2.750 HETATM 4 S 1.000 3.500 2.500 HETATM 5 S 2.000 4.000 2.000 HETATM 6 S 13.000 1.000 2.000 HETATM 7 S 14.000 1.500 2.500 HETATM 8 S 14.500 2.500 2.750 HETATM 9 S 14.500 3.500 2.500 HETATM 10 S 13.500 4.000 2.000 HETATM 11 N 3.500 0.500 0.500 HETATM 12 N 3.500 4.500 0.500 HETATM 13 N 12.000 0.500 0.500 HETATM 14 N 12.000 4.500 0.500 HETATM 15 Cl 12.000 3.000 0.500 HETATM 16 Cl 12.000 1.500 0.500 HETATM 17 Cl 3.500 3.000 0.500 HETATM 18 Cl 3.500 1.500 0.500 HETATM 19 O 9.500 2.500 1.500 CONECT 1 2 6 18 19 CONECT 2 1 3 CONECT 3 2 4 CONECT 4 3 5 CONECT 5 4 10 19 CONECT 6 1 7 19 14 16 CONECT 7 6 8 CONECT 8 7 9 CONECT 9 8 10 CONECT 10 9 5 15 19 CONECT 11 18 CONECT 12 17 CONECT 13 15 CONECT 14 16 CONECT 15 16 13 10 CONECT 16 14 6 15 CONECT 17 18 5 12 CONECT 18 1 17 11 CONECT 19 10 5 6 CONECT 19 1 END --Boundary_(ID_YNdncP58JirzmvD679HtIw) Content-disposition: inline; filename=plane.PDB COMPND plane.pdb HETATM 1 S 0.000 14.000 5.000 HETATM 2 S 11.000 18.000 5.000 HETATM 3 S 13.000 18.000 5.000 HETATM 4 S 16.000 25.000 5.000 HETATM 5 S 19.000 25.000 5.000 HETATM 6 S 22.000 18.000 5.000 HETATM 7 S 24.000 18.000 5.000 HETATM 8 S 34.000 14.000 5.000 HETATM 9 S 34.000 9.000 5.000 HETATM 10 S 23.000 9.000 5.000 HETATM 11 S 19.000 0.000 5.000 HETATM 12 S 13.000 0.000 5.000 HETATM 13 S 12.000 9.000 5.000 HETATM 14 S 0.000 9.000 5.000 HETATM 15 N 14.000 9.000 0.000 HETATM 16 N 14.000 18.000 0.000 HETATM 17 N 16.000 23.000 0.000 HETATM 18 N 19.000 23.000 0.000 HETATM 19 N 21.000 18.000 0.000 HETATM 20 N 21.000 9.000 0.000 HETATM 21 N 18.000 1.000 0.000 HETATM 22 N 16.000 1.000 0.000 CONECT 1 2 14 CONECT 2 1 3 CONECT 3 2 4 16 CONECT 4 3 5 17 CONECT 5 4 6 18 CONECT 6 5 7 19 CONECT 7 6 8 CONECT 8 7 9 CONECT 9 8 10 CONECT 10 9 11 20 CONECT 11 10 12 21 CONECT 12 11 13 22 CONECT 13 12 14 15 CONECT 14 1 13 CONECT 15 13 16 22 CONECT 16 3 15 17 CONECT 17 4 16 18 CONECT 18 5 17 19 CONECT 19 6 18 20 CONECT 20 10 19 21 CONECT 21 11 20 22 CONECT 22 12 15 21 23 END --Boundary_(ID_YNdncP58JirzmvD679HtIw) Content-description: Card for Cindy Klevickis Content-disposition: attachment; filename=klevicca.vcf begin:vcard n:Klevickis;Cindy tel;home:office phone: 540-568-2726 tel;work:James Madison University x-mozilla-html:FALSE adr:;;;;;; version:2.1 email;internet:klevicca@jmu.edu x-mozilla-cpt:;-22192 fn:Cindy Klevickis end:vcard --Boundary_(ID_YNdncP58JirzmvD679HtIw)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer 1.87 released Date: Tue, 03 Jul 2001 12:49:29 -0400 To: rasmol@lists.umass.edu I have released a small upgrade of the freeware Protein Explorer (http://proteinexplorer.org). The 1-Hour QuickTour has been improved, and expanded with a section "Beyond QuickTour". The Help/Index/Glossary/FAQ has been augmented to >150 terms. An all-new introduction to homology modeling has been added. In QuickViews, DISPLAY Contacts now shows a short movie, building the final image in stages, to make it more understandable. The new version is now downloadable. I hope I didn't break anything -- let me know! -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-- <429FEE3FD9597E4788D82B2966AD8F7C07DBC9@ils099.uopnet.plymouth.ac.uk> X-MIMEOLE: Produced By Microsoft Exchange V6.0.4417.0 Thread-Topic: Chime, JavaScript and JCAMP spectra Thread-Index: AcEFZGA3gm3CjnFLEdWHowBQ2kZrVQ== content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: Anthony Lewis Subject: Chime, JavaScript and JCAMP spectra Date: Thu, 05 Jul 2001 16:10:58 +0100 To: rasmol@lists.umass.edu Colleagues, I apologise for this slightly off topic question but the MDL Chime Message Forum has not, so far, produced any replies... Is there a way of calling a JavaScript function from a JCAMP spectrum? I know how to communicate between a spectrum and structure; however, I would also like to change other parts of the page/window that holds the structure. For example, I might have a link between a signal on a spectrum and the atoms/groups responsible... but what if I also wanted to add words to say "the signal at ... is a result of ... etc." and that the phrase changes depending upon which signal the user clicks on. I cannot see how this may be done directly and, consequently, I wonder if there is a way to obtain the name of the pdb file which could then be used to load the additional information, rather than call a script from the spectrum? Many thanks for any help, Anthony Lewis C. Anthony Lewis Petroleum & Environmental Geochemistry Group, Department of Environmental Sciences, University of Plymouth, Plymouth, Devon PL4 8AA, U.K. tel: +44 (0)1752 233000 ext. 2988 FAX: +44 (0)1752 233035 e-mail: calewis@plymouth.ac.uk ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: testers please Date: Sat, 14 Jul 2001 21:45:01 -0400 (EDT) To: rasmol@lists.umass.edu If you are familiar with building RasMol on a Mac and are interested in testing a version of RasMol for the mac which uses zlib to decompress compressed data files, please take a look at: http://www.openRasMol.org/#features_2_7_2_1_zlib http://www.bernstein-plus-sons.com/software/RasMol_2.7.2.1/.src_zlib/README.txt http://www.bernstein-plus-sons.com/software/RasMol_2.7.2.1/.src_zlib/ Mamoru Yamanishi (yama@biotech.okayama-u.ac.jp) has contributed patches to the source of RasMol 2.7.2.1 to support use of decompression using the zlib (http://www.gzip.org/zlib) library, which should allow decompression of compressed data files on non-Unix platforms. These new modifications are being studied for inclusion in a future RasMol standard release for use on systems for which a pipe to a standard decompression utility is not practical to use. Built versions for the mac should follow later this month. ===================================================== **** 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 ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Rekha.Iyer@asu.edu Subject: query Date: Tue, 17 Jul 2001 12:20:10 -0700 (MST) To: rasmol@lists.umass.edu Hi: I am trying to connect to Rasmol through a program written in Delphi 5. As mentioned in the manual I am using the DDE protocol. When I try to set the link between the two applications, Rasmol accepts only a file name string and does not accept 'script' commands. I think I am able to connect only to the graphics window and not the command line. Do you have any suggestions on how I can pass a command to the command line and where I can find commands to run the program on dos. Thanks Rekha ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Cindy Klevickis Subject: Web Molecules? Date: Fri, 27 Jul 2001 15:05:47 -0400 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_Tn8OSPIUNxCoMy96jzwWwg) Hello from Cindy Klevickis, Does anyone know where www.webmolecules.com went to? They are are great source of pdb files for over 210,000 small molecules and I would hate to loose their address. Thanks in advance. --Boundary_(ID_Tn8OSPIUNxCoMy96jzwWwg) Content-description: Card for Cindy Klevickis Content-disposition: attachment; filename=klevicca.vcf begin:vcard n:Klevickis;Cindy tel;work:540-568-2726 x-mozilla-html:FALSE adr:;;;;;; version:2.1 email;internet:klevicca@jmu.edu fn:Cindy Klevickis end:vcard --Boundary_(ID_Tn8OSPIUNxCoMy96jzwWwg)-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 X-MSMail-priority: Normal References: <3B61BB8B.3F6979DD@jmu.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Roy Fultun Subject: Re: Web Molecules? Date: Fri, 27 Jul 2001 12:36:53 -0700 To: rasmol@lists.umass.edu www.webmolecules.com seems to not be up, not today at least. There are plenty of references to it in Google. The apparently related www.molecules.com has references to it. Also, Phil Stevens phils@molecules.com is listed in references as a contact person. Please let us know if you come up with any useful alternate links. ----- Original Message ----- Sent: Friday, July 27, 2001 12:05 PM From: "Cindy Klevickis" Subject: Web Molecules? To: > Hello from Cindy Klevickis, > > Does anyone know where www.webmolecules.com went to? > They are are great source of pdb files for over 210,000 small molecules > and I would hate to loose their address. > > Thanks in advance. > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_A8KsFUt/EZdJx/GEs2SrZA)" ++++------+------+------+------+------+------+------+------+------+------+ From: "Seetharamulu, P. (Seetha)" Subject: Remove Date: Mon, 30 Jul 2001 08:43:44 -0500 To: "'rasmol@lists.umass.edu'" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --Boundary_(ID_A8KsFUt/EZdJx/GEs2SrZA) -----Original Message----- Sent: Friday, July 27, 2001 2:37 PM From: Roy Fultun [mailto:royf@loop.com] Subject: Re: Web Molecules? To: rasmol@lists.umass.edu www.webmolecules.com seems to not be up, not today at least. There are plenty of references to it in Google. The apparently related www.molecules.com has references to it. Also, Phil Stevens phils@molecules.com is listed in references as a contact person. Please let us know if you come up with any useful alternate links. ----- Original Message ----- Sent: Friday, July 27, 2001 12:05 PM From: "Cindy Klevickis" Subject: Web Molecules? To: > Hello from Cindy Klevickis, > > Does anyone know where www.webmolecules.com went to? > They are are great source of pdb files for over 210,000 small molecules > and I would hate to loose their address. > > Thanks in advance. > This email may contain confidential and privileged material for the sole use of the intended recipient. Any review or distribution by others is strictly prohibited. If you are not the intended recipient please contact the sender and delete all copies. --Boundary_(ID_A8KsFUt/EZdJx/GEs2SrZA) Remove

-----Original Message-----
From: Roy Fultun [mailto:royf@loop.com]
Sent: Friday, July 27, 2001 2:37 PM
To: rasmol@lists.umass.edu
Subject: Re: Web Molecules?


www.webmolecules.com seems to not be up, not today at least.  There are
plenty of references to it in Google.

The apparently related www.molecules.com has references to it.  Also, Phil
Stevens phils@molecules.com  is listed in references as a contact person.

Please let us know if you come up with any useful alternate links.


----- Original Message -----
From: "Cindy Klevickis" <klevicca@jmu.edu>
To: <rasmol@lists.umass.edu>
Sent: Friday, July 27, 2001 12:05 PM
Subject: Web Molecules?


> Hello from Cindy Klevickis,
>
> Does anyone know where www.webmolecules.com went to?
> They are are great source of pdb files for over 210,000 small molecules
> and I would hate to loose their address.
>
> Thanks in advance.
>


This email may contain confidential and privileged material for the sole use of the intended recipient. Any review or distribution by others is strictly prohibited.  If you are not the intended recipient please contact the sender and delete all copies.

--Boundary_(ID_A8KsFUt/EZdJx/GEs2SrZA)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Robert Dickey Subject: Chime users- important announcement from MDL Date: Fri, 03 Aug 2001 10:28:08 -0700 To: "'rasmol@lists.umass.edu'" Dear Chime and Chime Pro users: MDL has learned that a new service pack of the Microsoft Internet Explorer browser (5.5 SP2) has been released today without support for the Netscape plug-in interface used by Chime and Chime Pro. Our understanding is that future versions of Microsoft Internet Explorer will also lack this interface. This would mean that the Chime and Chime Pro plug-ins would not be supported on these new versions of Microsoft Internet Explorer (including 6.0) until further notice. This issue does not affect the Netscape Communicator 4.7 browser. MDL is working closely with Microsoft to evaluate alternatives for supporting Chime and Chime Pro with new versions of Internet Explorer. Until further notice, Chime and Chime Pro users should continue to use older versions of Internet Explorer (5.5 SP1 and lower) or Netscape Communicator 4.7, which are supported with Chime and Chime Pro 2.6 SP2. MDL will post updates to this information and the Hardware and Software requirements on its MDL Chime site at the following URL: http://www.mdlchime.com/chime/ Thank you for your patience and understanding while we address these issues. Regards, MDL Chime Product Management ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Robley Light Subject: RE: Chime users- important announcement from MDL Date: Fri, 03 Aug 2001 16:10:03 -0400 To: rasmol@lists.umass.edu Eric, How many people are on this list? Do you think it would help if everyone sent notes of complaint to both Microscoft and Netscape about the lack of chime support? Robley Light ************************************************************* Robley J. Light Professor of Chemistry Department of Chemistry Phone: (850) 644-3844 Florida State University Email: rlight@chem.fsu.edu Tallahassee, FL 32306-4390 Fax: (850) 644-8281 Home Page: http://chemweb.chem.fsu.edu/editors/rlight > -----Original Message----- > From: owner-rasmol@lists.umass.edu > [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Robert Dickey > Sent: Friday, August 03, 2001 1:28 PM > To: 'rasmol@lists.umass.edu' > Subject: Chime users- important announcement from MDL > > > Dear Chime and Chime Pro users: > MDL has learned that a new service pack of the Microsoft Internet Explorer > browser (5.5 SP2) has been released today without support for the Netscape > plug-in interface used by Chime and Chime Pro. Our understanding is that > future versions of Microsoft Internet Explorer will also lack this > interface. This would mean that the Chime and Chime Pro plug-ins would not > be supported on these new versions of Microsoft Internet Explorer > (including > 6.0) until further notice. This issue does not affect the Netscape > Communicator 4.7 browser. > MDL is working closely with Microsoft to evaluate alternatives for > supporting Chime and Chime Pro with new versions of Internet Explorer. > Until further notice, Chime and Chime Pro users should continue > to use older > versions of Internet Explorer (5.5 SP1 and lower) or Netscape Communicator > 4.7, which are supported with Chime and Chime Pro 2.6 SP2. > MDL will post updates to this information and the Hardware and Software > requirements on its MDL Chime site at the following URL: > http://www.mdlchime.com/chime/ > Thank you for your patience and understanding while we address > these issues. > > > Regards, > MDL Chime Product Management > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.2) Gecko/20010628 X-Accept-Language: es-AR, es, en, hr ++++------+------+------+------+------+------+------+------+------+------+ From: davinci Subject: New browser without support Date: Fri, 03 Aug 2001 23:12:58 -0300 To: RasMol Hi! I have recieved this email (see bottom). Maybe it's time for a Open Chime under GNU Project running under more OS (for example, GNU/Linux). Somebody is working in some project related? Regards, August 3, 2001 Dear Chime and Chime Pro users: MDL has learned that a new service pack of the Microsoft Internet Explorer browser (5.5 SP2) has been released today without support for the Netscape plug-in interface used by Chime and Chime Pro. Our understanding is that future versions of Microsoft Internet Explorer will also lack this interface. This would mean that the Chime and Chime Pro plug-ins would not be supported on these new versions of Microsoft Internet Explorer (including 6.0) until further notice. This issue does not affect the Netscape Communicator 4.7 browser. MDL is working closely with Microsoft to evaluate alternatives for supporting Chime and Chime Pro with new versions of Internet Explorer. Until further notice, Chime and Chime Pro users should continue to use older versions of Internet Explorer (5.5 SP1 and lower) or Netscape Communicator 4.7, which are supported with Chime and Chime Pro 2.6 SP2. MDL will post updates to this information and the Hardware and Software requirements on its MDL Chime site at the following URL: http://www.mdlchime.com/chime/ Thank you for your patience and understanding while we address these issues. Regards, MDL Chime Product Management ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: New browser without support Date: Sat, 04 Aug 2001 09:18:19 -0400 (EDT) To: RasMol As the current coordinator of RasMol releases, I would be delighted to cooperate in the reintegration of Chime's features into the mainstream of RasMol open source development. MDL made Chime some years ago using a now-obsolete version of RasMol, but they treat the resulting program as closed-source, strictly licensed, proprietary intellectual property. To reintegrate MDL's changes to RasMol into the current version of RasMol, we would need formal permission from MDL and, hopefully, their cooperation. We would be happy to give MDL appropriate credit for their contribution. Exciting things are happening with RasMol. Members of the community have contributed translations into Spanish, French and Italian and a Japanese translation is in the works. Members of the community test new versions, and, because they have access to the source code, are able to provide detailed fixes and new features. I would encourage members of the community who want to see all the best features of RasMol and Chime combined into one open-source software package to contact MDL and urge them to move in that direction. -- Herbert J. Bernstein ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Fri, 3 Aug 2001, davinci wrote: > Hi! > > I have recieved this email (see bottom). Maybe it's time for a Open Chime under GNU Project running under more OS (for example, GNU/Linux). Somebody is working in some project related? > Regards, > > > August 3, 2001 > > Dear Chime and Chime Pro users: > > MDL has learned that a new service pack of the Microsoft Internet Explorer browser (5.5 SP2) has been released today without support for the Netscape plug-in interface used by Chime and Chime Pro. Our understanding is that future versions of Microsoft Internet Explorer will also lack this interface. This would mean that the Chime and Chime Pro plug-ins would not be supported on these new versions of Microsoft Internet Explorer (including 6.0) until further notice. This issue does not affect the Netscape Communicator 4.7 browser. > > MDL is working closely with Microsoft to evaluate alternatives for supporting Chime and Chime Pro with new versions of Internet Explorer. Until further notice, Chime and Chime Pro users should continue to use older versions of Internet Explorer (5.5 SP1 and lower) or Netscape Communicator 4.7, which are supported with Chime and Chime Pro 2.6 SP2. > > MDL will post updates to this information and the Hardware and Software requirements on its MDL Chime site at the following URL: > > http://www.mdlchime.com/chime/ > Thank you for your patience and understanding while we address these issues. > > Regards, > MDL Chime Product Management > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.2) Gecko/20010628 X-Accept-Language: es-AR, es, en, hr References: ++++------+------+------+------+------+------+------+------+------+------+ From: davinci Subject: Re: New browser without support Date: Sat, 04 Aug 2001 14:47:45 -0300 To: rasmol@lists.umass.edu Hi! Well... Really, I'm thinking in an Open Chime using the new RasMol version with modular features like non-english interfase support, new tools, for example. It could be a hard and slow work but the goal will be worthwile. Unfortunately, my knowlegment in C is limitated, but I'm learning in my free time. Regards, Herbert J. Bernstein wrote: >As the current coordinator of RasMol releases, I would be delighted >to cooperate in the reintegration of Chime's features into the mainstream >of RasMol open source development. MDL made Chime some years ago using a >now-obsolete version of RasMol, but they treat the resulting program as >closed-source, strictly licensed, proprietary intellectual property. To >reintegrate MDL's changes to RasMol into the current version of RasMol, >we would need formal permission from MDL and, hopefully, their cooperation. >We would be happy to give MDL appropriate credit for their contribution. > >Exciting things are happening with RasMol. Members of the community have >contributed translations into Spanish, French and Italian and a Japanese >translation is in the works. Members of the community test new versions, >and, because they have access to the source code, are able to provide >detailed fixes and new features. > >I would encourage members of the community who want to see all the best >features of RasMol and Chime combined into one open-source software >package to contact MDL and urge them to move in that direction. > > -- Herbert J. Bernstein > >===================================================== >**** BERNSTEIN + SONS >* * INFORMATION SYSTEMS CONSULTANTS >**** P.O. BOX 177, BELLPORT, NY 11713-0177 >* * *** >**** * Herbert J. Bernstein > * *** yaya@bernstein-plus-sons.com > *** * > * *** 1-631-286-1339 FAX: 1-631-286-1999 >===================================================== > >On Fri, 3 Aug 2001, davinci wrote: > >>Hi! >> >>I have recieved this email (see bottom). Maybe it's time for a Open >> >Chime under GNU Project running under more OS (for example, GNU/Linux). >Somebody is working in some project related? > >>Regards, >> >> >>August 3, 2001 >> >>Dear Chime and Chime Pro users: >> >>MDL has learned that a new service pack of the Microsoft Internet >> >Explorer browser (5.5 SP2) has been released today without support for >the Netscape plug-in interface used by Chime and Chime Pro. Our >understanding is that future versions of Microsoft Internet Explorer will >also lack this interface. This would mean that the Chime and Chime Pro >plug-ins would not be supported on these new versions of Microsoft >Internet Explorer (including 6.0) until further notice. This issue does >not affect the Netscape Communicator 4.7 browser. > >>MDL is working closely with Microsoft to evaluate alternatives for >> >supporting Chime and Chime Pro with new versions of Internet Explorer. >Until further notice, Chime and Chime Pro users should continue to use >older versions of Internet Explorer (5.5 SP1 and lower) or Netscape >Communicator 4.7, which are supported with Chime and Chime Pro 2.6 SP2. > >>MDL will post updates to this information and the Hardware and Software >> >requirements on its MDL Chime site at the following URL: > >>http://www.mdlchime.com/chime/ >>Thank you for your patience and understanding while we address these issues. >> >>Regards, >>MDL Chime Product Management >> >> >> >> >> >> > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: DNA structure in Spanish Date: Sat, 04 Aug 2001 13:43:17 -0400 To: rasmol@lists.umass.edu M. Gonzalo Claros of the University of Malaga has translated into Spanish my Chime tutorial on DNA structure: http://www.nitrogeno.uma.es/proyectocd/Contenido/Pract/Pr_DNA/index.htm This DNA tutorial has buttons to highlight various structural features of the DNA double helix. It has sections on base pairs and hydrogen bonding, the code, strands and helical backbone, ends and antiparallelism. The format of this tutorial is unique -- you can press the buttons in any order, and what they do depends on the buttons pressed previously. The original is at http://www.umass.edu/microbio/chime/dna/index.htm Claros has also written (in Spanish) a tutorial on protein secondary structure. At his site http://www.nitrogeno.uma.es/bmbq/av_bma/index.html click on the Practicas button at the left middle. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en,es-ES ++++------+------+------+------+------+------+------+------+------+------+ From: shalpine@earthlink.net Subject: Jim Blinn at SIGGRAPH Date: Mon, 13 Aug 2001 08:17:23 -0700 To: "'rasmol@lists.umass.edu'" It was great to meet many of the list members in person during the Gordon Research Conference. I'm attending SIGGRAPH this week in LA. Jim Blinn came up with many algorithms for chemical visualization while working at CalTech. He is now working at Microsoft. I hope to speak to Jim regarding information for an article. Perhaps I can approach him about the Netscape/Chime plug-in issue as well. Personally, I think an open-source molecular web viewer is long over due, but perhaps Jim can help us forestall the inevitable. (Please respond to me directly (or cc:) as I get the weekly encapsulated RasMol listserve and will not see your response until after the conference is over.) Susana Women Chemists Committee Chair, American Chemical Society Los Angeles Section Susana Maria Halpine Artist-Biochemist 8640 Gulana Ave., J-1016 Playa del Rey, CA 90293 (310) 306-8399 shalpine@earthlink.net http://home.earthlink.net/~shalpine ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer 1.90 Released Date: Sun, 26 Aug 2001 18:41:29 -0400 To: rasmol@lists.umass.edu, edmolvis@lists.umass.edu Protein Explorer 1.90 is now available (http://proteinexplorer.org) -- free, works on Windows, Macintosh, in a Win4Lin subsystem on linux, and is downloadable for off-line use. Why should you and your students use Protein Explorer? Protein Explorer can do what RasMol or Chime can do, much more easily, and a great deal beyond, all without learning any RasMol-style commands. (Nevertheless, if you know some RasMol commands, they can be used in Protein Explorer.) All common visualization tasks can be accomplished from menus, such as rendering (cartoon, backbone, ball and stick, etc.), coloring (secondary structure, hydrophobic vs. polar, ATGCU, etc.), and hiding. There is an extensive menu for selecting subsets of atoms, and you can select atoms, residues, or chains by clicking on them (all without knowing any commands). There is a clickable sequence to structure mapping, and convenience buttons for zooming, unzooming, centering any part of the molecule, etc. Every menu operation automatically displays an explanation and in some cases, links to related resources. For example, the Polarity5 color scheme uses 5 colors for hydrophobic, polar, backbone, anionic, cationic, and has a link to a site that calculates the pI, and net charge at various pH's, from the sequence. Selecting nucleic acid provides a routine to distinguish DNA from RNA. In addition to common visualization operations, some more advanced operations are also achieved with a few menu clicks, including: contact surface displays that show all noncovalent bonding interactions with any selected moiety; cation-pi orbital interactions; salt bridges; using a multiple sequence alignment to color a protein to reveal conserved regions in the 3D structure. Since the last release of Protein Explorer that I announced on this list (1.87 on July 3), the following enhancements have been added: - Lesson Plans, including a new generic set of questions that can be used as a worksheet for any macromolecule (linked to the FrontDoor page, under About PE). A list of over 20 suitable PDB files is included. (This is in addition to the Form for Recording Observations that has been available for some time.) If you're looking for a tutorial on a particular molecule in Chime, PE's lesson plan guide reminds you to look at http://molvisindex.org, where over 100 molecule-specific tutorials are now indexed. - Assessment of your students' perception of how much Protein Explorer helped their learning. A printable list of 7 questions is provided to hand out to your class, or you can use a customizable website for on-line student assessment of your entire class, or just the Protein Explorer portion of the class. See the new link "Assessment" on the FrontDoor, under "About PE".) - Step by step control during building of Contact Surfaces. Contact surfaces show noncovalent bonding interactions to any moiety you select, in one click. For example, load myoglobin (1MBO), SELECT Ligand, DISPLAY Contacts. You will see right away that most of the heme is contacted hydrophobically by protein carbon; that two histidine nitrogens contact the ferric ion; that molecular oxygen is bound to the ferric iron; that water and some polar protein moieties contact the heme carboxyls. Contact surfaces have been available in PE for quite a while. What is new is the ability to build them step by step, so you can visualize the relation of the final image to what you started with. This is very helpful for beginners because the final contact surfaces image can be somewhat complex. Also, you can stop before adding all layers to the image, in order to keep a simpler image. DISPLAY Contacts is available at the QuickViews menus. - MSA3D: The ability to color a protein to reveal regions of evolutionary conservation, using a multiple protein sequence alignment, has been available for some time. This routine now runs much faster. A new and very pretty ready-made example has been added: translation repressor PUF, that binds to the 3' untranslated region of mRNA (thanks to David S. Bernstein, U. Wisconsin, Madison). The built-in alignment includes sequences from human, xenopus, drosophila, yeast, Dictyostelium, and C. elegans. Conservation is visible in the concavity believed to be the binding site for mRNA. To see this yourself: Run Protein Explorer from the Quick-Start on the FrontDoor (http://proteinexplorer.org). Click 'Explore More with QuickViews'. Click 'Advanced Explorer' (near the bottom of the top frame). Click 'MSA3D'. Click 'ready-made demonstrations'. Click 'Translation repressor PUF', accepting the offer to load PDB file 1IB2. Scroll up a little and click the button [Color Alignment and Molecule]. At the 'MSA3D Result' page, click Identical, Similar, Different to see a beautiful image! - A new animation has been added, showing lipase opening its hydrophobic pocket for binding fat substrate (thanks to Byron Rubin). At the top left of the FrontDoor page, click on the animated image of an EF hand binding calcium -- this takes you to the list of animation examples. - There is a new FAQ. The Help/Index/Glossary is growing, and now includes links to instructions on homology modeling, mutating a PDB file, and entries on 'Limitations of Protein Explorer', 'Troubleshooting', and over 180 other terms. Links to the FAQ and Help/Index/Glossary are on the FrontDoor page, under 'About PE'. -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: Sharron Bransburg - Zabary Subject: running PE on PC unix Date: Mon, 27 Aug 2001 10:12:38 +0300 To: rasmol@lists.umass.edu Cc: edmolvis@lists.umass.edu My name is Sharron Zabary, and I'm the Sys. Admin. of the Tel Aviv Bioinformatics unit. We are using the PE while running VMware under FreeBSD, and it seems like a very good solution. The system is stable, and there is no need to boot it (something that unix users really dislike). Actually it seems like windows is even more stable when running under VMware, in other words let the unix people handle the kernel... Best, --Sharron. Sharron Bransburg-Zabary E-mail: sharron@life2.tau.ac.il Tel: 972-3-6405099 Fax: 972-3-6405098 THE BIOINFORMATICS UNIT - TEL AVIV UNIVERSITY, ISRAEL ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: MSA3D bug when 1st residue number <1 Date: Fri, 31 Aug 2001 11:47:57 -0400 To: rasmol@lists.umass.edu, edmolvis@lists.umass.edu MSA3D is a section of Protein Explorer that colors a 3D protein model to show regions of conservation or mutation, based on an externally created multiple protein sequence alignment. Yesterday, Hannah Wexler of UCLA reported a serious bug that affects only PDB files where the sequence number of the first residue is less than one. For example, 1BXW's first residue is numbered zero, and 1AVQ's first residue is numbered -1. In such cases, the PDB sequence is misnumbered (starting at 1) in the alignment listing, and the colors representing identity, similarity, or difference are applied to the wrong residues. This bug has been present since MSA3D was first released a little over a year ago. I apologize, and remind users of Protein Explorer to check results carefully before publishing. (Actually, that is wise for any software package.) In this case, Dr. Wexler noticed that certain conserved residues, identified by clicking on them, were not colored as conserved in the alignment listing. Another harmless but annoying bug produced spurious error messages when the ready-made MSA3D examples were run. These bugs have been fixed in Protein Explorer 1.901, released today. You don't need to upgrade your downloaded copy unless you plan to use MSA3D. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: chime scripts for animated transitions Date: Mon, 17 Sep 2001 08:29:36 -0400 To: RasMol List Cc: oberhols@messiah.edu hello chime developers, the chime "movies" that I create make frequent use of transitions from one view to another. I accomplish these transitions via a set of custom "fade" scripts, chime scripts that animate a smooth change from the current view to the desired new view. (for example, the script "backbone2spacefill.spt" changes the currently selected set from a backbone view to a spacefill view.) in response to several requests, I have made these scripts publically available. you may download, use, and modify these scripts for your own purposes without restriction. if you do use the fade scripts, I ask only that you please email me the web site (or media) where they appear, so I can assess their utility. the scripts are named to reflect their purpose - the current view, followed by the number 2, followed by the new view. the current set of scripts use the following standards: backbone, wireframe, trace, and ball & stick bonds are 0.2A. spacefill is proportional and based on van der waal radii. of course, these values can be modified for your own purposes. downloading the original scripts: ******************************************** anonymous FTP: dir /public MAC archive: fades.sea.hqx -or- PC archive: fades.zip -or- individual scripts available in the dir /public/fades/ HTTP: -or- ******************************************** no warranties are implied concerning these scripts; they are provided on an "as is" basis, and molvisions.com is not responsible for problems that may arise from their use (or misuse). if you do use these scripts: 1. if you find a bug in the original scripts, notify us at and we will make every effort to correct the problem. 2. if you want to make additional contributions to the existing set, we will be happy to add your scripts to ours. however, please be advised that all such scripts will be available to the public without restriction. 3. finally, molvisions.com will provide nominal (and free) tech support regarding the use of these scripts; email any questions to . regards, tim _________________________________________ god bless america 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 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: Molecular sculpture and early computers Date: Mon, 17 Sep 2001 16:10:38 -0400 To: rasmol@lists.umass.edu I've tried to send this to the list about six times. It is bouncing because the first line contains a special word misinterpreted by the list processor. Hope it goes thru this time ... --Recent enhancements to the page entitled "History of Visualization of Biological Macromolecules" by myself and Eric Francoeur http://www.umass.edu/microbio/rasmol/history.htm include a historical anecdote on the importance of wire backbone models made with Byron's Bender in the first recognition of the immunoglobulin superfamily fold, a photo of a 1996 molecular sculpture in the Smithsonian, on-line digitized excerpts from 16 mm movies of very early protein computer graphics taken in Cyrus Levinthal's group at MIT in the mid 1960's, and a paragraph on the $250,000 Evans & Sutherland computers used in the mid-1980's for fitting models into electron density maps. This page has been indexed under Galleries at http://molvisindex.org There are new links to Michael J. Connolly's excellent "Molecular Surfaces: A Review" (http://www.netsci.org/Science/Compchem/feature14.html) We are seeking photographs, with permission to use on our website, of Kendrew models, Richards Boxes, screenshots of early "electronic Richards boxes" (e.g. Evans & Sutherland running FRODO), and related material suitable for our site. Suggestions for corrections or improvements of our pages are also 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-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Pradeep Subject: File Open dialog Date: Tue, 18 Sep 2001 09:33:14 +0800 To: rasmol@lists.umass.edu Hi, I am using Rasmol v 2.6 beta on Sun Solaris 8. The source code compiled ok and the Rasmol main window opens up on execution. However when I try to choose a file using the File -> Open menu, the file chooser dialog box does not show up. Instead the pdb file name has to be provided on the console window. Is this how it's supposed to be or am I missing some libraries ? Thanks in advance for your help. Pradeep. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Robert Dickey Subject: Chime and IE 5.5 SP2 announcement Date: Wed, 19 Sep 2001 10:55:44 -0700 To: "'rasmol@lists.umass.edu'" MDL Information Systems, Inc. 14600 Catalina Street San Leandro, CA 94577 September 19, 2001 Chime and Chime Pro/Microsoft Internet Explorer 5.5 SP2 Update On August 3, we warned our customers and user community that Microsoft had unexpectedly removed support for the plug-in interface and was therefore incompatible with existing versions of Chime and Chime Pro. At the time, we asked our customers to hold off upgrading to Internet Explorer 5.5 SP2 or any later version. We are pleased to announce that we are now confident of delivering a short-term solution to this problem as part of Chime and Chime Pro 2.6 Service Pack 3 (SP3). We expect to release this within the next two weeks. This service pack is designed to work with IE 5.5 SP2, and we expect to be able to extend compatibility to 6.0 at a later date. When used with IE 5.5 SP2 (but not 6.0), this service pack should also have the benefit of fixing the printing problems that have been reported against previous versions of IE 5.5. For the longer term, the Chime team will be continuing to work on architectural changes that will allow Chime to be more independent of the underlying browser technologies. We will release details of these changes on the Chime website once they are firm. Thanks, MDL Chime Product team ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Richards' box extant? Date: Mon, 24 Sep 2001 21:24:39 -0400 To: pdb-l@rcsb.org, rasmol@lists.umass.edu I had the pleasure of speaking with Fred Richards recently. (He and Wyckoff led one of the first two teams that solved protein crystal structures in the USA, ribonucleases, in the mid 1960's). He said he is not aware of any Richards' box ("Fred's Folly") that remains assembled (complete with Kendrew-style brass model, transparent plates with slices of the electron density map, and half-silvered mirrors). These were used in the '60's and '70's until computers became able to support fitting the polypeptide into the electron density ("electronic Richards' boxes"). Does anyone know of a physical Richards' box that remains assembled, anywhere in the world? I hope at least one can be preserved, and that eventually a museum of crystallographic history will house it (or possibly a museum such as the US Smithsonian Institution). I am also interested in where Kendrew-style brass models remain assembled -- a few of these will hopefully be preserved. Also, to reiterate a request I made here recently, I am still looking for photographs of a Richards Box and of Kendrew brass models suitable for my website History of Visualization of Biological Macromolecules, http://www.umass.edu/microbio/rasmol/history.htm -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: Netcape 6.1? Date: Tue, 25 Sep 2001 15:49:53 -0400 To: rasmol@lists.umass.edu Has anyone tested Netscape 6.1 with Chime? Does it solve any of the numerous problems that prevented Netscape 6.0 from working with Chime? I notice that Netscape has released two upgrades of the Communicator series, 4.77 and 4.78, since the release of 6.0. Both work fine with my Chime resources, as has the entire 4.X series, all the way back to 4.08. -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-- X-Accept-Language: fr,en-US References: <200109251933.f8PJXM316180@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Jean-Philippe Demers Subject: Re: Netcape 6.1? Date: Tue, 25 Sep 2001 20:23:58 -0400 To: rasmol@lists.umass.edu Mr Martz, > Has anyone tested Netscape 6.1 with Chime? Yes, I tested it with Windows 2000. > Does it solve any of the > numerous problems that prevented Netscape 6.0 from working with Chime? No. It has the same behavior (e.g. the structure appears, but neither spt buttons nor LiveConnect work) Jean-Philippe Demers By the way, have you received the second draft of the pdbheader project? ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.3) Gecko/20010801 X-Accept-Language: es-AR, es, en, hr References: <200109251933.f8PJXM316180@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: davinci Subject: Re: Netcape 6.1? Date: Tue, 25 Sep 2001 22:36:44 -0300 To: rasmol@lists.umass.edu Hi, I have tested Chime under Win 98 SE and Mozilla 0.9.X Web browser. The "embed molecule" appears and right buttom is fine but the "embed scripts" (application/x-stp) don't work. Regards, Eric Martz wrote: >Has anyone tested Netscape 6.1 with Chime? Does it solve any of the >numerous problems that prevented Netscape 6.0 from working with Chime? > >I notice that Netscape has released two upgrades of the Communicator >series, 4.77 and 4.78, since the release of 6.0. Both work fine with my >Chime resources, as has the entire 4.X series, all the way back to 4.08. > >-Eric Martz > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- charset=us-ascii X-Accept-Language: en,fr-FR X-Apparently-From: SydnyShll@aol.com References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Dr. Sydney Shall" Subject: Re: Richards' box extant? Date: Wed, 26 Sep 2001 14:19:18 +0100 To: rasmol@lists.umass.edu I suggest that you try asking Max Perutz and Aaron Klug at the MRC Molecular Biology unit, Cambridge, (UK). Good Luck, I remember them well. There is [or certainly was] a sculpture in the foyer of the Karolinska Institutet, in Stockholm derived from the sculptor seeing the myoglobin model in Cambridge, UK. Sydney Shall Eric Martz wrote: > I had the pleasure of speaking with Fred Richards recently. (He and Wyckoff > led one of the first two teams that solved protein crystal structures in > the USA, ribonucleases, in the mid 1960's). He said he is not aware of any > Richards' box ("Fred's Folly") that remains assembled (complete with > Kendrew-style brass model, transparent plates with slices of the electron > density map, and half-silvered mirrors). These were used in the '60's and > '70's until computers became able to support fitting the polypeptide into > the electron density ("electronic Richards' boxes"). Does anyone know of a > physical Richards' box that remains assembled, anywhere in the world? > > I hope at least one can be preserved, and that eventually a museum of > crystallographic history will house it (or possibly a museum such as the US > Smithsonian Institution). > > I am also interested in where Kendrew-style brass models remain assembled > -- a few of these will hopefully be preserved. > > Also, to reiterate a request I made here recently, I am still looking for > photographs of a Richards Box and of Kendrew brass models suitable for my > website History of Visualization of Biological Macromolecules, > http://www.umass.edu/microbio/rasmol/history.htm > > -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 > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > -- Dr. Sydney Shall, Department of Molecular Medicine, GKT School of Medicine, The Rayne Institute, 123 Coldharbour Lane, LONDON, SE5 9NU, ENGLAND. TEL: 020 7848 5901; FAX: 020 7733 3877 E-Mail: sydney.shall@kcl.ac.uk ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: Todd Carlson Subject: new feature for chime Date: Wed, 26 Sep 2001 16:35:28 -0400 To: rasmol@lists.umass.edu Dear Chime Users: I want to let potential Chime web page authors know about a feature for Chime that I have developed, in collaboration with Clark Wells of our Math Department. This feature, which I have called MoveTo, allows the web page author to include a button which calls a javascript function that causes a Chime image on the page to rotate, zoom and translate to any desired orientation independent of the starting orientation of the image. Anyone who uses Chime's move command in a Chime tutorial knows that the animation dictated by Move is relative to the starting position. Thus, if you have determined a move command to generate a desired view, you will only get the correct view if the image is in the correct starting orientation. We have also put together a utility page which will calculate the move command needed to go directly from one orientation to another. The third page is a simple page with all the necessary scripts in one document. You can access these pages at: http://faculty.gvsu.edu/carlsont/grant/moveto/moveto.htm http://faculty.gvsu.edu/carlsont/grant/moveutil/moveutil.htm http://faculty.gvsu.edu/carlsont/grant/simple/simple.htm I would like to know if you can get these pages to work and if they would be of use to you. I am not sure of compatibility issues. I am using Chime 2.0.3 in Netscape Communicator 4.51. The feature makes use of View Set and Message Callback commands in a series of javascript functions. I was hoping to have this listed in the World Index of Molecular Visualization and/or sent to the Chime developers for possible inclusion in Chime as a built in script function. Thanks in advance for any feedback. Todd Carlson Dept of Chemistry Grand Valley State University Allendale MI 49401 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Frieda Reichsman Subject: Re: new feature for chime Date: Wed, 26 Sep 2001 18:27:21 -0400 To: rasmol@lists.umass.edu Todd, I have tried the MoveTo page with the default myoglobin pdb file that you provide. It works like a charm!! I am so impressed! Really neat system - well thought out - allowing you two windows to choose beginning and ending positions independently. This is something that Chime developers have needed for a long time - it will not only save a huge amount of time when scripting a tutorial, but due to the ease of testing the commands out (literally seconds to see your command/wish come true!!), your method will enable investigating multiple approaches to moving to several different angles of view at a new position. Congratulations - this is surely a major boon to Chimers everywhere!!! Best wishes, and THANKS!!! Frieda -- Frieda Reichsman, Ph.D. 30 South Whitney Street Molecules In Motion Amherst MA 01002 USA Interactive Molecular Structures (413) 253-2405 http://www.MoleculesInMotion.com ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: Steven Verhey Subject: Re: new feature for chime Date: Wed, 26 Sep 2001 16:00:50 -0700 To: rasmol@lists.umass.edu Hi Todd, moveto sounds great, but FWIW it doesn't work on my machine, a Mac G3 with Netscape 4.7 and Chime 2.6. Thanks for all your work on this, Steve Steven Verhey, Ph.D Assistant Professor Department of Biology Central Washington University Ellensburg, WA 98926 509.963.3431 office 509.963.2730 fax verheys@cwu.edu >>> carlsont@gvsu.edu - 9/26/01 1:35 PM >>> Dear Chime Users: I want to let potential Chime web page authors know about a feature for Chime that I have developed, in collaboration with Clark Wells of our Math Department. This feature, which I have called MoveTo, allows the web page author to include a button which calls a javascript function that causes a Chime image on the page to rotate, zoom and translate to any desired orientation independent of the starting orientation of the image. Anyone who uses Chime's move command in a Chime tutorial knows that the animation dictated by Move is relative to the starting position. Thus, if you have determined a move command to generate a desired view, you will only get the correct view if the image is in the correct starting orientation. We have also put together a utility page which will calculate the move command needed to go directly from one orientation to another. The third page is a simple page with all the necessary scripts in one document. You can access these pages at: http://faculty.gvsu.edu/carlsont/grant/moveto/moveto.htm http://faculty.gvsu.edu/carlsont/grant/moveutil/moveutil.htm http://faculty.gvsu.edu/carlsont/grant/simple/simple.htm I would like to know if you can get these pages to work and if they would be of use to you. I am not sure of compatibility issues. I am using Chime 2.0.3 in Netscape Communicator 4.51. The feature makes use of View Set and Message Callback commands in a series of javascript functions. I was hoping to have this listed in the World Index of Molecular Visualization and/or sent to the Chime developers for possible inclusion in Chime as a built in script function. Thanks in advance for any feedback. Todd Carlson Dept of Chemistry Grand Valley State University Allendale MI 49401 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Pradeep Subject: File Open dialog Date: Thu, 27 Sep 2001 08:58:20 +0800 To: rasmol@lists.umass.edu Hi, I am using Rasmol v 2.6 beta on Sun Solaris 8. The source code compiled ok and the Rasmol main window opens up on execution. However when I try to choose a file using the File -> Open menu, the file chooser dialog box does not show up. Instead the pdb file name has to be provided on the console window. Is this how it's supposed to be or am I missing some libraries ? Thanks in advance for your help. Pradeep. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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 V5.00.2615.200 boundary="Boundary_(ID_C0valBLVNNMCAsOObjCHgg)" X-MSMail-priority: Normal References: X-Authentication-warning: dep.chem.rug.nl: Host biof18.chem.rug.nl [129.125.35.193] claimed to be biof18 ++++------+------+------+------+------+------+------+------+------+------+ From: Tjaard Pijning Subject: Re: new feature for chime Date: Thu, 27 Sep 2001 08:06:56 +0200 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_C0valBLVNNMCAsOObjCHgg) Hi Todd, This utility works well on my system (Win98 with Netscape 4.7 and Chime 2.03). It is really very useful and probably saves most of the Chime users a lot of puzzling with the move command ! I hope to be able to use it for my Chime presentations which I plan to put on the web in the future. Thank you for having developed this great utility ! Kind regards, Ing. Tjaard Pijning -------------------------------------------------------------------------- Protein Crystallography Group Dept. of Chemistry, RU Groningen Nijenborgh 4 9747 AG Groningen The Netherlands tel. (31)(0)50 3634385 email t.pijning@chem.rug.nl --Boundary_(ID_C0valBLVNNMCAsOObjCHgg)
Hi Todd,
 
This utility works well on my system (Win98 with
Netscape 4.7 and Chime 2.03). It is really very useful 
and probably saves most of the Chime users a lot of
puzzling with the move command !
I hope to be able to use it for my Chime presentations
which I plan to put on the web in the future.
Thank you for having developed this great utility !
 
Kind regards,
 
Ing. Tjaard Pijning

Protein Crystallography Group
Dept. of Chemistry, RU Groningen
Nijenborgh 4  9747 AG Groningen
The Netherlands
tel. (31)(0)50 3634385
email t.pijning@chem.rug.nl

Subject: New User Date: Thu, 27 Sep 2001 18:08:05 +0000 To: rasmol@lists.umass.edu Greetings, Molers! I'm a web developer in Atlanta who's new to the list. Looking forward to communicating with ya'll, and perhaps even helping occasionally. Pat O'Hern _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: Todd Carlson Subject: Re: new feature for chime Date: Thu, 27 Sep 2001 14:29:07 -0400 To: "<" MoveTo users: Thanks for the positive feedback. If you are having some troubles, consider this. If you got one page to work and the others don't work, it is possible that there is some error due to having more than one window open at one time. If you have all three pages open on three different windows, you will have the same javascript functions on all three windows with the same variable names, etc. Also, you will have three chime windows with the same name, which I know to be a problem. Sometimes, when I call a MoveTo js function in one window, it works, but on the chime image in another window. Probably bad scripting on my part, but I wanted to get this out to see if anyone likes it before doing more. Try loading only one page at a time in one window at a time and see if that works. Todd ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: Todd Carlson Subject: Re: new feature for chime Date: Thu, 27 Sep 2001 14:31:26 -0400 To: rasmol@lists.umass.edu Steve You are the second Mac G3 person to report a problem. I am not a Mac kind of guy but the biochemisty down the hall is. I will consult with her. Todd >>> Steven.Verhey@cwu.EDU 09/26/01 07:00PM >>> Hi Todd, moveto sounds great, but FWIW it doesn't work on my machine, a Mac G3 with Netscape 4.7 and Chime 2.6. Thanks for all your work on this, Steve Steven Verhey, Ph.D Assistant Professor Department of Biology Central Washington University Ellensburg, WA 98926 509.963.3431 office 509.963.2730 fax verheys@cwu.edu >>> carlsont@gvsu.edu - 9/26/01 1:35 PM >>> Dear Chime Users: I want to let potential Chime web page authors know about a feature for Chime that I have developed, in collaboration with Clark Wells of our Math Department. This feature, which I have called MoveTo, allows the web page author to include a button which calls a javascript function that causes a Chime image on the page to rotate, zoom and translate to any desired orientation independent of the starting orientation of the image. Anyone who uses Chime's move command in a Chime tutorial knows that the animation dictated by Move is relative to the starting position. Thus, if you have determined a move command to generate a desired view, you will only get the correct view if the image is in the correct starting orientation. We have also put together a utility page which will calculate the move command needed to go directly from one orientation to another. The third page is a simple page with all the necessary scripts in one document. You can access these pages at: http://faculty.gvsu.edu/carlsont/grant/moveto/moveto.htm http://faculty.gvsu.edu/carlsont/grant/moveutil/moveutil.htm http://faculty.gvsu.edu/carlsont/grant/simple/simple.htm I would like to know if you can get these pages to work and if they would be of use to you. I am not sure of compatibility issues. I am using Chime 2.0.3 in Netscape Communicator 4.51. The feature makes use of View Set and Message Callback commands in a series of javascript functions. I was hoping to have this listed in the World Index of Molecular Visualization and/or sent to the Chime developers for possible inclusion in Chime as a built in script function. Thanks in advance for any feedback. Todd Carlson Dept of Chemistry Grand Valley State University Allendale MI 49401 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: John Tweedie Subject: Re: new feature for chime Date: Fri, 28 Sep 2001 16:53:38 +1200 To: rasmol@lists.umass.edu Todd I am having the same problem with a beige 266 mH G3 Mac. Netscape 4.76 and Chime 2.6 John Tweedie >Steve > >You are the second Mac G3 person to report a problem. I am not a Mac kind >of guy but the biochemisty down the hall is. I will consult with her. > >Todd > > >>>> Steven.Verhey@cwu.EDU 09/26/01 07:00PM >>> > >Hi Todd, > >moveto sounds great, but FWIW it doesn't work on my machine, a Mac G3 with >Netscape 4.7 and Chime 2.6. > >Thanks for all your work on this, > >Steve > >Steven Verhey, Ph.D >Assistant Professor >Department of Biology >Central Washington University >Ellensburg, WA 98926 >509.963.3431 office >509.963.2730 fax >verheys@cwu.edu > >>>> carlsont@gvsu.edu - 9/26/01 1:35 PM >>> >Dear Chime Users: > >I want to let potential Chime web page authors know about a feature for >Chime that I have developed, in collaboration with Clark Wells of our Math >Department. This feature, which I have called MoveTo, allows the web page >author to include a button which calls a javascript function that causes a >Chime image on the page to rotate, zoom and translate to any desired >orientation independent of the starting orientation of the image. Anyone >who uses Chime's move command in a Chime tutorial knows that the animation >dictated by Move is relative to the starting position. Thus, if you have >determined a move command to generate a desired view, you will only get >the correct view if the image is in the correct starting orientation. We >have also put together a utility page which will calculate the move >command needed to go directly from one orientation to another. The third >page is a simple page with all the necessary scripts in one document. You >can access these pages at: > >http://faculty.gvsu.edu/carlsont/grant/moveto/moveto.htm > >http://faculty.gvsu.edu/carlsont/grant/moveutil/moveutil.htm > >http://faculty.gvsu.edu/carlsont/grant/simple/simple.htm > >I would like to know if you can get these pages to work and if they would >be of use to you. I am not sure of compatibility issues. I am using >Chime 2.0.3 in Netscape Communicator 4.51. The feature makes use of View >Set and Message Callback commands in a series of javascript functions. I >was hoping to have this listed in the World Index of Molecular >Visualization and/or sent to the Chime developers for possible inclusion >in Chime as a built in script function. > >Thanks in advance for any feedback. > >Todd Carlson >Dept of Chemistry >Grand Valley State University >Allendale MI 49401 > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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 f91GuJW20843 ++++------+------+------+------+------+------+------+------+------+------+ From: Todd Carlson Subject: MoveTo Update Date: Mon, 01 Oct 2001 12:53:52 -0400 To: rasmol@lists.umass.edu Last week I posted info on my MoveTo pages, which generated a bit of interest. Several Mac users said they couldn't get the feature to work. I debugged the page by putting in a temporary text box to have the javascript feed back info to the screen so I could trace its progress and see where things were going wrong. I had a biochemist down the hall with a Mac G3 try my page. The problem seem to be that the view show view chime command that is executed by the MoveTo js function was causing any feedback to go to the echo js function. Echo is then supposed to call the MoveToCalc js function which calculates and executes the move. I confirmed that the view show view command works on G3 using Protein Explorer. However, I noticed that on my PC (where the debugging page worked), the echo function indicated that it was being called by another chime script at the same time it was executing the View Show View chime script command. I determined that this chime script was the Chime button that was used to call the the original MoveTo js function. When I used a form button instead of a chime button to call the js, the page worked on both PC and Mac G3. I have put an updated version of the MoveTo and Simple MoveTo pages on the web with form buttons instead of Chime buttons. If you couldn't get MoveTo to work last week, I would appreciated it if you could try these revised pages and let me know what happens. Remember that you can only have one Netscape window open at a time for the current versions to work. This is because I have used the same name for the Chime plug-ins on each page. I can fix that problem later. People using IE also reported problem, which could be due to the same problem or a problem with different js or the view show view chime command. What are the IE compatability issues? Finally, has anyone else had problems when chime is called to execute two commands simultaneously? Todd Carlson GVSU ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Rekha.Iyer@asu.edu Subject: helix start residue Date: Tue, 02 Oct 2001 11:00:52 -0700 (MST) To: rasmol@lists.umass.edu Is the first residue of an alpha helix as listed in the PDB file an N-cap residue, that is, the interface residue half in and half out of the helix or is it the N1 residue (N-cap + 1)? Rekha ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: fr,en-US References: ++++------+------+------+------+------+------+------+------+------+------+ From: Jean-Philippe Demers Subject: Re: new feature for chime Date: Tue, 02 Oct 2001 20:31:54 -0400 To: rasmol@lists.umass.edu Mr. Carlson, The problem is maybe that you have given the same name tag to more than one plugin. For example, if pages 'moveutil.htm' and 'simple.htm' are opened at the same time and you send a script to the 'myoglobin' plug-in, then Netscape won't know which plugin to send the script to. A solution might just be to rename the different plugins. Jean-Philippe Demers ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: Todd Carlson Subject: Re: new feature for chime Date: Wed, 03 Oct 2001 08:54:54 -0400 To: rasmol@lists.umass.edu I know about this and warned people of this earlier. The easy fix is to just have one window open. If that doesn't solve the problem, then it must be something else. But I should fix this so others don't have to worry about it. I will try to get to it soon. Todd >>> diane.demers@sympatico.ca 10/02/01 08:31PM >>> Mr. Carlson, The problem is maybe that you have given the same name tag to more than one plugin. For example, if pages 'moveutil.htm' and 'simple.htm' are opened at the same time and you send a script to the 'myoglobin' plug-in, then Netscape won't know which plugin to send the script to. A solution might just be to rename the different plugins. Jean-Philippe Demers ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: Todd Carlson Subject: moveto update Date: Wed, 03 Oct 2001 11:52:11 -0400 To: rasmol@lists.umass.edu I have posted some updated versions of my pages at: http://faculty.gvsu.edu/carlsont/ I fixed a few glitches: The simple and moveto pages now have different names for the chime images which should end the problem of having more than one page open at a time The simple and moveto pages also have a command to prevent translations of more than 100, which fail when executing the chime move command All pages now have an option of avoiding the use of the executeScript command, which isn't supported by IE. Instead, a chime button is written in a dummy frame and executed immediately. This fix was supplied by Paul Pillot. (thanks). Also, make sure your javascript is turned on. I hope we can get a version that works for everyone. Todd ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 boundary="Boundary_(ID_7KhkjnFyXGSFYyArgtrHYg)" X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: paul pillot Subject: Compatibility between Chime and IE 6.0 Date: Thu, 04 Oct 2001 10:19:29 +0200 To: rasmol@lists.umass.edu C'est un message de format MIME en plusieurs parties. --Boundary_(ID_7KhkjnFyXGSFYyArgtrHYg) Hello to all chimeleons ! I've updated chime to version 2.6 SP3, and it works fine with IE 5.5 SP2 (congratulations to the Chime team !) I'd like to know if somebody tried this chime version with IE 6.0. Thanks Paul Pillot --Boundary_(ID_7KhkjnFyXGSFYyArgtrHYg)

Hello to all chimeleons !
 
I've updated chime to version 2.6 SP3, and it works fine with IE 5.5 SP2 (congratulations to the Chime team !)
 
I'd like to know if somebody tried this chime version with IE 6.0.
 
Thanks
 
Paul Pillot
--Boundary_(ID_7KhkjnFyXGSFYyArgtrHYg)-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Giulio Vistoli Subject: Announcing VEGA 1.3.1 OpenGL Edition Date: Wed, 10 Oct 2001 18:01:35 +0200 To: rasmol@lists.umass.edu we are glad to announce that the final 1.3.1 release of VEGA package is now ready for free download on our web server (http://users.unimi.it/~ddl). VEGA was developed to create a bridge between most of the molecular software packages, like Quanta/CHARMm, Insight II, MoPac, BioDock, etc. In this tool have been also implemented some features that are useful to analyze, display and manage the 3D structures of molecules. The most important features implemented in VEGA are: - Several file formats supported for input and output. - Multiple files load for assemblies creation. - Atomic charge attribution. - Force field attribution. - Calculation of molecular surfaces. - Calculation of ligand-receptor interaction energy. - Evaluation of logP and lipole. - Dynamic trajectory analysis. - Molecule solvatation. Available OpenGL packages: - VEGA Win32 1.3.0 OpenGL Edition. Available standard packages: - VEGA AmigaOS 1.3.0 - VEGA Linux x86 (1.3.0) - VEGA Silicon Graphics IRIX 6.x (1.3.0) The VEGA OpenGL version allows to visualize 3D molecular structures in several draw mode (wireframe, CPK solid & wireframe, Van der Waals solid & wireframe) using an high optimized graphical engine. The VEGA OpenGL can calculate and display any type of molecular surface: Van der Waals, surface accessible to solvent (SAS), molecular electrostatic potential (MEP), hydropathicity surface (ILM), molecular lypophilicity surface (MLP), etc. Each surface can be colored in several modes (by atom, by molecule, by property, custom). The most significant features are: **** 3D Graphics **** - Strong hardware acceleration (depending on your graphic card). - 3D molecule view (wireframe, CPK wireframe, CPK solid, VdW wireframe, VdW solid). - 3D surface view with most coloring methods (property, atom type and custom). - 3D object manipulation. - Lighting (available with hardware acceleration only). - Smooth animations. - Color properties. - Labels (atom name, element, atom type, atom number and atomic charge). - Mouse control for rotations, translations, scale operations and animations. **** Graphic User Interface **** - All VEGA functions are available trough menu and/or requesters. - Extended menu with accelerators. - Context menu. - Buttons, radio buttons, combo boxes, list boxes, check boxes and sliders. - Copy & Paste operations. - Integrated Html help. **** Calculation Tools **** - Analysis of molecular dynamics trajectory files. - Graphic interface for BioDock 3.0. - Graphic interface for MoPac 6 (included in the package). - Molecular properties. **** Extra Tools **** - Integrated Mini Text Editor. - Integrated Graph Editor. - Task manager. **** External Tools **** - File decompressor (WinDD). - SendVegaCmd console command for batch file creation. **** Other **** - Communication port for batch file scripting (see SendVegaCmd utility). - Full language localization (locale.dll). - Pentium optimized code for maximum performances. - Demo. The VEGA OpenGL package was developed for Windows 9x/ME/NT/2000 only and in the future can be available for other operating systems with OpenGL API support. New in this release: - Win32: improved CPK visualization. - Win32: added VdW Dotted and Liquorice visualization modes. - Win32: some configuration parameters (window size and position, menu checkmarks, etc) are stored when the program is closed. - Win32: menu history of the opened files. - Win32: added window popup menu to resize the main. - Win32: more than one VEGA session can be opened at the same time. - Win32: drag & drop function to open the molecules. - SendVegaCmd can control more than one VEGA session. - SendVegaCmd asyncronous mode. Thank you for your attention. Giulio Vistoli & Alessandro Pedretti -- Dr. Giulio Vistoli Ist. di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano (Italy) Tel. +39-02-58357522 Fax +39-02-58357565 E-Mail: giulio.vistoli@unimi.it WWW: http://users.unimi.it/~ddl ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <200110081738.f98HcZW27734@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Chime sites in IE Date: Wed, 10 Oct 2001 15:36:02 -0400 To: Vickie Mckee Cc: rasmol@lists.umass.edu Re: IE and Chime. It is a big problem because Chime is a "netscape plugin" and IE has never supported these well. The most important thing is that if the computers have IE5.5 SP2, you MUST use Chime 2.6 SP3 released a couple of weeks ago. Microsoft removed more plugin support in IE5.5 SP2, and luckily MDL was able to solve this problem in SP3 of Chime. Earlier versions of IE5.5 (through SP1) work to some extent with Chime 2.6 SP2. Chime 2.6 SP3 should work with the earlier versions of IE as well as the most recent. Some websites designed for Netscape will not work in IE unless redesigned. This involves changes in the javascript and html of the websites and is not trivial. If you're interested in details, subscribe to the MolVis freeware email list (below) where these technicalities are discussed. At present, there is no website I know about where all the Chime vs. IE issues are documented. One is needed, but the recent changes have made this even more difficult. We believe we can make Protein Explorer work in IE and getting that capability released is a current priority. It has been complicated by Microsoft's recent changes in policy, but it again looks feasable now, thanks to volunteer efforts (Paul Pillot and Jean-Philippe Demers). At 10/08/2001, you wrote: >Eric, > Thanks. I have downloaded protein explorer and it is working fine. > Question for you: Do you know of any source of hints for running CHIME >on Explorer? I am using Netscape but my university computer centre controls >all the student-access computer labs very strictly and they run only >Explorer (even worse - they run a "corporate desktop" version). I have >assorted CHIME stuff running more-or-less but the combination of Explorer >and university computer security protocols keep throwing up niggly >problems - which someone else must have also seen. >***************************************************** >Vickie McKee >Chemistry Department >Loughborough University >Loughborough >Leics LE11 3TU >email: v.mckee@lboro.ac.uk >http://www-staff.lboro.ac.uk/~cmvm >Phone: +44 (0)1509 222565 >Fax (Dept): +44 (0)1509 223925 >***************************************************** > >> > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - 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-- boundary="Boundary_(ID_CP9DqYFnH0hkKbzsAR4NHg)" X-Accept-Language: de,en ++++------+------+------+------+------+------+------+------+------+------+ From: Scharfenberg Franz-Josef Subject: Chime Tutorials in German Date: Thu, 11 Oct 2001 16:50:13 +0200 To: rasmol@lists.umass.edu --Boundary_(ID_CP9DqYFnH0hkKbzsAR4NHg) Hi everyone working with Chime, I will announce some tutorials in Chime. I have developed two organic chemistry tutorials in chime by myself and translated and changed some other tutorials developed by Americans in German language. All authors have given permission to me to publish the translated tutorials at our school homepage Virtuelle Moleküle (Tutorials in Chime) . Their is also a link to my sites in http://molvis.sdsc.edu/visres/#noneng . If there will be any change in organisation of our school homepage by the webmaster, the link in this list will be changed too. Sincererly Franz-Josef Scharfenberg Richard-Wagner-Gymnasium Wittelsbacherring 9 D-95444 Bayreuth (Germany) --Boundary_(ID_CP9DqYFnH0hkKbzsAR4NHg) Hi everyone working with Chime,


I will announce some tutorials in Chime.
I have developed two organic chemistry tutorials in chime by myself and translated  and changed some other tutorials developed by Americans in German language. All authors have given permission to me to publish the translated tutorials at our school 
homepage  Virtuelle Moleküle (Tutorials in Chime) .
Their is also a link to my sites in  http://molvis.sdsc.edu/visres/#noneng . 
If there will be any change in organisation of our school homepage by the webmaster,  the  link  in this list will be changed too.
Sincererly
Franz-Josef Scharfenberg
Richard-Wagner-Gymnasium
Wittelsbacherring 9
D-95444 Bayreuth (Germany) --Boundary_(ID_CP9DqYFnH0hkKbzsAR4NHg)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Problems with Chime in Internet Explorer Date: Sat, 13 Oct 2001 19:44:58 -0400 To: rasmol@lists.umass.edu, webmaster@mdlchime.com, bdickey@mdli.com I've had mixed results with the new Chime 2.6SP3 in the new IE 5.5SP2. I'd like to know what others have found, and especially any tricks to work around the various problems mentioned below. My few tests confirmed that older Chime versions don't work in IE5.5SP2, even when they did work in earlier versions of IE. On all systems I've tested, I used the IE menu Tools, Windows Upgrade to upgrade to IE5.5SP2. In general, I've used the custom upgrade option to avoid installing Outlook Express -- possibly there is something that is not obvious that I must install to get IE to cooperate with Chime? All sites and computers mentioned below work perfectly in Netscape 4.08 or later with Chime 2.0.3/2.0a or later. Below are my results with IE5.5SP2 + Chime2.6SP3. -----------PARTIAL FUNCTION IN WINDOWS 98----------- On one Windows 98 computer (Desktop P3/667MHz, martz8, 4.10.2222.A 2nd edition) I find that Chime works with buttons that have literal scripts within the embed tag. These sites that work include (at http://www.umass.edu/microbio/chime) -Chime, How To Use It [THIS IS THE TEST PAGE I USED FOR THE 2 COMPUTERS BELOW] -Amino Acid Quizzer -Infrared Spectrum with Animated Molecular Vibrations -Programming Chime Web Pages from Scratch What does not work are sites in which the buttons call script files. That is, the embed tag script string is for example "script globin1.spt", and the command script is in file globin1.spt. Scripts seem to get truncated in the middle, so only the early commands get executed, and in some cases, it appears that a command is truncated in the middle, so an error message reports an invalid command, which is in fact half of a valid command in the script file. Unfortunately, most of my sites use script files, for example (also at http://www.umass.edu/microbio/chime) -DNA -Hemoglobin -Knots in proteins -Lipid Bilayers and Gramicidin Channel -----------NO BUTTON FUNCTION IN WINDOWS 98------------- On another Windows 98 computer (Dell notebook, P2/300MHz, martz5, 4.10.1998, not 2nd edition), I've never been able to get Chime buttons to work in IE. (However, I've seen them work in other Win98 1st edition installations.) Chime is invoked and shows the initial image, but buttons don't work at all (IE5.0, Chime 2.6, no service packs). Months ago, I upgraded to IE5.5SP1 and ran the repair routine (offered under Add/Remove Programs, Uninstall, IE). I spent hours trying to uninstall and reinstall IE (the best could do was delete lots of files and run the repair routine), to no avail. Today I upgraded to IE5.5SP2 and Chime 2.6SP3. Still, the Chime buttons don't work. Furthermore, after displaying any page with Chime and closing IE, I reproducibly get "this program has performed an illegal operation". Although upgrading to Chime 2.6SP3 enabled IE5.5SP2 to invoke Chime and show a molecule (before, it showed the broken plugin), Chime reported its version as 2.6 (not 2.6SP3). However, among the 11 npchime.dll files on my disk, only the one in c:\program files\internet explorer\plugins has a write date of 9/10/2001. So I did an uninstall for all 3 Chimes listed in my Add/Remove Programs Uninstall list (IE, Communicator, Navigator). Then I reinstalled 2.6SP3 into all 3 browser categories. Now IE does report the Chime it is invoking as SP3; however, the buttons still don't work. ------------NO BUTTON FUNCTION IN WINDOWS 2000------------- I have a 20G disk with Windows 2000 installed on it solely for testing Chime and Chime website functions. The original Win2K installation included IE5.0, and worked to some extent with Chime 2.0.3. I upgraded to IE5.5SP2, and Chime 2.6SP3. Chime is invoked and displays the initial molecule view, but Chime buttons have no effect (don't work). (This Win2K disk is in completely different hardware than the above Win98 system that has identical symptoms.) The Win98 system where I can't get Chime buttons to work in IE has a long history -- it is my primary work site. Conceivably something I did in the past could account for the problem (though I would have hoped that the IE repair function would have fixed it). However, the Win2K system has only been booted a few times, and used only for a few tests. So the fact that the IE5.5SP2/Chime2.6SP3 combination fails there gives me low confidence that this combination will work widely, or be supportable. Paul Pillot has modified Protein Explorer so that most of it works in IE5.5SP2 with Chime2.6SP3. I was optimistic that we could release a Protein Explorer fully compatible with IE. (If necessary, we could move the few script files that it uses into javascript variables.) However, in view of the Win2K result above, I'm less optimistic. I'd like to know what other people have observed, especially with Windows 2000 after an upgrade from IE 5.0. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: paul pillot Subject: Re: Problems with Chime in Internet Explorer Date: Sun, 14 Oct 2001 13:07:47 +0200 To: rasmol@lists.umass.edu, webmaster@mdlchime.com, bdickey@mdli.com As I haven't got Win2k, I won't be able to answer to specific questions about it. Indeed, if you read the Chime message forum on mdl's site, you'll find several questions about it. Concerning the script files in the buttons, you matched : > What does not work are sites in which the buttons call script files. That > is, the embed tag script string is for example "script globin1.spt", and > the command script is in file globin1.spt. Scripts seem to get truncated in > the middle, so only the early commands get executed, and in some cases, it > appears that a command is truncated in the middle, so an error message > reports an invalid command, which is in fact half of a valid command in the > script file. Unfortunately, most of my sites use script files, for example > (also at http://www.umass.edu/microbio/chime) > -DNA > -Hemoglobin > -Knots in proteins > -Lipid Bilayers and Gramicidin Channel > In Protein Explorer, heavy script files such as contact.spt, wich calculates contact surfaces, work with IE and Chime. So I don't think that the lentgh of the script is the main problem. When Tim Dricolls has made his fade scripts available, I tried them, and even if some of them are small, they are always broken after few instructions, except if all 'delay' commands are discarded (but then his beautifull scripts have no more interest, because there is no more fade effect). I matched also that after a load command or a script command the scripts are broken in IE. In globin1.spt, the script begins by this : zap background [0,0,0] load pdb "2hhd.pdb" set ambient 60 set specular off So, after the load pdb command, no more instructions could be executed. In fact, I discovered that the following instructions in scripts are kept in memory and reappeared when another load or script command is called. In conclusion, in script files, the instructions which cause troubles are at least : - load - script - delay As long as these instructions don't exist in the Protein explorer's script files, it should run correctly with Internet Explorer. I'd like to know if somebody else has matched this buggs or others... It could be a great idea to check off all IE buggs and the tricks to avoid them. Paul Pillot ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 X-MSMail-priority: Normal References: ++++------+------+------+------+------+------+------+------+------+------+ From: Tamas Gunda Subject: Re: Problems with Chime in Internet Explorer Date: Sun, 14 Oct 2001 19:19:13 +0200 To: rasmol@lists.umass.edu Eric, You did not mentioned a very important thing in connection with the test (or did I overlook it?): What were the security settings in IE? There are several options there, which can substantially influence the result. Did you gave a try when the security was in the lowest position? Best regards Tamas ------------------------------------- Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Academy of Sciences University of Debrecen, POBox 36 H-4010 Debrecen Hungary ----- Original Message ----- Sent: Sunday, October 14, 2001 1:44 AM From: "Eric Martz" Subject: Problems with Chime in Internet Explorer To: ; ; > I've had mixed results with the new Chime 2.6SP3 in the new IE 5.5SP2. I'd > like to know what others have found, and especially any tricks to work > around the various problems mentioned below. > > My few tests confirmed that older Chime versions don't work in IE5.5SP2, > even when they did work in earlier versions of IE. > ..... ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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-Lboro-Filtered: mailer2.lut.ac.uk, Sun, 14 Oct 2001 18:23:29 +0100 References: <001601c154d4$58b80760$0200a8c0@cthulhu> ++++------+------+------+------+------+------+------+------+------+------+ From: Vickie Mckee Subject: Re: Problems with Chime in Internet Explorer Date: Sun, 14 Oct 2001 18:20:37 +0100 To: rasmol@lists.umass.edu Some IE security problems can be evaded by supplying an absolute URL for any page including chime - doesn't do much for portability, though. ***************************************************** Vickie McKee Chemistry Department Loughborough University Loughborough Leics LE11 3TU email: v.mckee@lboro.ac.uk http://www-staff.lboro.ac.uk/~cmvm Phone: +44 (0)1509 222565 Fax (Dept): +44 (0)1509 223925 ***************************************************** ----- Original Message ----- Sent: Sunday, October 14, 2001 6:19 PM From: "Tamas Gunda" Subject: Re: Problems with Chime in Internet Explorer To: > Eric, > > You did not mentioned a very important thing in connection with the test > (or did I overlook it?): > > What were the security settings in IE? There are several options there, > which > can substantially influence the result. Did you gave a try when the security > was in > the lowest position? > > Best regards > > Tamas > ------------------------------------- > Dr Tamas E. Gunda > Research Group for Antibiotics > of the Hungarian Academy of Sciences > University of Debrecen, POBox 36 > H-4010 Debrecen > Hungary > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: Problems with Chime in Internet Explorer II Date: Sun, 14 Oct 2001 19:53:53 +0200 To: rasmol@lists.umass.edu On the Chime buttons under IE 5.5 SP1. Eric, I use Chime and IE on two PCs, at home Win2000, at the university Win98 2nd edition. Both have IE5.5 SP1 + all (4 or 5) security updates installed, and Chime 2.6 SP2. I have no problem with Chime and its buttons. What I realized quite a time ago that buttons does not work if the script is in a separate file. But when I embedded the scripts, as it is shown below, they work without any problem. Try it directly from my home page: http://www.klte.hu/~gundat/blaktam_rev/klavam1.htm It is written in Hungarian, anyway, at the bottom of the page there is broad button in the middle, this starts it. Best regards Tamas ----------------- Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Academy of Sciences University of Debrecen, POBox 36 H-4010 Debrecen Hungary The script = "script klav.scr" solution did not work under IE ----- Original Message ----- Sent: Sunday, October 14, 2001 1:44 AM > ------------NO BUTTON FUNCTION IN WINDOWS 2000------------- > I have a 20G disk with Windows 2000 installed on it solely for testing > Chime and Chime website functions. The original Win2K installation included > IE5.0, and worked to some extent with Chime 2.0.3. I upgraded to IE5.5SP2, > and Chime 2.6SP3. Chime is invoked and displays the initial molecule view, > but Chime buttons have no effect (don't work). (This Win2K disk is in > completely different hardware than the above Win98 system that has > identical symptoms.) > ... From: "Eric Martz" Subject: Problems with Chime in Internet Explorer To: ; ; ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 X-MSMail-priority: Normal References: <004101c154d9$308e40b0$0200a8c0@cthulhu> ++++------+------+------+------+------+------+------+------+------+------+ From: paul pillot Subject: Re: Problems with Chime in Internet Explorer II Date: Sun, 14 Oct 2001 22:23:27 +0200 To: rasmol@lists.umass.edu Tamas, I tried to create two scripts based on your embed script : one with the delay command included (called gunda.scr), and another without these commands (called gunda2.scr) (delay is used twice in your script). For the gunda.scr, it breaks and fails after the first delay command. For the second script, it runs till the end, and no error occurs. But the transition is of course discarded. If you want to test this, i could post you these files. In conclusion, the delay command, when included in an external script file, causes Chime in IE to failed Paul ----- Original Message ----- Sent: Sunday, October 14, 2001 7:53 PM From: "Tamas Gunda" Subject: Re: Problems with Chime in Internet Explorer II To: > On the Chime buttons under IE 5.5 SP1. > > Eric, > > I use Chime and IE on two PCs, at home Win2000, at the university Win98 2nd > edition. Both > have IE5.5 SP1 + all (4 or 5) security updates installed, and Chime 2.6 SP2. > I have no problem with Chime and its buttons. > What I realized quite a time ago that buttons does not work if the script is > in a separate file. But when > I embedded the scripts, as it is shown below, they work without any problem. > > Try it directly from my home page: > http://www.klte.hu/~gundat/blaktam_rev/klavam1.htm > > It is written in Hungarian, anyway, at the bottom of the page there is broad > button in the middle, this starts it. > > Best regards > > Tamas > ----------------- > Dr Tamas E. Gunda > Research Group for Antibiotics > of the Hungarian Academy of Sciences > University of Debrecen, POBox 36 > H-4010 Debrecen > Hungary > > > button=push target="cepht" > script="background [0,0,0];set ambient 66 > select *; spacefill off; strands off; dots off; backbone off; labels > off;spin off > reset;color atoms CPK; wireframe on > rotate y 42 > rotate x -100 > zoom 420 > translate y -30 > translate x 30 > delay > select tem > colour cpk > wireframe .2 > delay 2 > select ser70 > wireframe .1 > select ser70.OG > cpk .5 > select atomno==312 > colour label white > label %n%r" > > > > The script = "script klav.scr" solution did not work under IE > > > ----- Original Message ----- > From: "Eric Martz" > To: ; ; > Sent: Sunday, October 14, 2001 1:44 AM > Subject: Problems with Chime in Internet Explorer > > ------------NO BUTTON FUNCTION IN WINDOWS 2000------------- > > I have a 20G disk with Windows 2000 installed on it solely for testing > > Chime and Chime website functions. The original Win2K installation > included > > IE5.0, and worked to some extent with Chime 2.0.3. I upgraded to IE5.5SP2, > > and Chime 2.6SP3. Chime is invoked and displays the initial molecule view, > > but Chime buttons have no effect (don't work). (This Win2K disk is in > > completely different hardware than the above Win98 system that has > > identical symptoms.) > > ... > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 X-MSMail-priority: Normal References: <004101c154d9$308e40b0$0200a8c0@cthulhu> ++++------+------+------+------+------+------+------+------+------+------+ From: paul pillot Subject: Re: Problems with Chime in Internet Explorer III Date: Mon, 15 Oct 2001 00:05:16 +0200 To: rasmol@lists.umass.edu Tamas, as the delay command doesn't seem to work, i tried to replace it in your script with a single move command : move -100 42 0 420 30 -30 0 0 1 and it causes the same troubles. I decreased the delay to 0, with no effects. I tried a script file with only this move command : the script is being loaded, the command seems to be processed by the plug-in (the messageCallback function reports this command), but nothing happens, and it's impossible to get chime work again. So, the list of the commands that may not being used in script file with IE, is growing ! - delay - move - script x.spt... - load x.pdb... (the two last commands seem to cause no troubles if they are used at the end of a script) Best Regards Paul Pillot . > What I realized quite a time ago that buttons does not work if the script is > in a separate file. But when > I embedded the scripts, as it is shown below, they work without any problem. > > Try it directly from my home page: > http://www.klte.hu/~gundat/blaktam_rev/klavam1.htm > > It is written in Hungarian, anyway, at the bottom of the page there is broad > button in the middle, this starts it. > > Best regards > > Tamas > ----------------- > Dr Tamas E. Gunda > Research Group for Antibiotics > of the Hungarian Academy of Sciences > University of Debrecen, POBox 36 > H-4010 Debrecen > Hungary > > > button=push target="cepht" > script="background [0,0,0];set ambient 66 > select *; spacefill off; strands off; dots off; backbone off; labels > off;spin off > reset;color atoms CPK; wireframe on > rotate y 42 > rotate x -100 > zoom 420 > translate y -30 > translate x 30 > delay > select tem > colour cpk > wireframe .2 > delay 2 > select ser70 > wireframe .1 > select ser70.OG > cpk .5 > select atomno==312 > colour label white > label %n%r" > > > > The script = "script klav.scr" solution did not work under IE ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: fr,en-US References: <004101c154d9$308e40b0$0200a8c0@cthulhu> <000701c154fc$5392b5a0$b3d8fac1@fti36qrh9z> ++++------+------+------+------+------+------+------+------+------+------+ From: Jean-Philippe Demers Subject: Re: Problems with Chime in Internet Explorer III Date: Sun, 14 Oct 2001 22:05:45 -0400 To: rasmol@lists.umass.edu Hi Paul, I had problems a few weeks ago with scripts containing a "show pdbheader" command, no matter if the command was included in a script file or not. I think that this bug was dependent on the length of the PDB header of the file. I was wondering if you had the same problem... Bonne chance dans votre travail... Jean-Philippe Demers ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Chime under x86 linux Date: Tue, 16 Oct 2001 12:26:53 -0400 To: rasmol@lists.umass.edu Erik Luijten (luijten@uiuc.edu) has kindly provided a page that describes how to use the commercial (US$20) Codeweavers' CrossOver Plugin to run Windows-Chime in native x86 linux Netscape (http://ariadne.mse.uiuc.edu/Info/chime_linux.html). This method does not require booting a Windows subsystem. He reports that Chime itself works, but that Protein Explorer (PE) fails to load the specified molecule. I have accordingly updated at my site "Chime: Browsers, Platforms, Installation, Troubleshooting" (http://www.umass.edu/microbio/chime/neccsoft.htm), and the document explaining options for using PE under linux (http://molvis.sdsc.edu/protexpl/platform.htm), and the document displayed when PE detects a platform other than Windows or Macintosh (http://molvis.sdsc.edu/protexpl/needplat.htm). At the latter I've provided information on how to bypass platform testing in order to start PE under native linux. These documents also describe two methods that do enable PE to work in a Windows subsystem booted under linux. If anyone wishes to volunteer to devise workarounds within Protein Explorer to get it to work in this native mode under x86 linux, I'll be happy to point out portions of PE's javascript relevant to sticking points you identify. (When you download PE, you get its entire javascript source code.) I myself have not tested this mode, because I believe the number of people who would prefer to use this mode of PE will be few. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: PDB files needed... Date: Mon, 22 Oct 2001 10:09:38 -0400 To: RasMol List hello all, I am in need of three PDB files that I can not find in the usual places (RCSB, Klotho, EBI, etc.). Can anyone help? the structures are: 1. sucrose (alternatively maltose, or lactose, or any disaccharaide). 2. cyclic GMP. 3. aspirin, but in PDB format (I am aware that RasMol ships with the aspirin structure, but it is a MOL file). any help is greatly appreciated. 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-- Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: Todd Carlson Subject: Re: PDB files needed... Date: Mon, 22 Oct 2001 10:46:35 -0400 To: rasmol@lists.umass.edu http://www.nyu.edu/pages/mathmol/library/sugars/ http://www.nyu.edu:80/pages/mathmol/library/drugs/ I found sucrose and aspirin at the above links using google. I found a cGMP.pdb file, but it was only GMP, not cyclic. I did find some cAMP files. I suppose you could change them. Or find a protein with cGTP bound (if any exist) and delete the protein. Todd >>> driscoll@molvisions.com 10/22/01 10:09AM >>> hello all, I am in need of three PDB files that I can not find in the usual places (RCSB, Klotho, EBI, etc.). Can anyone help? the structures are: 1. sucrose (alternatively maltose, or lactose, or any disaccharaide). 2. cyclic GMP. 3. aspirin, but in PDB format (I am aware that RasMol ships with the aspirin structure, but it is a MOL file). any help is greatly appreciated. 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-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: PDB files needed... Date: Mon, 22 Oct 2001 12:50:56 -0400 To: rasmol@lists.umass.edu thanks to Todd and Suzanne, who tie for the fastest response ;-). I now have all the PDB files that I need except cGMP, which is proving more difficullt to track down. I did search the PDB for cGMP-binding proteins and found two (plus one theoretical model). unfortunately, none of them included cGMP, so the search continues... thanks again, tim On 10.22.01 at 10:46 AM, carlsont@gvsu.edu (Todd Carlson) wrote: > > > http://www.nyu.edu/pages/mathmol/library/sugars/ > > http://www.nyu.edu:80/pages/mathmol/library/drugs/ > > > I found sucrose and aspirin at the above links using google. > I found a cGMP.pdb file, but it was only GMP, not cyclic. > > I did find some cAMP files. I suppose you could change them. Or find a protein > with cGTP bound (if any exist) and delete the protein. > > Todd > > > > >>> driscoll@molvisions.com 10/22/01 10:09AM >>> > hello all, > > I am in need of three PDB files that I can not find in the usual places (RCSB, > Klotho, EBI, etc.). Can anyone help? > > the structures are: > > 1. sucrose (alternatively maltose, or lactose, or any disaccharaide). > 2. cyclic GMP. > 3. aspirin, but in PDB format (I am aware that RasMol ships with the aspirin > structure, but it is a MOL file). > > > any help is greatly appreciated. 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 > > > > > > _________________________________________ 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-MIMETrack: Serialize by Router on CDCLNPH1/Pharma_MHUB(Release 5.0.8 |June 18, 2001) at 10/22/2001 01:16:12 PM ++++------+------+------+------+------+------+------+------+------+------+ From: James.L.Meek@dupontpharma.com Subject: Re: PDB files needed... Date: Mon, 22 Oct 2001 13:16:09 -0400 To: rasmol@lists.umass.edu > driscoll@molvisions.com 10/22/01 10:09AM >>> >hello all, >I am in need of three PDB files that I can not find in the usual places (RCSB, >Klotho, EBI, etc.). Can anyone help? >the structures are: >1. sucrose (alternatively maltose, or lactose, or any disaccharaide). >2. cyclic GMP. >3. aspirin, but in PDB format (I am aware that RasMol ships with the aspirin There's lots of files with guanine nucleotides (though I couldn't find cGMP), sucrose and maltose. The following were obtained using the website http://exlnt.com/search_pdb/index.htm Note that the website is still under construction, one of the search tools is not yet available, and the multi-language support is still in progress. PDB HET TITLE CLASSIFICATION Searching for hetnam contains 'sucrose' 1a0t SUC, CA Sucrose-Specific Porin OUTER MEMBRANE PROTEIN 1ex2 SUC, PO4 Protein Maf STRUCTURAL GENOMICS 1fe0 CD, SUC, SO4 Copper Transport Protein Atox1 METAL TRANSPORT 1fe4 IUM, SUC, HG, SO4, PLA Copper Transport Protein Atox1 METAL TRANSPORT 1fee CU1, SUC, SO4 Copper Transport Protein Atox1 TRANSPORT PROTEIN For het = 'suc' 1a0t SUC, CA Sucrose-Specific Porin OUTER MEMBRANE PROTEIN 1ex2 SUC, PO4 Protein Maf STRUCTURAL GENOMICS 1fe0 CD, SUC, SO4 Copper Transport Protein Atox1 METAL TRANSPORT 1fe4 IUM, SUC, HG, SO4, PLA Copper Transport Protein Atox1 METAL TRANSPORT 1fee CU1, SUC, SO4 Copper Transport Protein Atox1 TRANSPORT PROTEIN 1r1r SUC Ribonucleotide Reductase R2 Protein OXIDOREDUCTASE For het= 'mal' 1a7l MAL, NAD Male-B363 TRANSPORT 1ahp GOL, SO4, MAL, PLP E. Coli Maltodextrin Phosphorylase ECOLI 1at1 ZN, MAL, PAM Aspartate Carbamoyltransferase (Aspartate Tr TRANSFERASE (CARBAMOYL-P,ASPARTATE) 1b9z CA, SO4, ACT, MAL Beta-Amylase HYDROLASE 1cdg CA, DZF, MAL Cyclodextrin Glycosyltransferase (E.C. 2.4.1 TRANSFERASE(GLUCANOTRANSFERASE) 1cgv CA, MAL Cyclomaltodextrin Glucanotransferase (E.C. 2 GLYCOSYLTRANSFERASE 1cgw CA, MAL Cyclomaltodextrin Glucanotransferase (Cgtase GLYCOSYLTRANSFERASE 1cgx CA, MAL Cyclomaltodextrin Glucanotransferase (Cgtase GLYCOSYLTRANSFERASE 1cgy CA, MAL Cyclomaltodextrin Glucanotransferase (Cgtase GLYCOSYLTRANSFERASE 1csc CMC, MAL Citrate Synthase (E.C. 4.1.3.7)- L-Malat OXO-ACID-LYASE 1cxe CA, GLC, MAL Cyclodextrin Glycosyltransferase GLYCOSYLTRANSFERASE 1cxf CA, GLC, MAL, ACX Cyclodextrin Glycosyltransferase GLYCOSYLTRANSFERASE 1cxh CA, GLC, MAL Cyclodextrin Glycosyltransferase GLYCOSYLTRANSFERASE 1cxi CA, MAL Cyclodextrin Glycosyltransferase GLYCOSYLTRANSFERASE 1iud MAL Maltodextrin-Binding Protein Male-B133 HYDRID PROTEIN 1mdp MAL Maltodextrin-Binding Protein (Male178 Mutant SUGAR TRANSPORT 1mdq MAL Maltodextrin-Binding Protein (Male322) (Malt SUGAR TRANSPORT 1mg1 ZN, CL, MAL Htlv-1 Gp21 Ectodomain/Maltose-Binding Prote LEUKEMIA VIRUS TYPE 1 1mpd MAL Maltodextrin-Binding Protein PERIPLASMIC BINDING PROTEIN 1qho CA, ABD, SO4, MAL Alpha-Amylase HYDROLASE 1qhp CA, SO4, MAL Alpha-Amylase HYDROLASE 2at1 ZN, MAL, PAM Aspartate Carbamoyltransferase (Aspartate Tr TRANSFERASE (CARBAMOYL-P,ASPARTATE) 2csc CMC, MAL Citrate Synthase (E.C. 4.1.3.7)- D-Malat OXO-ACID-LYASE 3csc ACO, MAL Citrate Synthase (E.C. 4.1.3.7)- L-Malat OXO-ACID-LYASE 4csc ACO, MAL Citrate Synthase (E.C. 4.1.3.7)- D-Malat OXO-ACID-LYASE 7at1 ATP, ZN, MAL, PAM Aspartate Carbamoyltransferase (Aspartate Tr TRANSFERASE (CARBAMOYL-P,ASPARTATE) 8at1 CTP, ZN, MAL, PAM Aspartate Carbamoyltransferase (Aspartate Tr TRANSFERASE (CARBAMOYL-P,ASPARTATE) For het = 'GMP ' (there do not appear to be any with cGMP: 1rga CA, GMP Ribonuclease T1 (E.C. 3.1.27.3) Isozyme Comp HYDROLASE(ENDORIBONUCLEASE) 1wah GMP, CTP, 5GP, SO4 DNA COMPLEX (NUCLEOTIDYLTRANSFERASE/DNA) 2sar GMP, SO4 Ribonuclease Sa (E.C. 3.1.4.8) Complex With 3 HYDROLASE (ENDORIBONUCLEASE) For all GxP nucleotides: 1a2k GDP, MG, SO4 Ran COMPLEX (TRANSPORT/NUCLEAR PROTEIN) 1a4r GDP, MG, GNH G25K GTP-Binding Protein HYDROLASE 1a8r GTP GTP Cyclohydrolase I HYDROLASE 1a9c GTP GTP Cyclohydrolase I HYDROLASE 1aac CU, GDP Amicyanin ELECTRON TRANSPORT 1agr CIT, ALF, MG, GDP Rgs4 COMPLEX (SIGNAL TRANSDUCTION/REGULATOR) 1an0 MG, MSE, GDP Cdc42Hs-GTP GTPASE 1as2 PO4, GDP Gia1 SIGNAL TRANSDUCTION 1as3 SO4, GDP Gia1 SIGNAL TRANSDUCTION 1awl FOK, MG, GTP Photoreceptor Guanylyl Cyclase LYASE 1awn MG, GTP Guanylyl Cyclase LYASE 1bhn GDP, 35G Nucleoside Diphosphate Transferase PHOSPHOTRANSFERASE 1bof MG, SO4, GDP Gi Alpha 1 SIGNAL TRANSDUCTION PROTEIN 1byu MG, GDP GTP-Binding Protein Ran TRANSPORT PROTEIN 1c1y CA, MG, GTP Proto-Onkogene Serine/Threonine Protein Kinas SIGNALING PROTEIN 1c4k GTP, PLP Ornithine Decarboxylase LYASE 1cc1 NI, FCO, CSE, GDP, H2S, FS4, FE2 Hydrogenase (Large Subunit) OXIDOREDUCTASE 1cg0 MG, IMO, GDP, HDA Adenylosuccinate Synthetase LIGASE 1cg1 MG, IMO, GDP, HDA Adenylosuccinate Synthetase LIGASE 1cg3 MG, IMO, GDP, HDA Adenylosuccinate Synthetase LIGASE 1cg4 MG, IMO, GDP Adenylosuccinate Synthetase LIGASE 1cib NO3, MG, IMP, SEO, GDP, HDA Adenylosuccinate Synthetase LIGASE 1ckm GTP Mrna Capping Enzyme CAPPING ENZYME 1ckn GPL, SO4, MN, GTP Mrna Capping Enzyme CAPPING ENZYME 1clq CA, GDP DNA (5'-D(ApGpTpApGpTpTpCpCpGpCpG)- 3') TRANSFERASE/DNA 1crp MG, GDP C-H-Ras P21 Protein (Catalytic Domain, Resid ONCOGENE PROTEIN 1crq MG, GDP C-H-Ras P21 Protein (Catalytic Domain, Resid ONCOGENE PROTEIN 1crr MG, GDP C-H-Ras P21 Protein (Catalytic Domain, Resid ONCOGENE PROTEIN 1d2e MO4, GDP, MO2 Elongation Factor Tu (Ef-Tu) RNA BINDING PROTEIN 1d4r MO4, A23, GDP, MO3 29-Mer Of Modified Srp RNA Helix 6 RIBONUCLEIC ACID 1d5c MG, MSE, GDP Rab6 Gtpase ENDOCYTOSIS/EXOCYTOSIS 1d8t MG, ACE, GDP, GEA Elongation Factor Tu RNA BINDING PROTEIN 1dar GDP Elongation Factor G TRANSLATIONAL GTPASE 1dg1 MG, GDP Elongation Factor Tu RNA BINDING PROTEIN 1dj5 HGU, HEM, GDP Cytochrome C Peroxidase OXIDOREDUCTASE 1doa MG, CMT, HEM, GDP, GER GTP-Dissociation Inhibitor 1 CELL CYCLE 1dpf GDP Rhoa GENE REGULATION/SIGNALING PROTEIN 1ds6 MG, GDP Rho GTP-Dissociation Inhibitor 2 SIGNALING PROTEIN 1e0s NH4, GDP, DTT Adp-Ribosylation Factor 6 G PROTEIN 1e8o SO4, GDP 7Sl RNA, 5'-R(GdpGpGpCpCpGpGpGpCpGpCpGp G ALU RIBONUCLEOPROTEIN PARTICLE 1e96 MG, GTP Neutrophil Cytosol Factor 2 (Ncf-2) Tpr Doma SIGNALLING COMPLEX 1efc MG, GDP Elongation Factor RNA BINDING PROTEIN 1efh A3P, GDP Hydroxysteroid Sulfotransferase TRANSFERASE 1efn GDP, PBM Hiv-1 Nef Protein COMPLEX (SH3 DOMAIN/VIRAL ENHANCER) 1ek0 MHO, GNP, MG, NI, GDP, PDI GTP-Binding Protein Ypt51 ENDOCYTOSIS/EXOCYTOSIS 1etu GDP Elongation Factor Tu (Domain I) - Guanos TRANSPORT AND PROTECTION PROTEIN 1ffx GTP, GDP Stathmin-Like Domain Of Rb3 STRUCTURAL PROTEIN 1ffy MRC, ZN, K, MO2, MO4, MO5, MO6, GDP Isoleucyl-tRNA LIGASE/RNA 1fnm MG, GDP Elongation Factor G TRANSLATION 1fqj ALF, MG, GDP Regulator Of G-Protein Signaling 9 SIGNALING PROTEIN 1fqk ALF, MG, GDP Regulator Of G-Protein Signaling 9 SIGNALING PROTEIN 1frw ZN, GTP, NI, ACT, MN Molybdopterin-Guanine Dinucleotide Biosynthe METAL BINDING PROTEIN 1fsz GDP Ftsz CELL-DIVISION PROTEIN 1fzq CA, MES, NH4, SO4, GDP Adp-Ribosylation Factor-Like Protein 3 SIGNALING PROTEIN 1g16 MSE, CO, GDP Ras-Related Protein Sec4 SIGNALING PROTEIN,ENDOCYTOSIS/EXOCYTOSIS 1g4u MG, AF3, GDP Ras-Related C3 Botulinum Toxin Substrate 1 SIGNALING PROTEIN 1g7s GDP Translation Initiation Factor If2/Eif5B TRANSLATION 1gdd ZN, SO4, GDP Gi Alpha 1 SIGNAL TRANSDUCTION PROTEIN 1gfi ALF, MG, GDP Guanine Nucleotide-Binding Protein G(I), Alp SIGNAL TRANSDUCTION PROTEIN 1gg2 GDP G Protein Gi Gamma 2 COMPLEX (GTP-BINDING/TRANSDUCER) 1gim IMP, HAD, NO3, MG, GDP Adenylosuccinate Synthetase LIGASE (SYNTHETASE) 1gin IMP, HAD, NO3, MG, GDP Adenylosuccinate Synthetase LIGASE 1git PO4, GDP G Protein Gi Alpha 1 GTP-BINDING PROTEIN 1got MSE, GDP Gt-Gamma COMPLEX (GTP-BINDING/TRANSDUCER) 1gp2 GDP G Protein Gi Gamma 2 COMPLEX (GTP-BINDING/TRANSDUCER) 1grn MG, AF3, ETA, GDP Rho Gtpase Activating Protein GENE REGULATION 1he1 MG, NI, AF3, GDP Ras-Related C3 Botulinum Toxin Substrate 1 SIGNALLING COMPLEX 1hur MG, GDP Molecule: Human Adp-Ribosylation Factor 1; S PROTEIN TRANSPORT 1hwx GLU, GTP, NAI, BPI Glutamate Dehydrogenase OXIDOREDUCTASE 1hwz NDP, GLU, GTP Glutamate Dehydrogenase OXIDOREDUCTASE 1hx1 GTP, TRS Bag-Family Molecular Chaperone Regulator-1 CHAPERONE/CHAPERONE INHIBITOR 1ksz PGS, HAD, MG, GDP Adenylosuccinate Synthetase LIGASE 1mre ZN, IMD, GDP Igg Jel 103 Fab Fragment Complexed With Guan IMMUNOGLOBULIN 1ng1 CD, MO4, MO6, EDO, GDP, ACY Signal Sequence Recognition Protein Ffh SIGNAL RECOGNITION 1nht SPG, HAD, MG, GDP Adenylosuccinate Synthetase LIGASE 1nue MG, GDP Nucleoside Diphosphate Kinase PHOSPHOTRANSFERASE 1plk GTP, MG C-H-Ras P21 Protein Mutant With Gly 12 Repla ONCOGENE PROTEIN 1plq HG, GDP Proliferating Cell Nuclear Antigen (Pcna) (S DNA-BINDING 1q21 MG, GDP c-H-Ras p21 Protein Catalytic Domain Complex ONCOGENE PROTEIN 1qf4 RPD, PO4, MG, GDP Adenylosuccinate Synthetase LIGASE 1qf5 RPL, PO4, MG, GDP Adenylosuccinate Synthetase LIGASE 1qg2 MO4, PTR, GDP Ran GTPASE 1qg4 MO4, GDP Ran GTPASE 1qln GTP RNA (5- R(PppGpGpG)-3) NUCLEOTIDYLTRANSFERASE 1qra GTP, MG Transforming Protein P21/H-Ras-1 SIGNALING PROTEIN 1rga CA, GMP Ribonuclease T1 (E.C. 3.1.27.3) Isozyme Comp HYDROLASE(ENDORIBONUCLEASE) 1rrg MG, GDP Rat Adp-Ribosylation Factor-1 TRANSPORT PROTEIN 1tad CA, CAC, ALF, GDP Transducin-Alpha (Gt-Alpha-GTP-Alf, T-Alpha- GTP-BINDING PROTEIN 1tag MG, GDP Transducin-Alpha Complexed With GTP and Magn GTP-BINDING PROTEIN 1tub GTP, GDP Tubulin MICROTUBULES 1tui MG, GDP Elongation Factor Tu ELONGATION FACTOR 1tx4 ALF, MG, GDP Transforming Protein Rhoa COMPLEX(GTPASE ACTIVATN/PROTO-ONCOGENE) 1wah GMP, CTP, 5GP, SO4 DNA COMPLEX (NUCLEOTIDYLTRANSFERASE/DNA) 1wq1 MG, AF3, GDP P120Gap COMPLEX (GTP-BINDING/GTPASE ACTIVATION) 1zbd MSE, ZN, GTP, MG Rabphilin-3A COMPLEX (GTP-BINDING/EFFECTOR) 2efg GDP Elongation Factor G Domain 3 PROTEIN BINDING 2gep FS4, NA, SRM, SO3, GDP Sulfite Reductase Hemoprotein OXIDOREDUCTASE 2ng1 DOX, HEC, EDO, GDP Signal Sequence Recognition Protein Ffh SIGNAL RECOGNITION 2ngr MG, AF3, GDP Gtpase Activating Protein (Rhg) HYDROLASE 2q21 MG, GDP c-H-Ras p21 Protein Catalytic Domain (Mutant ONCOGENE PROTEIN 2rap GTP, MG Rap2A G PROTEIN 2sar GMP, SO4 Ribonuclease Sa (E.C. 3.1.4.8) Complex With 3 HYDROLASE (ENDORIBONUCLEASE) 3ran MG, GDP GTP-Binding Nuclear Protein Ran TRANSPORT PROTEIN 3rap GTP, MG G Protein Rap2A SIGNALING PROTEIN 4q21 MG, GDP c-H-Ras p21 Protein Catalytic Domain Complex ONCOGENE PROTEIN 4r1r TTP, GDP Ribonucleotide Reductase R2 Protein COMPLEX (OXIDOREDUCTASE/PEPTIDE) 4rcr FE, BCL, U10, BPH, GDP Photosynthetic Reaction Center - Chain H PHOTOSYNTHETIC REACTION CENTER 521p GTP H-Ras P21 Protein Mutant With Gly 12 Replace ONCOGENE PROTEIN select pdb, het, title, header from pdb where het regexp "G[MDT]P" ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: KRW Subject: RE: PDB files needed... Date: Mon, 22 Oct 2001 19:24:28 +0200 To: rasmol@lists.umass.edu Cc: driscoll@molvisions.com This is a multi-part message in MIME format. --Boundary_(ID_CN11z6LGfVvtQZGlQ0RAYg) Guanosine 3',5'-cyclic monophosphate.pdb attached ------------------------------------ Keith Wilkinson LRSC Head of Science International School of Lusaka 6945 Nangwenya Road PO Box 50121 RIDGEWAY Lusaka, Zambia --------------------------- Keith Wilkinson "All it requires for evil to flourish is that good men remain silent" Edmund Burke -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of timothy driscoll Sent: 22 October 2001 16:10 From: owner-rasmol@lists.umass.edu Subject: PDB files needed... To: RasMol List hello all, I am in need of three PDB files that I can not find in the usual places (RCSB, Klotho, EBI, etc.). Can anyone help? the structures are: 1. sucrose (alternatively maltose, or lactose, or any disaccharaide). 2. cyclic GMP. 3. aspirin, but in PDB format (I am aware that RasMol ships with the aspirin structure, but it is a MOL file). any help is greatly appreciated. thanks! tim _________________________________________ timothy driscoll molvisions.com - 3D molecular visualization 80 fiske ave, waltham, ma 02453 usa e: p: 508.864.6516 f: 781.899.4108 ------------------------------------------------------------- god bless america --Boundary_(ID_CN11z6LGfVvtQZGlQ0RAYg) Content-disposition: attachment; filename=cGMP.PDB COMPND cGMP.PDB = =20 HETATM 1 O 3.504 4.715 2.665 =20 HETATM 2 C 2.953 4.217 1.713 =20 HETATM 3 C 1.446 4.142 1.553 =20 HETATM 4 N 3.626 3.644 0.667 =20 HETATM 5 C 0.969 3.551 0.453 =20 HETATM 6 N 0.363 4.600 2.410 =20 HETATM 7 C 3.347 3.057 -0.423 =20 HETATM 8 N 1.891 3.004 -0.542 =20 HETATM 9 N -0.493 3.546 0.453 =20 HETATM 10 C -1.019 4.190 1.655 =20 HETATM 11 N 4.225 2.610 -1.208 =20 HETATM 12 C -0.943 2.147 0.453 =20 HETATM 13 O -2.343 2.081 0.453 =20 HETATM 14 C -0.533 1.455 -0.820 =20 HETATM 15 C -2.630 0.709 0.453 =20 HETATM 16 C -1.472 0.081 -0.276 =20 HETATM 17 O -1.231 2.057 -1.876 =20 HETATM 18 C -2.636 0.242 1.884 =20 HETATM 19 O -1.982 -0.563 -1.412 =20 HETATM 20 O -2.764 -1.154 1.869 =20 HETATM 21 P -3.062 -1.732 -1.138 =20 HETATM 22 P -2.167 -3.675 -1.600 =20 HETATM 23 O -4.627 -1.211 -1.674 =20 HETATM 33 H 4.627 3.702 0.803 =20 HETATM 34 H 1.482 2.554 -1.398 =20 HETATM 35 H -2.062 4.361 1.960 =20 HETATM 27 H 3.781 2.177 -2.020 =20 HETATM 36 H -0.602 1.686 1.404 =20 HETATM 30 H 0.548 1.205 -0.772 =20 HETATM 32 H -3.557 0.577 -0.145 =20 HETATM 31 H -0.869 -0.519 0.438 =20 HETATM 26 H -0.967 1.617 -2.665 =20 HETATM 28 H -3.537 0.640 2.398 =20 HETATM 29 H -1.653 0.468 2.349 =20 HETATM 24 H -3.128 -4.715 -1.355 =20 HETATM 25 H -1.321 -4.083 -0.511 =20 CONECT 1 2 =20 CONECT 2 1 3 4 =20 CONECT 3 2 5 6 =20 CONECT 4 2 7 33 =20 CONECT 5 3 8 9 =20 CONECT 6 3 10 =20 CONECT 7 4 8 11 =20 CONECT 8 5 7 34 =20 CONECT 9 5 10 12 =20 CONECT 10 6 9 35 =20 CONECT 11 7 27 =20 CONECT 12 9 13 14 36 =20 CONECT 13 12 15 =20 CONECT 14 12 16 17 30 =20 CONECT 15 13 16 18 32 =20 CONECT 16 14 15 19 31 =20 CONECT 17 14 26 =20 CONECT 18 15 20 28 29 =20 CONECT 19 16 21 =20 CONECT 20 18 21 =20 CONECT 21 19 20 22 23 =20 CONECT 22 21 24 25 =20 CONECT 23 21 =20 CONECT 33 4 =20 CONECT 34 8 =20 CONECT 35 10 =20 CONECT 27 11 =20 CONECT 36 12 =20 CONECT 30 14 =20 CONECT 32 15 =20 CONECT 31 16 =20 CONECT 26 17 =20 CONECT 28 18 =20 CONECT 29 18 =20 CONECT 24 22 =20 CONECT 25 22 =20 END =20 --Boundary_(ID_CN11z6LGfVvtQZGlQ0RAYg)-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Michael Bruist Subject: RE: PDB files needed... Date: Mon, 22 Oct 2001 13:36:33 -0400 To: rasmol@lists.umass.edu Tim, I took a quick look and found cGMP in the PDB. I used the standard search page and searched on "cyclic guanosine monophosphate" as text. This gave one hit: 1BE4. Using a text editor, delete everything from that file except cGMP. Those atoms are in lines begining HETATM. Also keep the CONNECT lines that include atom numbers (the first # after HETATM) for cAGMP. This method can be used to extract any ligand bound to a macromolecule in the PDB. Mike Bruist -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Todd Carlson Sent: Monday, October 22, 2001 10:47 AM From: owner-rasmol@lists.umass.edu Subject: Re: PDB files needed... To: rasmol@lists.umass.edu http://www.nyu.edu/pages/mathmol/library/sugars/ http://www.nyu.edu:80/pages/mathmol/library/drugs/ I found sucrose and aspirin at the above links using google. I found a cGMP.pdb file, but it was only GMP, not cyclic. I did find some cAMP files. I suppose you could change them. Or find a protein with cGTP bound (if any exist) and delete the protein. Todd >>> driscoll@molvisions.com 10/22/01 10:09AM >>> hello all, I am in need of three PDB files that I can not find in the usual places (RCSB, Klotho, EBI, etc.). Can anyone help? the structures are: 1. sucrose (alternatively maltose, or lactose, or any disaccharaide). 2. cyclic GMP. 3. aspirin, but in PDB format (I am aware that RasMol ships with the aspirin structure, but it is a MOL file). any help is greatly appreciated. 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-- ++++------+------+------+------+------+------+------+------+------+------+ From: Jim Perkins Subject: Re: PDB files needed... Date: Mon, 22 Oct 2001 14:18:23 -0500 To: rasmol@lists.umass.edu Timothy said: >3. aspirin, but in PDB format (I am aware that RasMol ships with the aspirin >structure, but it is a MOL file). Can't you just open the aspirin MOL file in Rasmol and save it as a PDB? In my copy of Rasmol (2.6 for Mac) it lets you save any file as a Brookhaven PDB, Alchemy, or MDL MOL format. Jim ___________________________________________________________ James A. Perkins, MS, MFA Assistant Professor of Medical Illustration College of Imaging Arts and Sciences/School of Art Rochester Institute of Technology 73 Lomb Memorial Drive Rochester, NY 14623 716-475-2443 fax: 716-475-6447 japfaa@rit.edu ___________________________________________________________ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Michel Guilloton Subject: Re: PDB files needed... Date: Mon, 22 Oct 2001 19:53:28 +0200 To: rasmol@lists.umass.edu --Boundary_(ID_Y2xrOpKfPSNbERd7N3y/9A) Hi all, As an alternate way to obtain cGMP or any simple molecule as a pdb file,=20 one can - draw it using for example Isisdraw, - save as .skc file (see attachment), - open it with Weblab, - save as .pdb file (see attachment). Michel Guilloton At 10:09 22/10/01 -0400, vous avez =E9crit: >hello all, > >I am in need of three PDB files that I can not find in the usual places= (RCSB, >Klotho, EBI, etc.). Can anyone help? > >the structures are: > >1. sucrose (alternatively maltose, or lactose, or any disaccharaide). >2. cyclic GMP. >3. aspirin, but in PDB format (I am aware that RasMol ships with the= aspirin >structure, but it is a MOL file). > > >any help is greatly appreciated. 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 > > --Boundary_(ID_Y2xrOpKfPSNbERd7N3y/9A) Content-disposition: attachment; filename=cGMP.skc AQMABAIEAAEAYQMAAFgFAAAAAFkFAAAAAAsLAAVBcmlhbHgAAAMDAAwwBgD///// EwIAAgQAOQBhAwAAAwMAIRYKAFZuG0U32RxFFwQACADoBAABTxoEAAIAJQQABADQ BAAPAOAEAMYA4QQAIQDpAwAHAwMAIRYKAPiDAEV75BxFFwQACADoBAABTxoEAAMA JQQABADQBAAPAOAEAMYA4QQAIQDpAwAHAwMAIRYKAPquDUWQwv9EFwQACADoBAAB TxoEAAQAJQQABADQBAAPAOAEAMYA4QQAIQDpAwAHAwMAIRYKAMk24USuRw1FFwQA CADoBAABTxoEAAUAJQQABADQBAAPAOAEAMYA4QQAIQDpAwAHAwMAIRYKAErcF0WF WwdF6AQAAUMaBAAGACUEAAQA0AQADwDgBADGAOEEACEA6QMABwMDACEWCgA6FBRF L90SRegEAAFDGgQABwAlBAAEANAEAA8A4AQAxgDhBAAhAOkDAAcDAwAhFgoA1ZgH RS/dEkXoBAABQxoEAAgAJQQABADQBAAPAOAEAMYA4QQAIQDpAwAHAwMAIRYKAKim A0UGIQdF6AQAAUMaBAAJACUEAAQA0AQADwDgBADGAOEEACEA6QMABwMDACEWCgBk 2+9EaHEDRegEAAFDGgQACgAlBAAEANAEAA8A4AQAxgDhBAAhAOkDAAcDAwAgBQMA BycGAAcAAgAqAwACzgQAIQADAwAgBQMABycGAAcABgAqAwACzgQAIQADAwAgBQMA BycGAAIABAAqAwACzgQAIQADAwAgBQMABycGAAYABQAqAwACzgQAIQADAwAgBQMA BycGAAQABQAqAwACzgQAIQADAwAgBQMABycGAAcACAApAwABKgMAAs8EABsAzgQA IQADAwAgBQMABycGAAgAAwAqAwACzgQAIQADAwAgBQMABycGAAUAAAApAwAGzwQA GwDOBAAhAAMDACAFAwAHJwYABgABACkDAAYqAwACzwQAGwDOBAAhAAMDACAFAwAH JwYAAwATACoDAALOBAAhAAMDACEWCgBK4uJE2rMaRRcEAA8A6AQAAVAaBAALACUE AAQA0AQADwDgBADGAOEEACEA6QMABwMDACAFAwAHJwYAAQATACoDAALOBAAhAAMD ACEWCgDezdVEF0YoRRcEAAgA6AQAAU8aBAAMACUEAAQA0AQADwADAwAgBQMABycG ABMAFQADAwAhFgoAh73IRHq0GkUXBAAIAOgEAAFPGgQADQAlBAAEANAEAA8AAwMA IAUDAAcnBgATABcAKAMAAgMDACEWCgB4FSZFXSv+RBcEAAcA6AQAAU4aBAAUACUE AAQA0AQADwDgBADGAOkDAAcDAwAgBQMABycGAAQAGQApAwABzgQAIQADAwAhFgoA NG0qRa5rvUROBgAQ+nJB6AQAAUMaBAAPACUEAAQA0AQADwADAwAgBQMABycGACoA GwAqAwACAwMAIRYKAF/lLEV5o9VETgYAQPGbQOgEAAFDGgQAEAAlBAAEANAEAA8A AwMAIAUDAAcnBgAbAB0AKgMAAgMDACEWCgDYoDhFWoLdRE4GAMDnxkAXBAAHAOgE AAFOGgQAEQAlBAAEANAEAA8AAwMAIAUDAAcnBgAdAB8AKgMAAgMDACEWCgASoiNF Y/zlRE4GAAAI2cDoBAABQxoEABIAJQQABADQBAAPAAMDACAFAwAHJwYAHQAhACgD AAIqAwACAwMAIRYKAJrmF0WCHd5ETgYAQP8BwRcEAAcA6AQAAU4aBAATACUEAAQA 0AQADwADAwAgBQMABycGACEAIwAqAwACAwMAIAUDAAcnBgAhABkAKgMAAgMDACEW CgCRORxFAlWdRE4GABhAwUEXBAABAOgEAAFIGgQAFQAlBAAEANAEAA8AAwMAIAUD AAcnBgAqACYAAwMAIRYKAG9uFUW35cVETgYAwAcMQOgEAAFDGgQAFwAlBAAEANAE AA8AAwMAIAUDAAcnBgAjACgAKAMAAioDAAIDAwAhFgoAvLEeRc2MtUROBgDAfl1B FwQABwDoBAABThoEAA4AJQQABADQBAAPAAMDACAFAwAHJwYAKAAqACoDAAIDAwAh FgoA97IJRdYGvkROBgAAa1g/FwQABwDoBAABThoEABgAJQQABADQBAAPAAMDACAF AwAHJwYAKAAsAAMDACEWCgCBsDNFxBKtRE4GAGC71kEXBAAIAOgEAAFPGgQAGQAl BAAEANAEAA8AAwMAIAUDAAcnBgAbAC4AKAMAAgMDACEWCgB1QjdFJhr/RE4GAKBk NcHoBAABQxoEABoAJQQABADQBAAPAAMDACAFAwAHJwYAHwAwACgDAAIqAwACAwMA IAUDAAcnBgAZADAAKgMAAgMDACEWCgDMOgdFC8+lRE4GADCIMkEXBAABAOgEAAFI GgQAGwAlBAAEANAEAA8AAwMAIAUDAAcnBgAsADMAAwMAIRYKAKpvAEXAX85ETgYA 4PUswRcEAAEA6AQAAUgaBAAcACUEAAQA0AQADwADAwAgBQMABycGACwANQADAwAh FgoA/PM7RZiWBUVOBgCoRoLBFwQAAQDoBAABSBoEAB0AJQQABADQBAAPAAMDACAF AwAHJwYAMAA3ABQCAP8ECAAEAEE0UAAUAgA= --Boundary_(ID_Y2xrOpKfPSNbERd7N3y/9A) Content-disposition: attachment; filename=cGMP.pdb REMARK MSI WebLab Viewer PDB file REMARK Created: Mon Oct 22 19:45:22 Paris, Madrid (heure d'=E9t=E9) 2001 ATOM 1 O1 MOL 1 19.561 -18.841 -1.189 1.00 0.00 = =20 ATOM 2 O2 MOL 1 16.998 -19.767 0.155 1.00 0.00 = =20 ATOM 3 O3 MOL 1 17.875 -16.368 0.531 1.00 0.00 = =20 ATOM 4 O4 MOL 1 14.754 -18.344 0.134 1.00 0.00 = =20 ATOM 5 C5 MOL 1 19.005 -16.840 -0.133 1.00 0.00 = =20 ATOM 6 C6 MOL 1 19.064 -18.374 0.062 1.00 0.00 = =20 ATOM 7 C7 MOL 1 17.567 -18.514 0.428 1.00 0.00 = =20 ATOM 8 C8 MOL 1 16.927 -17.357 -0.084 1.00 0.00 = =20 ATOM 9 C9 MOL 1 15.567 -17.274 0.546 1.00 0.00 = =20 ATOM 10 P10 MOL 1 15.481 -19.682 -0.065 1.00 0.00 = =20 ATOM 11 O11 MOL 1 14.748 -20.825 0.578 1.00 0.00 = =20 ATOM 12 O12 MOL 1 15.256 -20.035 -1.335 1.00 0.00 = =20 ATOM 13 N13 MOL 1 20.182 -16.050 -0.086 1.00 0.00 = =20 ATOM 14 C14 MOL 1 22.355 -14.109 1.813 1.00 0.00 = =20 ATOM 15 C15 MOL 1 21.688 -14.830 0.777 1.00 0.00 = =20 ATOM 16 N16 MOL 1 22.031 -15.000 -0.583 1.00 0.00 = =20 ATOM 17 C17 MOL 1 20.584 -15.464 1.030 1.00 0.00 = =20 ATOM 18 N18 MOL 1 19.970 -15.499 2.275 1.00 0.00 = =20 ATOM 19 H19 MOL 1 22.149 -13.664 3.855 1.00 0.00 = =20 ATOM 20 C20 MOL 1 20.497 -14.883 3.260 1.00 0.00 = =20 ATOM 21 N21 MOL 1 21.737 -14.142 3.088 1.00 0.00 = =20 ATOM 22 N22 MOL 1 19.847 -14.943 4.512 1.00 0.00 = =20 ATOM 23 O23 MOL 1 23.412 -13.495 1.611 1.00 0.00 = =20 ATOM 24 C24 MOL 1 21.113 -15.742 -1.114 1.00 0.00 = =20 ATOM 25 H25 MOL 1 20.227 -14.479 5.302 1.00 0.00 = =20 ATOM 26 H26 MOL 1 18.993 -15.463 4.604 1.00 0.00 = =20 ATOM 27 H27 MOL 1 21.068 -16.042 -2.067 1.00 0.00 = =20 ATOM 28 H58 MOL 1 19.640 -19.837 -1.166 1.00 0.00 = =20 ATOM 29 H60 MOL 1 18.918 -16.691 -1.118 1.00 0.00 = =20 ATOM 30 H62 MOL 1 19.628 -18.868 0.723 1.00 0.00 = =20 ATOM 31 H64 MOL 1 17.428 -18.531 1.418 1.00 0.00 = =20 ATOM 32 H66 MOL 1 16.781 -17.272 -1.070 1.00 0.00 = =20 ATOM 33 H68 MOL 1 15.666 -17.303 1.541 1.00 0.00 = =20 ATOM 34 H70 MOL 1 15.135 -16.413 0.278 1.00 0.00 = =20 TER --Boundary_(ID_Y2xrOpKfPSNbERd7N3y/9A) Michel Guilloton Laboratoire de Chimie des Substances Naturelles Facult=E9 des Sciences Universit=E9 de Limoges 123, Avenue Albert Thomas 87060 Limoges France Tel : 33 (0)5 55 45 74 64 Fax : 33 (0)5 55 45 72 02 mailto:guilloton@unilim.fr --Boundary_(ID_Y2xrOpKfPSNbERd7N3y/9A)-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: RE: PDB files needed... Date: Mon, 22 Oct 2001 14:17:03 -0400 To: m.bruist@usip.edu Cc: RasMol List thanks, mike! I must've mistyped the entry; my search for this text at the RCSB came up empty. I guess I should learn to proofread, even when I'm in a hurry! again, thanks to everyone who responded; I now have all of the structures that I need. best, tim On 10.22.01 at 1:36 PM, m.bruist@usip.edu (Michael Bruist) wrote: > Tim, > > I took a quick look and found cGMP in the PDB. I used the standard search > page and searched on "cyclic guanosine monophosphate" as text. This gave > one hit: 1BE4. Using a text editor, delete everything from that file except > cGMP. Those atoms are in lines begining HETATM. Also keep the CONNECT > lines that include atom numbers (the first # after HETATM) for cAGMP. > > This method can be used to extract any ligand bound to a macromolecule in > the PDB. > > Mike Bruist > > -----Original Message----- > From: owner-rasmol@lists.umass.edu > [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Todd Carlson > Sent: Monday, October 22, 2001 10:47 AM > To: rasmol@lists.umass.edu > Subject: Re: PDB files needed... > > > > > http://www.nyu.edu/pages/mathmol/library/sugars/ > > http://www.nyu.edu:80/pages/mathmol/library/drugs/ > > > I found sucrose and aspirin at the above links using google. > I found a cGMP.pdb file, but it was only GMP, not cyclic. > > I did find some cAMP files. I suppose you could change them. Or find a > protein with cGTP bound (if any exist) and delete the protein. > > Todd > > > > >>> driscoll@molvisions.com 10/22/01 10:09AM >>> > hello all, > > I am in need of three PDB files that I can not find in the usual places > (RCSB, > Klotho, EBI, etc.). Can anyone help? > > the structures are: > > 1. sucrose (alternatively maltose, or lactose, or any disaccharaide). > 2. cyclic GMP. > 3. aspirin, but in PDB format (I am aware that RasMol ships with the aspirin > structure, but it is a MOL file). > > > any help is greatly appreciated. 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 > > > > > > > > _________________________________________ 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 MimeOLE V5.00.2314.1300 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: KRW Subject: RE: PDB files needed... Date: Tue, 23 Oct 2001 00:16:44 +0200 To: m.bruist@usip.edu, rasmol@lists.umass.edu >one hit: 1BE4. Using a text editor, delete everything from that file except >cGMP. Those atoms are in lines begining HETATM. Also keep the CONNECT >lines that include atom numbers (the first # after HETATM) for cAGMP. Sounds unnecessarily complicated. I checked out ChemIndex the database that comes with ChemOffice/ChemDraw, which if you don't have it, you can access off the web at: www.chemfinder.com All the mentioned compounds are there (database has about 80,000 compounds) I saved the molecule as .pdb, and posted it. The Okenagen Uni site is the other principal archive of .pdb's. Keith Wilkinson This method can be used to extract any ligand bound to a macromolecule in the PDB. Mike Bruist -----Original Message----- [mailto:owner-rasmol@lists.umass.edu]On Behalf Of Todd Carlson Sent: Monday, October 22, 2001 10:47 AM From: owner-rasmol@lists.umass.edu Subject: Re: PDB files needed... To: rasmol@lists.umass.edu http://www.nyu.edu/pages/mathmol/library/sugars/ http://www.nyu.edu:80/pages/mathmol/library/drugs/ I found sucrose and aspirin at the above links using google. I found a cGMP.pdb file, but it was only GMP, not cyclic. I did find some cAMP files. I suppose you could change them. Or find a protein with cGTP bound (if any exist) and delete the protein. Todd >>> driscoll@molvisions.com 10/22/01 10:09AM >>> hello all, I am in need of three PDB files that I can not find in the usual places (RCSB, Klotho, EBI, etc.). Can anyone help? the structures are: 1. sucrose (alternatively maltose, or lactose, or any disaccharaide). 2. cyclic GMP. 3. aspirin, but in PDB format (I am aware that RasMol ships with the aspirin structure, but it is a MOL file). any help is greatly appreciated. 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-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: PDB files needed... Date: Mon, 22 Oct 2001 19:07:35 -0400 To: rasmol@lists.umass.edu At 10/22/2001, Tim Driscoll wrote: >1. sucrose (alternatively maltose, or lactose, or any disaccharaide). >2. cyclic GMP. >3. aspirin, but in PDB format (I am aware that RasMol ships with the aspirin >structure, but it is a MOL file). I'm pleased that several of our subscribers promptly offered good solutions to Tim's questions. In addition, I'd like to remind everyone that http://molvisindex.org has a category "Molecules: Sources of PDB Files", which currently lists 20 sources. Furthermore, if you know of a good source that is not listed, any VISITOR to this site can add a new entry (no account or password required) simply by filling out a form. You are all encouraged to add to this set of 'visitor-maintained indices'. Listed there, in the Subject index, under 'drugs', is Dave Woodcock's site Molecular Models from Chemistry at Okanagan University College. I found sucrose and aspirin (complete with double bonds!) there. I didn't find cGMP quickly, and Michael Bruist's solution was an excellent one (cutting it out of a protein-ligand file from the Protein Data Bank). The largest category at molvisindex.org is for ready-to-use Chime tutorials, where over 100 sites are now listed, with nearly 1,000 subject terms (e.g. molecules). The second most-visited category is molecular visualization freeware, where currently 27 software packages are listed, 2 with snapshots (and most have galleries at their home sites). molvisindex.org is currently being visited by over 2,000 people/month. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Importance: Normal X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: KRW Subject: RE: PDB files needed... Date: Tue, 23 Oct 2001 12:24:25 +0200 To: rasmol@lists.umass.edu But there's no mention of energy minimisation to get the bond angles right, or are biologists quite happy to present a non-optimised molecule as real? >As an alternate way to obtain cGMP or any simple molecule as a pdb file, >one can >- draw it using for example Isisdraw, >- save as .skc file (see attachment), >-open it with Weblab, >- save as .pdb file (see attachment). > >------------------------------------------------------------- >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-- Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: Todd Carlson Subject: cGMP and downloading pdb files from the web Date: Tue, 23 Oct 2001 11:52:11 -0400 To: rasmol@lists.umass.edu It's worth noting that you have to use caution downloading files from the web. Some people may find this file named cGMP.PDB http://www.isat.jmu.edu/common/coursedocs/isat454/midterm/Viagra/cGMP.PDB but if you look at the structure, it isn't cyclic. It's just 5`-GMP I have found several "bad" structures over the web. I once had my students find an aspartame pdb file so they can see the geometry of the planar peptide group geometry, but half the students found aspartame models with trigonal pyramidal geometry around the amide nitrogen. Now I warn them and they have to make sure they have a correct pdb file (of course half still get it wrong, ug). Compare http://education.llnl.gov/msds/pdb/ASPARTAME.PDB incorrect To http://www.okanagan.bc.ca/chem/molecule/aspartam.pdb correct Todd ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Gale Rhodes Subject: Intergrating Molecular Graphics Into Biochemistry Teaching Date: Tue, 23 Oct 2001 14:10:45 -0400 To: rasmol@lists.umass.edu, pdb-l@rcsb.org Hi! I recently posted a web article on molecular graphics as an essential skill for students in introductory biochemistry. To many of you, this might be coals to Newcastle, but if you're looking for some why and how, and perhaps some ammunition for convincing colleagues, see http://www.usm.maine.edu/~rhodes/Manifesto/index.html I will appreciate your comments. Cheers! ~*~*~*~*~*~*~*~*~*~*~* Gale Rhodes Professor of Chemistry University of Southern Maine PO Box 9300 Portland, Maine 04104-9300 207-780-4736 http://www.usm.maine.edu/~rhodes ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Cindy Klevickis Subject: Re: cGMP and downloading pdb files from the web Date: Wed, 24 Oct 2001 08:02:08 -0400 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_nHNIq7lfMHSwgiSWjsg+Yg) OOPs, the incorrect cGMP that you noted is on one of my student's old project pages. I will fix it. Cindy Klevickis Todd Carlson wrote: > It's worth noting that you have to use caution downloading files from the web. Some people may find this file named cGMP.PDB > > http://www.isat.jmu.edu/common/coursedocs/isat454/midterm/Viagra/cGMP.PDB > > but if you look at the structure, it isn't cyclic. It's just 5`-GMP > > I have found several "bad" structures over the web. I once had my students find an aspartame pdb file so they can see the geometry of the planar peptide group geometry, but half the students found aspartame models with trigonal pyramidal geometry around the amide nitrogen. Now I warn them and they have to make sure they have a correct pdb file (of course half still get it wrong, ug). > > Compare http://education.llnl.gov/msds/pdb/ASPARTAME.PDB incorrect > > To http://www.okanagan.bc.ca/chem/molecule/aspartam.pdb correct > > Todd > --Boundary_(ID_nHNIq7lfMHSwgiSWjsg+Yg) Content-description: Card for Cindy Klevickis Content-disposition: attachment; filename=klevicca.vcf begin:vcard n:Klevickis;Cindy tel;home:office phone: 540-568-2726 tel;work:James Madison University x-mozilla-html:FALSE adr:;;;;;; version:2.1 email;internet:klevicca@jmu.edu x-mozilla-cpt:;-22192 fn:Cindy Klevickis end:vcard --Boundary_(ID_nHNIq7lfMHSwgiSWjsg+Yg)-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: RE: PDB files needed... Date: Wed, 24 Oct 2001 07:59:40 -0400 To: rasmol@lists.umass.edu On 10.23.01 at 12:24 PM, experimentalsciences@yahoo.de (KRW) wrote: > But there's no mention of energy minimisation to get the bond angles right, > or are biologists quite happy to present a non-optimised molecule as real? > > >As an alternate way to obtain cGMP or any simple molecule as a pdb file, > >one can > > >- draw it using for example Isisdraw, > >- save as .skc file (see attachment), > >-open it with Weblab, > >- save as .pdb file (see attachment). > > I think the message was intended as a brief outline, not an exact protocol, and should be taken in good faith. your point about minimization, however indelicately phrased, is a good one. I would never presume to speak for all biologists, but for my own purposes, I want a structure as close to "real" as possible. is it more or less accurate to rely on the calculation of a structure within chemdraw, or the calculations used in solving a crystal structure? my own thought is that the former might be more idealized than the latter... I have never used IsisDraw; does that have minimization capabilities? how about $$$? 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-Originating-IP: [12.91.235.208] X-OriginalArrivalTime: 24 Oct 2001 12:52:18.0624 (UTC) FILETIME=[B6DCA400:01C15C8A] ++++------+------+------+------+------+------+------+------+------+------+ From: "Pat O'Hern" Subject: Re: Intergrating Molecular Graphics Into Biochemistry Teaching Date: Wed, 24 Oct 2001 12:52:18 +0000 To: rasmol@lists.umass.edu Gale: I read your Manifesto. It's very good-- well-organized, well-written and very persuasive. Thank you! I helped teach a biochemistry course at Emory University in Atlanta where the students had do a term paper using Chime/RasMol. I was similarly pleased with the educational outcome. Some of the students really loved it! There's our next generation of proteonomics professionals. Warren Gallagher at the University of Wisconsin Eau Claire is also a big advocate. Keep spreading the word. Patricia A. O'Hern, Ph.D. CyberScience Design 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 _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Gorga, Frank" Subject: CHIMEd Web Sites as Scholarly Works (was RE: PDB files needed...) Date: Wed, 24 Oct 2001 09:45:02 -0400 To: "'rasmol@lists.umass.edu'" Colleagues, Tim Driscoll's request and the ensuing discussion raises a two issues regarding CHIMEd websites that I have been thinking about for awhile. Both issues come from my view that CHIMEd websites could be viewed as scholarly works (emphasis on could!). Additionally, a large part of the solution to both problems could be solved by including proper references in a CHIMEd website. The issues I allude to both relate to the sources of data used in CHIMEd sites. Number One... Many many CHIMEd websites include no reference to the original source of the data, not even a simple mention of the PDB entry in the text, much less a literature reference. In my view this is simply intellectually dishonest... basic scholarly manners say the when one uses someone else's data one gives proper credit. Number Two... When structures that are not obtained from the PDB or other data bases (mainly small molecules, in my experience) I rarely if ever see any mention of how the structure was arrived at. I suspect that many of the structures of small molecules are unoptimised structures constructed with standard bond lengths and angles. There is nothing wrong with these if they suit your purpose, but this fact should be properly documented (referenced). Minimized structures are probably preferable for most uses, but these should also be documented with a mention of the type of calculation used and the program used for the calculation. There has been a suggestion that one can obtain structures by cutting data out of a pdb file. Again I see no problem with that as long as this is properly documented and referenced. (As an aside, the structure of small molecule bound to a protein may differ substantially from its solution structure. For many purposes this does not matter, but for others it might. Proper documentation and citation will go along way in helping others evaluate sites.) One might ask how these things should be documented... I modestly propose a two pronged approach. The data file itself should contain information as to the source of the structure as do all pdb files from the database. Additionally, each CHIMEd site should have a reference section (hopefully linked to the main text) that contains this information. For (imperfect) examples of a "properly" documented website one could take a look at either my site titled "Introduction to Protein Structure" (http://webhost.bridgew.edu/fgorga/proteins/default.htm) or my site titled "The Ras Oncogene Product" (http://webhost.bridgew.edu/fgorga/ras/default.htm). The references are included in the "Acknowledgements" section of both sites. Hopefully this message will stimulate some thought and maybe even some response. I look forward to the discussion. --- Frank P.S. As I mentioned at the beginning this view springs from my idea that CHIMEd presentations *could* be viewed as scholarly works... a mechanism for peer-review of CHIMEd websites would go along way towards improving the scholarly standing of website. Any thought or discussion of this idea would be welcome as well. ---------------------------------------------------------------------------- - Frank R. Gorga, Ph.D. Department of Chemical Sciences Bridgewater State College Bridgewater, MA 02325 508-531-2827 / 508-531-1785 (fax) fgorga@bridgew.edu webhost.bridgew.edu/fgorga ---------------------------------------------------------------------------- Comfort the troubled; trouble the comfortable. -- Dietrich Bonhoeffer, 1906-1945 http://www.dbonhoeffer.org/who-was-db2.htm -----Original Message----- Sent: Wednesday, October 24, 2001 8:00 AM From: timothy driscoll [mailto:driscoll@molvisions.com] Subject: RE: PDB files needed... To: rasmol@lists.umass.edu On 10.23.01 at 12:24 PM, experimentalsciences@yahoo.de (KRW) wrote: > But there's no mention of energy minimisation to get the bond angles right, > or are biologists quite happy to present a non-optimised molecule as real? > > >As an alternate way to obtain cGMP or any simple molecule as a pdb file, > >one can > > >- draw it using for example Isisdraw, > >- save as .skc file (see attachment), > >-open it with Weblab, > >- save as .pdb file (see attachment). > > I think the message was intended as a brief outline, not an exact protocol, and should be taken in good faith. your point about minimization, however indelicately phrased, is a good one. I would never presume to speak for all biologists, but for my own purposes, I want a structure as close to "real" as possible. is it more or less accurate to rely on the calculation of a structure within chemdraw, or the calculations used in solving a crystal structure? my own thought is that the former might be more idealized than the latter... I have never used IsisDraw; does that have minimization capabilities? how about $$$? 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: <9F5E83E17008D31193DD0090274E75050663345F@mailhost.bridgew.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Cindy Klevickis Subject: Re: CHIMEd Web Sites as Scholarly Works (was RE: PDB files needed...) Date: Wed, 24 Oct 2001 10:49:35 -0400 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_/G5tJMRBnP6XtCKrzoSw2A) Hello to All, Since proper reference citation is one of the things that I want my students to learn when they are doing Chime projects, I would like to use this message, with your permission, as a reinforcement of that idea. Cindy Klevickis "Gorga, Frank" wrote: > Colleagues, > > Tim Driscoll's request and the ensuing discussion raises a two issues > regarding CHIMEd websites that I have been thinking about for awhile. > > Both issues come from my view that CHIMEd websites could be viewed as > scholarly works (emphasis on could!). Additionally, a large part of the > solution to both problems could be solved by including proper references in > a CHIMEd website. > > The issues I allude to both relate to the sources of data used in CHIMEd > sites. > > Number One... Many many CHIMEd websites include no reference to the original > source of the data, not even a simple mention of the PDB entry in the text, > much less a literature reference. In my view this is simply intellectually > dishonest... basic scholarly manners say the when one uses someone else's > data one gives proper credit. > > Number Two... When structures that are not obtained from the PDB or other > data bases (mainly small molecules, in my experience) I rarely if ever see > any mention of how the structure was arrived at. I suspect that many of the > structures of small molecules are unoptimised structures constructed with > standard bond lengths and angles. There is nothing wrong with these if they > suit your purpose, but this fact should be properly documented (referenced). > Minimized structures are probably preferable for most uses, but these should > also be documented with a mention of the type of calculation used and the > program used for the calculation. There has been a suggestion that one can > obtain structures by cutting data out of a pdb file. Again I see no problem > with that as long as this is properly documented and referenced. (As an > aside, the structure of small molecule bound to a protein may differ > substantially from its solution structure. For many purposes this does not > matter, but for others it might. Proper documentation and citation will go > along way in helping others evaluate sites.) > > One might ask how these things should be documented... I modestly propose a > two pronged approach. The data file itself should contain information as to > the source of the structure as do all pdb files from the database. > Additionally, each CHIMEd site should have a reference section (hopefully > linked to the main text) that contains this information. > > For (imperfect) examples of a "properly" documented website one could take a > look at either my site titled "Introduction to Protein Structure" > (http://webhost.bridgew.edu/fgorga/proteins/default.htm) or my site titled > "The Ras Oncogene Product" > (http://webhost.bridgew.edu/fgorga/ras/default.htm). The references are > included in the "Acknowledgements" section of both sites. > > Hopefully this message will stimulate some thought and maybe even some > response. I look forward to the discussion. > > --- Frank > > P.S. As I mentioned at the beginning this view springs from my idea that > CHIMEd presentations *could* be viewed as scholarly works... a mechanism for > peer-review of CHIMEd websites would go along way towards improving the > scholarly standing of website. Any thought or discussion of this idea would > be welcome as well. > > ---------------------------------------------------------------------------- > - > Frank R. Gorga, Ph.D. > Department of Chemical Sciences > Bridgewater State College > Bridgewater, MA 02325 > 508-531-2827 / 508-531-1785 (fax) > fgorga@bridgew.edu > webhost.bridgew.edu/fgorga > ---------------------------------------------------------------------------- > Comfort the troubled; trouble the comfortable. > -- Dietrich Bonhoeffer, 1906-1945 > http://www.dbonhoeffer.org/who-was-db2.htm > > -----Original Message----- > From: timothy driscoll [mailto:driscoll@molvisions.com] > Sent: Wednesday, October 24, 2001 8:00 AM > To: rasmol@lists.umass.edu > Subject: RE: PDB files needed... > > On 10.23.01 at 12:24 PM, experimentalsciences@yahoo.de (KRW) wrote: > > > But there's no mention of energy minimisation to get the bond angles > right, > > or are biologists quite happy to present a non-optimised molecule as real? > > > > >As an alternate way to obtain cGMP or any simple molecule as a pdb file, > > >one can > > > > >- draw it using for example Isisdraw, > > >- save as .skc file (see attachment), > > >-open it with Weblab, > > >- save as .pdb file (see attachment). > > > > > I think the message was intended as a brief outline, not an exact protocol, > and > should be taken in good faith. your point about minimization, however > indelicately phrased, is a good one. I would never presume to speak for all > biologists, but for my own purposes, I want a structure as close to "real" > as > possible. is it more or less accurate to rely on the calculation of a > structure > within chemdraw, or the calculations used in solving a crystal structure? > my > own thought is that the former might be more idealized than the latter... > > I have never used IsisDraw; does that have minimization capabilities? how > about > $$$? > > > > 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 > --Boundary_(ID_/G5tJMRBnP6XtCKrzoSw2A) Content-description: Card for Cindy Klevickis Content-disposition: attachment; filename=klevicca.vcf begin:vcard n:Klevickis;Cindy tel;work:540-568-2726 x-mozilla-html:FALSE adr:;;;;;; version:2.1 email;internet:klevicca@jmu.edu fn:Cindy Klevickis end:vcard --Boundary_(ID_/G5tJMRBnP6XtCKrzoSw2A)-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Gorga, Frank" Subject: RE: CHIMEd Web Sites as Scholarly Works (was RE: PDB files needed ...) Date: Wed, 24 Oct 2001 11:11:24 -0400 To: "'rasmol@lists.umass.edu'" Cindy, I am not sure whether you request was directed at the list in general or me in particular... but either way, from my point of view... "permission granted" I am glad to hear that you stress proper citation in your CHIME projects... I know what a battle this is in regular term papers! --- Frank ---------------------------------------------------------------------------- - Frank R. Gorga, Ph.D. Department of Chemical Sciences Bridgewater State College Bridgewater, MA 02325 508-531-2827 / 508-531-1785 (fax) fgorga@bridgew.edu webhost.bridgew.edu/fgorga ---------------------------------------------------------------------------- Comfort the troubled; trouble the comfortable. -- Dietrich Bonhoeffer, 1906-1945 http://www.dbonhoeffer.org/who-was-db2.htm -----Original Message----- Sent: Wednesday, October 24, 2001 10:50 AM needed...) From: Cindy Klevickis [mailto:klevicca@jmu.edu] Subject: Re: CHIMEd Web Sites as Scholarly Works (was RE: PDB files To: rasmol@lists.umass.edu Hello to All, Since proper reference citation is one of the things that I want my students to learn when they are doing Chime projects, I would like to use this message, with your permission, as a reinforcement of that idea. Cindy Klevickis "Gorga, Frank" wrote: > Colleagues, > > Tim Driscoll's request and the ensuing discussion raises a two issues > regarding CHIMEd websites that I have been thinking about for awhile. > > Both issues come from my view that CHIMEd websites could be viewed as > scholarly works (emphasis on could!). Additionally, a large part of the > solution to both problems could be solved by including proper references in > a CHIMEd website. > > The issues I allude to both relate to the sources of data used in CHIMEd > sites. > > Number One... Many many CHIMEd websites include no reference to the original > source of the data, not even a simple mention of the PDB entry in the text, > much less a literature reference. In my view this is simply intellectually > dishonest... basic scholarly manners say the when one uses someone else's > data one gives proper credit. > > Number Two... When structures that are not obtained from the PDB or other > data bases (mainly small molecules, in my experience) I rarely if ever see > any mention of how the structure was arrived at. I suspect that many of the > structures of small molecules are unoptimised structures constructed with > standard bond lengths and angles. There is nothing wrong with these if they > suit your purpose, but this fact should be properly documented (referenced). > Minimized structures are probably preferable for most uses, but these should > also be documented with a mention of the type of calculation used and the > program used for the calculation. There has been a suggestion that one can > obtain structures by cutting data out of a pdb file. Again I see no problem > with that as long as this is properly documented and referenced. (As an > aside, the structure of small molecule bound to a protein may differ > substantially from its solution structure. For many purposes this does not > matter, but for others it might. Proper documentation and citation will go > along way in helping others evaluate sites.) > > One might ask how these things should be documented... I modestly propose a > two pronged approach. The data file itself should contain information as to > the source of the structure as do all pdb files from the database. > Additionally, each CHIMEd site should have a reference section (hopefully > linked to the main text) that contains this information. > > For (imperfect) examples of a "properly" documented website one could take a > look at either my site titled "Introduction to Protein Structure" > (http://webhost.bridgew.edu/fgorga/proteins/default.htm) or my site titled > "The Ras Oncogene Product" > (http://webhost.bridgew.edu/fgorga/ras/default.htm). The references are > included in the "Acknowledgements" section of both sites. > > Hopefully this message will stimulate some thought and maybe even some > response. I look forward to the discussion. > > --- Frank > > P.S. As I mentioned at the beginning this view springs from my idea that > CHIMEd presentations *could* be viewed as scholarly works... a mechanism for > peer-review of CHIMEd websites would go along way towards improving the > scholarly standing of website. Any thought or discussion of this idea would > be welcome as well. > > ---------------------------------------------------------------------------- > - > Frank R. Gorga, Ph.D. > Department of Chemical Sciences > Bridgewater State College > Bridgewater, MA 02325 > 508-531-2827 / 508-531-1785 (fax) > fgorga@bridgew.edu > webhost.bridgew.edu/fgorga > ---------------------------------------------------------------------------- > Comfort the troubled; trouble the comfortable. > -- Dietrich Bonhoeffer, 1906-1945 > http://www.dbonhoeffer.org/who-was-db2.htm > > -----Original Message----- > From: timothy driscoll [mailto:driscoll@molvisions.com] > Sent: Wednesday, October 24, 2001 8:00 AM > To: rasmol@lists.umass.edu > Subject: RE: PDB files needed... > > On 10.23.01 at 12:24 PM, experimentalsciences@yahoo.de (KRW) wrote: > > > But there's no mention of energy minimisation to get the bond angles > right, > > or are biologists quite happy to present a non-optimised molecule as real? > > > > >As an alternate way to obtain cGMP or any simple molecule as a pdb file, > > >one can > > > > >- draw it using for example Isisdraw, > > >- save as .skc file (see attachment), > > >-open it with Weblab, > > >- save as .pdb file (see attachment). > > > > > I think the message was intended as a brief outline, not an exact protocol, > and > should be taken in good faith. your point about minimization, however > indelicately phrased, is a good one. I would never presume to speak for all > biologists, but for my own purposes, I want a structure as close to "real" > as > possible. is it more or less accurate to rely on the calculation of a > structure > within chemdraw, or the calculations used in solving a crystal structure? > my > own thought is that the former might be more idealized than the latter... > > I have never used IsisDraw; does that have minimization capabilities? how > about > $$$? > > > > 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: <9F5E83E17008D31193DD0090274E75050663345F@mailhost.bridgew.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Judy Voet Subject: Re: CHIMEd Web Sites as Scholarly Works (was RE: PDB files needed...) Date: Wed, 24 Oct 2001 11:29:28 -0400 To: rasmol@lists.umass.edu Cc: bgordon@asbmb.faseb.org, voet@sas.upenn.edu >Dear Rasmolers, Frank Gorga's note is extremely timely. Next spring, the ASBMB, IUBMB and the journal Biochemistry and Molecular Biology Education (BAMBED) will begin constructing a digital library of peer-reviewed, web-based educational materials. We will start planning soon and would like as much input as possible on the best way to do it. If you would like to participate in this planning, please contact me. Best regards, Judy Voet, Co-Editor-in-chief, BAMBED >Colleagues, > >Tim Driscoll's request and the ensuing discussion raises a two issues >regarding CHIMEd websites that I have been thinking about for awhile. > >Both issues come from my view that CHIMEd websites could be viewed as >scholarly works (emphasis on could!). Additionally, a large part of the >solution to both problems could be solved by including proper references in >a CHIMEd website. > >The issues I allude to both relate to the sources of data used in CHIMEd >sites. > >Number One... Many many CHIMEd websites include no reference to the original >source of the data, not even a simple mention of the PDB entry in the text, >much less a literature reference. In my view this is simply intellectually >dishonest... basic scholarly manners say the when one uses someone else's >data one gives proper credit. > >Number Two... When structures that are not obtained from the PDB or other >data bases (mainly small molecules, in my experience) I rarely if ever see >any mention of how the structure was arrived at. I suspect that many of the >structures of small molecules are unoptimised structures constructed with >standard bond lengths and angles. There is nothing wrong with these if they >suit your purpose, but this fact should be properly documented (referenced). >Minimized structures are probably preferable for most uses, but these should >also be documented with a mention of the type of calculation used and the >program used for the calculation. There has been a suggestion that one can >obtain structures by cutting data out of a pdb file. Again I see no problem >with that as long as this is properly documented and referenced. (As an >aside, the structure of small molecule bound to a protein may differ >substantially from its solution structure. For many purposes this does not >matter, but for others it might. Proper documentation and citation will go >along way in helping others evaluate sites.) > >One might ask how these things should be documented... I modestly propose a >two pronged approach. The data file itself should contain information as to >the source of the structure as do all pdb files from the database. >Additionally, each CHIMEd site should have a reference section (hopefully >linked to the main text) that contains this information. > >For (imperfect) examples of a "properly" documented website one could take a >look at either my site titled "Introduction to Protein Structure" >(http://webhost.bridgew.edu/fgorga/proteins/default.htm) or my site titled >"The Ras Oncogene Product" >(http://webhost.bridgew.edu/fgorga/ras/default.htm). The references are >included in the "Acknowledgements" section of both sites. > >Hopefully this message will stimulate some thought and maybe even some >response. I look forward to the discussion. > >--- Frank > >P.S. As I mentioned at the beginning this view springs from my idea that >CHIMEd presentations *could* be viewed as scholarly works... a mechanism for >peer-review of CHIMEd websites would go along way towards improving the >scholarly standing of website. Any thought or discussion of this idea would >be welcome as well. > > > > >---------------------------------------------------------------------------- >- >Frank R. Gorga, Ph.D. >Department of Chemical Sciences >Bridgewater State College >Bridgewater, MA 02325 >508-531-2827 / 508-531-1785 (fax) >fgorga@bridgew.edu >webhost.bridgew.edu/fgorga >---------------------------------------------------------------------------- >Comfort the troubled; trouble the comfortable. > -- Dietrich Bonhoeffer, 1906-1945 > http://www.dbonhoeffer.org/who-was-db2.htm > > >-----Original Message----- >From: timothy driscoll [mailto:driscoll@molvisions.com] >Sent: Wednesday, October 24, 2001 8:00 AM >To: rasmol@lists.umass.edu >Subject: RE: PDB files needed... > > >On 10.23.01 at 12:24 PM, experimentalsciences@yahoo.de (KRW) wrote: > >> But there's no mention of energy minimisation to get the bond angles >right, >> or are biologists quite happy to present a non-optimised molecule as real? >> >> >As an alternate way to obtain cGMP or any simple molecule as a pdb file, >> >one can >> >> >- draw it using for example Isisdraw, >> >- save as .skc file (see attachment), >> >-open it with Weblab, >> >- save as .pdb file (see attachment). >> > > >I think the message was intended as a brief outline, not an exact protocol, >and >should be taken in good faith. your point about minimization, however >indelicately phrased, is a good one. I would never presume to speak for all >biologists, but for my own purposes, I want a structure as close to "real" >as >possible. is it more or less accurate to rely on the calculation of a >structure >within chemdraw, or the calculations used in solving a crystal structure? >my >own thought is that the former might be more idealized than the latter... > >I have never used IsisDraw; does that have minimization capabilities? how >about >$$$? > > > >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-- X-Accept-Language: en References: <9F5E83E17008D31193DD0090274E750506633463@mailhost.bridgew.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Erik Nordling Subject: tube representation Date: Wed, 24 Oct 2001 17:33:10 +0200 To: rasmol@lists.umass.edu Hi all Rasmoler out there! recently have I been searching for a program that manages to display helices as tubes, plain tubes without cones or arrows to show direction (thank you weblab viewer lite). If you happen to now any such software please let me know since all I find is som strange stuff which do not work as I hope. The platform is prefereble windows, but Irix or linux works just as fine. thanks in advance Sincerley yours, Erik Nordling -- Erik Nordling MBB, Karolinska Institutet E-mail: erik.nordling@mbb.ki.se ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: <9F5E83E17008D31193DD0090274E750506633463@mailhost.bridgew.edu> <3BD6DF36.1847E8ED@mbb.ki.se> ++++------+------+------+------+------+------+------+------+------+------+ From: Ilan Samish Subject: Re: tube representation Date: Wed, 24 Oct 2001 18:40:24 +0200 To: rasmol@lists.umass.edu Hi all, Both VMD and DINO have good representations for tubes. http://www.ks.uiuc.edu/Research/vmd/ http://www.biozentrum.unibas.ch/~xray/dino/ In DINO, under the quick-start tutorial you'll find the script needed - after loading, defining a name, putting the protein in the center and defining a graphical resolution, you need to write render tube,bw= Though the script is a few lines, it produces good results and can later be easily re-used as a procedure (@ and path of script saved). Good luck, Ilan Samish ~~~~~~~~~~~~~~~~~~~~ Ilan.samish@weizmann.ac.il Weizmann Institute of Science Rehovot, Israel 972-8-9344300 Erik Nordling wrote: > Hi all Rasmoler out there! > > recently have I been searching for a program that manages to display helices as > tubes, plain tubes without cones or arrows to show direction (thank you weblab > viewer lite). If you happen to now any such software please let me know since > all I find is som strange stuff which do not work as I hope. The platform is > prefereble windows, but Irix or linux works just as fine. > > thanks in advance > > Sincerley yours, > > Erik Nordling > > -- > Erik Nordling > MBB, Karolinska Institutet > E-mail: erik.nordling@mbb.ki.se > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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_3Uc5ej8L7jHgDhsTlvY6ew)" ++++------+------+------+------+------+------+------+------+------+------+ From: David Margulies Subject: RE: tube representation Date: Wed, 24 Oct 2001 15:46:52 -0400 To: "'rasmol@lists.umass.edu'" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --Boundary_(ID_3Uc5ej8L7jHgDhsTlvY6ew) You can do this in quanta. D > ---------- > From: Erik Nordling > Reply To: rasmol@lists.umass.edu > Sent: Wednesday, October 24, 2001 11:33 AM > To: rasmol@lists.umass.edu > Subject: tube representation > > Hi all Rasmoler out there! > > recently have I been searching for a program that manages to display > helices as > tubes, plain tubes without cones or arrows to show direction (thank you > weblab > viewer lite). If you happen to now any such software please let me know > since > all I find is som strange stuff which do not work as I hope. The platform > is > prefereble windows, but Irix or linux works just as fine. > > thanks in advance > > Sincerley yours, > > Erik Nordling > > -- > Erik Nordling > MBB, Karolinska Institutet > E-mail: erik.nordling@mbb.ki.se > > > > --Boundary_(ID_3Uc5ej8L7jHgDhsTlvY6ew) RE: tube representation

You  can do this in quanta.
D

    ----------
    From:   Erik Nordling
    Reply To:       rasmol@lists.umass.edu
    Sent:   Wednesday, October 24, 2001 11:33 AM
    To:     rasmol@lists.umass.edu
    Subject:        tube representation

    Hi all Rasmoler out there!

    recently have I been searching for a program that manages to display helices as
    tubes, plain tubes without cones or arrows to show direction (thank you weblab
    viewer lite). If you happen to now any such software please let me know since
    all I find is som strange stuff which do not work as I hope. The platform is
    prefereble windows, but Irix or linux works just as fine.

    thanks in advance

    Sincerley yours,

    Erik Nordling

    --
    Erik Nordling
    MBB, Karolinska Institutet
    E-mail: erik.nordling@mbb.ki.se



--Boundary_(ID_3Uc5ej8L7jHgDhsTlvY6ew)-- X-Accept-Language: en References: <9F5E83E17008D31193DD0090274E750506633463@mailhost.bridgew.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Cindy Klevickis Subject: Re: CHIMEd Web Sites as Scholarly Works (was RE: PDB files needed ...) Date: Wed, 24 Oct 2001 21:07:26 -0400 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_fyw577A1M2ET/1FN4iYFxA) Thanks, I am going to send an email to my class tonight with your note. They are just starting a Chime project and this might help with some quality control. Cindy Klevickis "Gorga, Frank" wrote: > Cindy, > > I am not sure whether you request was directed at the list in general or me > in particular... but either way, from my point of view... "permission > granted" > > I am glad to hear that you stress proper citation in your CHIME projects... > I know what a battle this is in regular term papers! > > --- Frank > > ---------------------------------------------------------------------------- > - > Frank R. Gorga, Ph.D. > Department of Chemical Sciences > Bridgewater State College > Bridgewater, MA 02325 > 508-531-2827 / 508-531-1785 (fax) > fgorga@bridgew.edu > webhost.bridgew.edu/fgorga > ---------------------------------------------------------------------------- > Comfort the troubled; trouble the comfortable. > -- Dietrich Bonhoeffer, 1906-1945 > http://www.dbonhoeffer.org/who-was-db2.htm > > -----Original Message----- > From: Cindy Klevickis [mailto:klevicca@jmu.edu] > Sent: Wednesday, October 24, 2001 10:50 AM > To: rasmol@lists.umass.edu > Subject: Re: CHIMEd Web Sites as Scholarly Works (was RE: PDB files > needed...) > > Hello to All, > > Since proper reference citation is one of the things that I want my students > to > learn when they are doing Chime projects, I would like to use this message, > with > your permission, as a reinforcement of that idea. > > Cindy Klevickis > > "Gorga, Frank" wrote: > > > Colleagues, > > > > Tim Driscoll's request and the ensuing discussion raises a two issues > > regarding CHIMEd websites that I have been thinking about for awhile. > > > > Both issues come from my view that CHIMEd websites could be viewed as > > scholarly works (emphasis on could!). Additionally, a large part of the > > solution to both problems could be solved by including proper references > in > > a CHIMEd website. > > > > The issues I allude to both relate to the sources of data used in CHIMEd > > sites. > > > > Number One... Many many CHIMEd websites include no reference to the > original > > source of the data, not even a simple mention of the PDB entry in the > text, > > much less a literature reference. In my view this is simply intellectually > > dishonest... basic scholarly manners say the when one uses someone else's > > data one gives proper credit. > > > > Number Two... When structures that are not obtained from the PDB or other > > data bases (mainly small molecules, in my experience) I rarely if ever see > > any mention of how the structure was arrived at. I suspect that many of > the > > structures of small molecules are unoptimised structures constructed with > > standard bond lengths and angles. There is nothing wrong with these if > they > > suit your purpose, but this fact should be properly documented > (referenced). > > Minimized structures are probably preferable for most uses, but these > should > > also be documented with a mention of the type of calculation used and the > > program used for the calculation. There has been a suggestion that one can > > obtain structures by cutting data out of a pdb file. Again I see no > problem > > with that as long as this is properly documented and referenced. (As an > > aside, the structure of small molecule bound to a protein may differ > > substantially from its solution structure. For many purposes this does not > > matter, but for others it might. Proper documentation and citation will go > > along way in helping others evaluate sites.) > > > > One might ask how these things should be documented... I modestly propose > a > > two pronged approach. The data file itself should contain information as > to > > the source of the structure as do all pdb files from the database. > > Additionally, each CHIMEd site should have a reference section (hopefully > > linked to the main text) that contains this information. > > > > For (imperfect) examples of a "properly" documented website one could take > a > > look at either my site titled "Introduction to Protein Structure" > > (http://webhost.bridgew.edu/fgorga/proteins/default.htm) or my site titled > > "The Ras Oncogene Product" > > (http://webhost.bridgew.edu/fgorga/ras/default.htm). The references are > > included in the "Acknowledgements" section of both sites. > > > > Hopefully this message will stimulate some thought and maybe even some > > response. I look forward to the discussion. > > > > --- Frank > > > > P.S. As I mentioned at the beginning this view springs from my idea that > > CHIMEd presentations *could* be viewed as scholarly works... a mechanism > for > > peer-review of CHIMEd websites would go along way towards improving the > > scholarly standing of website. Any thought or discussion of this idea > would > > be welcome as well. > > > > > ---------------------------------------------------------------------------- > > - > > Frank R. Gorga, Ph.D. > > Department of Chemical Sciences > > Bridgewater State College > > Bridgewater, MA 02325 > > 508-531-2827 / 508-531-1785 (fax) > > fgorga@bridgew.edu > > webhost.bridgew.edu/fgorga > > > ---------------------------------------------------------------------------- > > Comfort the troubled; trouble the comfortable. > > -- Dietrich Bonhoeffer, 1906-1945 > > http://www.dbonhoeffer.org/who-was-db2.htm > > > > -----Original Message----- > > From: timothy driscoll [mailto:driscoll@molvisions.com] > > Sent: Wednesday, October 24, 2001 8:00 AM > > To: rasmol@lists.umass.edu > > Subject: RE: PDB files needed... > > > > On 10.23.01 at 12:24 PM, experimentalsciences@yahoo.de (KRW) wrote: > > > > > But there's no mention of energy minimisation to get the bond angles > > right, > > > or are biologists quite happy to present a non-optimised molecule as > real? > > > > > > >As an alternate way to obtain cGMP or any simple molecule as a pdb > file, > > > >one can > > > > > > >- draw it using for example Isisdraw, > > > >- save as .skc file (see attachment), > > > >-open it with Weblab, > > > >- save as .pdb file (see attachment). > > > > > > > > I think the message was intended as a brief outline, not an exact > protocol, > > and > > should be taken in good faith. your point about minimization, however > > indelicately phrased, is a good one. I would never presume to speak for > all > > biologists, but for my own purposes, I want a structure as close to "real" > > as > > possible. is it more or less accurate to rely on the calculation of a > > structure > > within chemdraw, or the calculations used in solving a crystal structure? > > my > > own thought is that the former might be more idealized than the latter... > > > > I have never used IsisDraw; does that have minimization capabilities? how > > about > > $$$? > > > > > > > > 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 > > > --Boundary_(ID_fyw577A1M2ET/1FN4iYFxA) Content-description: Card for Cindy Klevickis Content-disposition: attachment; filename=klevicca.vcf begin:vcard n:Klevickis;Cindy tel;home:office phone: 540-568-2726 tel;work:James Madison University x-mozilla-html:FALSE adr:;;;;;; version:2.1 email;internet:klevicca@jmu.edu x-mozilla-cpt:;-22192 fn:Cindy Klevickis end:vcard --Boundary_(ID_fyw577A1M2ET/1FN4iYFxA)-- X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Marlene Kayne Subject: your rasmol list message Date: Wed, 24 Oct 2001 18:03:33 -0400 To: Judy Voet Dear Judy, If you think my experience with using modeling to teach biochem would be useful, I would be happy to volunteer. I have designed several exercises which are used in the Biochem for Chem majors and Biochem for Biology majors courses. I have put together packages using materials which are available on the web. I have not done any RasMol scripts myself. Say hello to Don. Regards, Marlene Kayne ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <9F5E83E17008D31193DD0090274E75050663345F@mailhost.bridgew.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Reichsman Subject: Re: CHIMEd Web Sites as Scholarly Works Date: Wed, 24 Oct 2001 18:12:43 -0400 To: rasmol@lists.umass.edu The Chime tutorials at the Lehninger Biochemistry in 3D site are a good example (if I do say so myself! :-> ) of well-referenced online tutorials. In some cases, the tutorials were also reviewed before release by an author of one or more of the structure papers used (e.g., hammerhead ribozyme). The PDB files and references are accessed in each tutorial's Control Panel (bottom of tutorial window), by clicking the "Misc" tab. This reveals References and Structure File links. Cheers, Frieda -- Frieda Reichsman, Ph.D. 30 South Whitney Street Molecules In Motion Amherst MA 01002 USA Interactive Molecular Structures (413) 253-2405 http://www.MoleculesInMotion.com ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: <3BD73AB5.4C1FEF1C@tcnj.edu> X-Authentication-warning: andromeda.alb.edu: Host [172.16.60.67] claimed to be alb.edu ++++------+------+------+------+------+------+------+------+------+------+ From: Frieda Texter Subject: Re: your rasmol list message Date: Thu, 25 Oct 2001 11:18:57 -0400 To: rasmol@lists.umass.edu I teach a junior/senior level biochemistry course which is taken by a combination of biochemistry/chemistry/ and biology majors. I have begun to introduce my students to RasMol and most recently Protein Explorer through the laboratory component of the course. I would be very much interested seeing the types of exercises you have incorporated into your courses if you would be willing to share them. Frieda L. Texter, Ph.D. Professor and Chair Department of Chemistry and Biochemistry Albright College 13th and Bern Streets P.O. Box 15234 Reading, PA 19612-5234 voice: 610-921-7747 fax: 610-921-7784 email: friedat@alb.edu Marlene Kayne wrote: > Dear Judy, > If you think my experience with using modeling to teach biochem would > be useful, I would be happy to volunteer. I have designed several > exercises which are used in the Biochem for Chem majors and Biochem for > Biology majors courses. I have put together packages using materials > which are available on the web. I have not done any RasMol scripts > myself. Say hello to Don. > Regards, > Marlene Kayne > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Karl Oberholser Subject: Re: your rasmol list message Date: Thu, 25 Oct 2001 11:27:36 -0400 To: rasmol@lists.umass.edu This is a MIME message. If you are reading this text, you may want to consider changing to a mail reader or gateway that understands how to properly handle MIME multipart messages. --Boundary_(ID_SN0nbrWigmumZtpzDanxvg) Content-disposition: inline Exercises that use Protein Explorer can be found at http://www.messiah.edu/molscilab/. Karl M. Oberholser, Ph.D. Phone: Professor of Chemistry Voice: 717-766-0512 Natural Sciences Dept. Fax: 717-691-6002 Messiah College e-mail: oberhols@messiah.edu P.O. Box 3030 One College Avenue Grantham, Pa 17027 >>> friedat@alb.edu 10/25/01 11:18AM >>> I teach a junior/senior level biochemistry course which is taken by a combination of biochemistry/chemistry/ and biology majors. I have begun to introduce my students to RasMol and most recently Protein Explorer through the laboratory component of the course. I would be very much interested seeing the types of exercises you have incorporated into your courses if you would be willing to share them. Frieda L. Texter, Ph.D. Professor and Chair Department of Chemistry and Biochemistry Albright College 13th and Bern Streets P.O. Box 15234 Reading, PA 19612-5234 voice: 610-921-7747 fax: 610-921-7784 email: friedat@alb.edu Marlene Kayne wrote: > Dear Judy, > If you think my experience with using modeling to teach biochem would > be useful, I would be happy to volunteer. I have designed several > exercises which are used in the Biochem for Chem majors and Biochem for > Biology majors courses. I have put together packages using materials > which are available on the web. I have not done any RasMol scripts > myself. Say hello to Don. > Regards, > Marlene Kayne > --Boundary_(ID_SN0nbrWigmumZtpzDanxvg) Content-disposition: attachment; filename="Karl Oberholser.vcf" BEGIN:VCARD VERSION:2.1 X-GWTYPE:USER FN:Oberholser, Karl EMAIL;WORK;PREF;NGW:Oberhols@messiah.edu ORG:;Faculty - Natural Sciences N:Oberholser;Karl END:VCARD --Boundary_(ID_SN0nbrWigmumZtpzDanxvg)-- Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: Todd Carlson Subject: Re: cGMP and downloading pdb files from the web Date: Thu, 25 Oct 2001 13:47:34 -0400 To: rasmol@lists.umass.edu Glad to be of service. Todd >>> klevicca@jmu.edu 10/24/01 07:55 AM >>> OOPs, the incorrect cGMP that you noted is on one of my student's old project pages. I will fix it. Cindy Klevickis Todd Carlson wrote: > It's worth noting that you have to use caution downloading files from the web. Some people may find this file named cGMP.PDB > > http://www.isat.jmu.edu/common/coursedocs/isat454/midterm/Viagra/cGMP.PDB > > but if you look at the structure, it isn't cyclic. It's just 5`-GMP > > I have found several "bad" structures over the web. I once had my students find an aspartame pdb file so they can see the geometry of the planar peptide group geometry, but half the students found aspartame models with trigonal pyramidal geometry around the amide nitrogen. Now I warn them and they have to make sure they have a correct pdb file (of course half still get it wrong, ug). > > Compare http://education.llnl.gov/msds/pdb/ASPARTAME.PDB incorrect > > To http://www.okanagan.bc.ca/chem/molecule/aspartam.pdb correct > > Todd > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Marlene Kayne Subject: Lab exercises using web materials Date: Thu, 25 Oct 2001 17:13:40 -0400 To: Frieda Texter Dear Dr. Texter, I would be very happy to share the exercises I have put together. As I wrote to Judy Voet, I have used materials from the Web and placed them together into a fairly reasonable package. I would be happy to send them to you. Regards, Marlene Kayne ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: CHIMEd Web Sites as Scholarly Works Date: Thu, 25 Oct 2001 16:11:42 -0400 To: rasmol@lists.umass.edu I applaud Frank Gorga's suggestion. I agree that authors of Chime websites should at least always give the PDB id codes for molecules shown, and that citing the literature reference in addition is even better (preferably hyperlinked to PubMed). (Undoubtedly I've fallen short of these ideals myself on some of my sites.) I do include literature citation in the instructions I give to my students (http://www.umass.edu/microbio/chime/prsswc/presreqt.htm) I am also interested in the idea of having Chime sites reviewed, and I'd like to suggest that one mechanism for making brief reviews widely available is to add them to the descriptions of the sites at http://molvisindex.org. One could include the key term "reviewed" in the cross-indexing/subject term list, so one could find all reviewed sites listed together in the subject index. Since the inception of the visitor-maintained indices software that manages MolVisIndex, I have wanted to add formal fields for evaluations and ratings. Also I have become convinced that Judy Voet's suggestion is correct that a search mechanism is desirable (now that we have nearly 1,000 subject terms in the Chime section!). If someone reading this list is interested in that project, and is good at programming java and java server pages, please contact me (payment for programming time is possible). -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <3BD73AB5.4C1FEF1C@tcnj.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Judy Voet Subject: Re: your rasmol list message Date: Thu, 25 Oct 2001 17:52:45 -0400 To: rasmol@lists.umass.edu >Dear Marlene, Good to hear from you. I'll put your name on the list of people interested in helping plan the digital library. It may be a few months before we actually get going, so don't hold your breath. Say to Fred, too. Regards, Judy >Dear Judy, > If you think my experience with using modeling to teach biochem would >be useful, I would be happy to volunteer. I have designed several >exercises which are used in the Biochem for Chem majors and Biochem for >Biology majors courses. I have put together packages using materials >which are available on the web. I have not done any RasMol scripts >myself. Say hello to Don. > Regards, > Marlene Kayne > -- 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-- X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Lettice AuYeung Subject: E-mail project questionnaire Date: Fri, 26 Oct 2001 09:53:08 +0800 To: rasmol@lists.umass.edu Dear Colleagues, Do you have some experiences, views and opinions to share about the use of email for ODL research, administration and teaching? If so, please visit this website and send us your response: http://www.ouhk.edu.hk/cridal/project/email/index.html Should you have any query about the instrument do please contact Ms Lettice Au Yeung (lau@ouhk.edu.hk) Thank you very much for your co-operation. Olugbemiro Olugbemiro Jegede, Ph.D Professor & Director Centre for Research in Distance & Adult Learning The Open University of Hong Kong 30 Good Shepherd Street, Homatin, Kowloon HONG KONG Tel: +852 2768 6700 Fax: +852 2715 9042 email: jegede@ouhk.edu.hk URL: http://www.ouhk.edu.hk/cridal/staff/jegede/ojj.html ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: <3BD73AB5.4C1FEF1C@tcnj.edu> <3BD82D61.4984DA5C@alb.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Cindy Klevickis Subject: Re: your rasmol list message Date: Thu, 25 Oct 2001 20:47:30 -0400 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_tHywwK9ek+2ocxGo2Vrx9A) Hello from Cindy Klevickis, Here is the web link for my Computer Applications in Biotechnology Class. http://www.isat.jmu.edu/users/klevicca/isat454/open.htm All of the activities are linked on the syllabus frame of this page. Students write illustrated essays, RasMol scripts, Chime Projects and a combination NMR/Chime project. The NMR project involves taking an NMR spectrum of an amino acid and making links between each peak in the spectrum and a Chime model of that amino acid. Another project for this class is called Shoebox Crystallography. For this project, students derive x,y and z coordinates from toys and use these coordinates to make their own pdb files. These students are not biochemistry or chemistry majors. Most are Integrated Science and Technology majors and some are CS majors. Thus, almost all of the biochemistry they learn comes solely from the experience of working on these projects. Cindy Klevickis Frieda Texter wrote: > I teach a junior/senior level biochemistry course which is taken by a combination > of biochemistry/chemistry/ and biology majors. I have begun to introduce my > students to RasMol and most recently Protein Explorer through the laboratory > component of the course. I would be very much interested seeing the types of > exercises you have incorporated into your courses if you would be willing to > share them. > > Frieda L. Texter, Ph.D. > Professor and Chair > Department of Chemistry and Biochemistry > Albright College > 13th and Bern Streets > P.O. Box 15234 > Reading, PA 19612-5234 > voice: 610-921-7747 > fax: 610-921-7784 > email: friedat@alb.edu > > Marlene Kayne wrote: > > > Dear Judy, > > If you think my experience with using modeling to teach biochem would > > be useful, I would be happy to volunteer. I have designed several > > exercises which are used in the Biochem for Chem majors and Biochem for > > Biology majors courses. I have put together packages using materials > > which are available on the web. I have not done any RasMol scripts > > myself. Say hello to Don. > > Regards, > > Marlene Kayne > > > --Boundary_(ID_tHywwK9ek+2ocxGo2Vrx9A) Content-description: Card for Cindy Klevickis Content-disposition: attachment; filename=klevicca.vcf begin:vcard n:Klevickis;Cindy tel;home:office phone: 540-568-2726 tel;work:James Madison University x-mozilla-html:FALSE adr:;;;;;; version:2.1 email;internet:klevicca@jmu.edu x-mozilla-cpt:;-22192 fn:Cindy Klevickis end:vcard --Boundary_(ID_tHywwK9ek+2ocxGo2Vrx9A)-- ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: CHIMEd Web Sites as Scholarly Works Date: Fri, 26 Oct 2001 06:59:02 -0400 (EDT) To: rasmol@lists.umass.edu If one is creating a scholarly work which uses molecular graphics, I hope that, in addition to citing the sources for the content of the images, the author will also cite the appropriate literature on the graphics program or programs used. -- HJB ===================================================== **** 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, 25 Oct 2001, Eric Martz wrote: > I applaud Frank Gorga's suggestion. I agree that authors of Chime websites > should at least always give the PDB id codes for molecules shown, and that > citing the literature reference in addition is even better (preferably > hyperlinked to PubMed). (Undoubtedly I've fallen short of these ideals > myself on some of my sites.) I do include literature citation in the > instructions I give to my students > (http://www.umass.edu/microbio/chime/prsswc/presreqt.htm) > ... > > -Eric ... > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz ... > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: referencing software (was CHIMEd Web Sites as Scholarly Works) Date: Fri, 26 Oct 2001 08:21:41 -0400 To: rasmol@lists.umass.edu On 10.26.01 at 6:59 AM, yaya@bernstein-plus-sons.com (Herbert J. Bernstein) wrote: > If one is creating a scholarly work which uses molecular graphics, I hope > that, in addition to citing the sources for the content of the images, the > author will also cite the appropriate literature on the graphics program > or programs used. -- HJB I agree with this concept for "freeware," if for no other reason than common courtesy, but certainly not commercial products. isn't that part of the $$$? that does bring up an interesting question, though; when a user signs/accepts a licence agreement to use a copy of a software program, does that mean the copy is "owned" by the user? so does the user need to reference its use? if the consensus answer is yes, I'd love an explanation that I can present to clients. many are unwilling to give up even a square pixel of screen space or bandwidth without much gnashing of teeth. -tim typed using an Apple Pro keyboard (), and composed in BareBones MailSmith (), before being sent via TCP/IP under Mac OS 9.1 () to an AppleShare IP mail server () across a Speakeasy DSL (http://www.speakeasy.org>) to the RasMol list (http://www.umass.edu/microbio/rasmol/raslist.htm>). powered by Dunkin Donuts coffee - large () :-) _________________________________________ 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-- charset=us-ascii X-Accept-Language: en References: <20011026082142-r01010800-f103386c-0910-010c@192.168.1.3> ++++------+------+------+------+------+------+------+------+------+------+ From: Alex Brown Subject: Re: referencing software (was CHIMEd Web Sites as Scholarly Works) Date: Fri, 26 Oct 2001 13:53:23 +0100 To: rasmol@lists.umass.edu If I may butt in - If the software is pertinent to your presentation or work, then commercial or otherwise, it should be acknowledged. Scientific journals are 'commercial' and the work of many (if not all) scientists is 'commercial' (they get paid for it - perhaps not enough, but they still get paid !!), and yet we all acknowledge the papers we reference in our submissions. Perhaps the same conciderations should be made for software (and perhaps hardware ?). For items such as word processors, perhaps not, as these shouldn't have any relevance to your work. With that in mind, this presentation was written without the use any Microsoft software :-) Cheers, Alex Brown timothy driscoll wrote: > On 10.26.01 at 6:59 AM, yaya@bernstein-plus-sons.com (Herbert J. Bernstein) > wrote: > > > I agree with this concept for "freeware," if for no other reason than common > courtesy, but certainly not commercial products. isn't that part of the $$$? > that does bring up an interesting question, though; when a user signs/accepts a > licence agreement to use a copy of a software program, does that mean the copy > is "owned" by the user? so does the user need to reference its use? > > if the consensus answer is yes, I'd love an explanation that I can present to > clients. many are unwilling to give up even a square pixel of screen space or > bandwidth without much gnashing of teeth. > > -tim > > typed using an Apple Pro keyboard (), > and composed in BareBones MailSmith (), > before being sent via TCP/IP under Mac OS 9.1 () > to an AppleShare IP mail server () > across a Speakeasy DSL (http://www.speakeasy.org>) > to the RasMol list (http://www.umass.edu/microbio/rasmol/raslist.htm>). > powered by Dunkin Donuts coffee - large () > > :-) > > _________________________________________ > 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 > -- ===================================================================== | Alex Brown ||e-mail: abrown@nimr.mrc.ac.uk | | MRC-T, || : abrown@hgmp.mrc.ac.uk | | 1-3 Burtonhole Lane, ||tel.: +44 (0)20 8 906 3811 x 6137 | | Mill Hill, London NW7 1AD. UK.||fax.: +44 (0)20 8 906 1395 | ===================================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: Todd Carlson Subject: Re: referencing software (was CHIMEd Web Sites as Scholarly Works) Date: Fri, 26 Oct 2001 10:58:37 -0400 To: rasmol@lists.umass.edu Good one Tim Someone once said that great ideas progress from being dismissed as crazy, to being hailed as brilliant, to being dismissed as obvious (I would like to reference this quote, but I can't recall where I read it!) In other words, ideas progress from cutting edge to routine with many grey areas in between. This influences references in research papers. We reference other's ideas that we may have used. However, when the idea has been around long enough, it becomes more of a tool. However we do reference the tools we have used if it is necessary information for someone trying to repeat our results. Eventually tools become so familiar and routine that references become irrelevant (have you ever referenced your NaCl supplier?). So by analogy, it seems that referencing a molecular modeling program used to generate an mol file would be wise as it is a tool that would be needed to repeat the work. If using someone else's javascript, that would be referenced as someone's idea. But the points at which an idea becomes a tool and when a tool becomes irrelevant seem to be a grey area, in some cases. Todd Carlson PS - I too have been negligent at referencing my Chime pages. It's been on my list of things to do for some time. Perhaps it will get bumped up the priority list now. -tim typed using an Apple Pro keyboard (), and composed in BareBones MailSmith (), before being sent via TCP/IP under Mac OS 9.1 () to an AppleShare IP mail server () across a Speakeasy DSL (http://www.speakeasy.org>) to the RasMol list (http://www.umass.edu/microbio/rasmol/raslist.htm>). powered by Dunkin Donuts coffee - large () :-) _________________________________________ 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-pair-Authenticated: 12.79.128.224 References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: referencing software (was CHIMEd Web Sites as Scholarly Works) Date: Fri, 26 Oct 2001 09:10:07 -0400 To: rasmol@lists.umass.edu Dear Collleagues, I vigorously disagree with the concept that one should not cite software simply because it is a "commercial product." As scholars, we are obliged by long academic tradition to give credit where credit is due. How can we teach our students to be honest in their submisssions to us if we are not scrupulously open and honest in our publications about the sources of what we present? Timithy Driscoll asks, "when a user signs/accepts a licence agreement to use a copy of a software program, does that mean the copy is "owned" by the user?" The answer to that question depends, of course, on the terms of the particular license, but in most cases the entire purpose of having a license is to grant to the user only certain rights to use the software for certain intended purposes and to retain for the grantor of the license most or all of the rights of "ownership". Would anyone seriously claim that when they buy a book at the bookstore they become the "owner" of the intellectual property contained in the book and need not give credit when to the ideas they use from that book? Buying a book is a highly commercial transaction, but we drum students out of school for using words or ideas from books without credit. Let us adhere to the same high scholarly standard when dealing with software. The argument that giving credit takes space and bandwidth is unsound. It is very easy to have a clearly identified bibliography or references page and to include cites as simple "[nnn]" anotations or hyperlinks. The creation of visualization tutorials is a valuable scholarly effort. The same standards we apply in writing textbooks and journal articles should be applied to creating tutorials. -- H. J. Bernstein At 8:21 -0400 10/26/01, timothy driscoll wrote: >On 10.26.01 at 6:59 AM, yaya@bernstein-plus-sons.com (Herbert J. Bernstein) >wrote: > >> If one is creating a scholarly work which uses molecular graphics, I hope >> that, in addition to citing the sources for the content of the images, the >> author will also cite the appropriate literature on the graphics program >> or programs used. -- HJB > > >I agree with this concept for "freeware," if for no other reason than common >courtesy, but certainly not commercial products. isn't that part of the $$$? >that does bring up an interesting question, though; when a user >signs/accepts a >licence agreement to use a copy of a software program, does that mean the copy >is "owned" by the user? so does the user need to reference its use? > >if the consensus answer is yes, I'd love an explanation that I can present to >clients. many are unwilling to give up even a square pixel of screen space or >bandwidth without much gnashing of teeth. > >-tim > >typed using an Apple Pro keyboard (), >and composed in BareBones MailSmith (), >before being sent via TCP/IP under Mac OS 9.1 () >to an AppleShare IP mail server () >across a Speakeasy DSL (http://www.speakeasy.org>) >to the RasMol list (http://www.umass.edu/microbio/rasmol/raslist.htm>). >powered by Dunkin Donuts coffee - large () > >:-) > >_________________________________________ >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 > > ===================================================== **** 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 ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Gorga, Frank" Subject: RE: referencing software (was CHIMEd Web Sites as Scholarly Works ) Date: Fri, 26 Oct 2001 09:14:03 -0400 To: "'rasmol@lists.umass.edu'" Colleagues, I agree that it is absolutely necessary to cite freeware software of any kind used to prepare scholarly works (including RasMol) this goes for print publications too. After all, such citation is the only compensation that authors get for writing and maintaining such software. It is probably also a good idea to notify the author of the software of your citation because, in some cases, funding for maintenance and further development depends on being able to prove that the software is generally useful. With commercial software the situation is somewhat more complicated... if all you are doing is using the software to make a graphic, I tend to agree with Tim. Your payment for the software is enough credit. However, if you use the software to perform any sort of calculations (e.g. to determine a minimized structure, or other property), you should cite both the software used and the type of calculation you did. This is simply a matter of intellectual (scholarly) rigor, after all not all calculations will result in the same answer and different programs implement the algorithms in slightly different ways. With regard to Tim's point about screen "real estate"... this sort of citation does not require significant space on the "main screen"... In my view a small link to a "footnote" on another page is all that is required... one can collect all of the "footnotes" on a separate page where the information is available for those who wish to view it. The point of all of this is not to provide software makers free advertisements, but to provide the information necessary to evaluate the rigor of a site and the validity of the claims being made. --- Frank ---------------------------------------------------------------------------- - Frank R. Gorga, Ph.D. Department of Chemical Sciences Bridgewater State College Bridgewater, MA 02325 508-531-2827 / 508-531-1785 (fax) fgorga@bridgew.edu webhost.bridgew.edu/fgorga ---------------------------------------------------------------------------- Comfort the troubled; trouble the comfortable. -- Dietrich Bonhoeffer, 1906-1945 http://www.dbonhoeffer.org/who-was-db2.htm ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: <9F5E83E17008D31193DD0090274E75050663345F@mailhost.bridgew.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Cindy Klevickis Subject: Electrostatic Potential Question Date: Sat, 27 Oct 2001 09:42:38 -0400 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_6iwvLy462VJCa0eEuhSnzw) Hello to All, One of the participants at a RasMol summer workshop wrote to ask this question: "I have been making some webpages and using chime to show the electrostatic potential. I used the red, white and blue color scheme. It works great for everything except methane, which unfortunately is one of the molecules I need to use. For some reason methane has the potentials backwards. That is the more positive hydrogens are red and for every other molecule, including ethane and propane, the more positive atoms are blue and the more negative atoms (in these cases carbons) are red. Do you know what is wrong? I downloaded methane from 3 different locations (some pdb some mol) and got the same results. Unfortunately my wife was showing methane to her class and they caught the "mistake" right away. I cannot find anything in the html that says which is more negative or positive. Do you know where that information is and how to change it? Any advise you can give would be appreciated." Thanks --Boundary_(ID_6iwvLy462VJCa0eEuhSnzw) Content-description: Card for Cindy Klevickis Content-disposition: attachment; filename=klevicca.vcf begin:vcard n:Klevickis;Cindy tel;home:office phone: 540-568-2726 tel;work:James Madison University x-mozilla-html:FALSE adr:;;;;;; version:2.1 email;internet:klevicca@jmu.edu x-mozilla-cpt:;-22192 fn:Cindy Klevickis end:vcard --Boundary_(ID_6iwvLy462VJCa0eEuhSnzw)-- X-Originating-IP: [12.91.235.111] X-OriginalArrivalTime: 27 Oct 2001 13:46:49.0110 (UTC) FILETIME=[D3767360:01C15EED] ++++------+------+------+------+------+------+------+------+------+------+ From: "Pat O'Hern" Subject: User-defined colors Date: Sat, 27 Oct 2001 13:46:48 +0000 To: rasmol@lists.umass.edu I'm working on a big RasMol/Chime project. The designer does not want to use the CPK color scheme (I don't know why). She wants phosphorus to be purple, nitrogen to be "darker blue", etc. Is there some way to change the RasMol default palette, or do I have to go into every script and change the atom colors? I know there's something called COLO as part of a .pdb file. Is that the way to go? Thanks, Pat Patricia A. O'Hern, Ph.D. CyberScience Design 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 _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: [12.91.235.170] X-OriginalArrivalTime: 27 Oct 2001 17:08:22.0083 (UTC) FILETIME=[FB6FB130:01C15F09] ++++------+------+------+------+------+------+------+------+------+------+ From: "Pat O'Hern" Subject: Re: referencing software (was CHIMEd Web Sites as Scholarly Works) Date: Sat, 27 Oct 2001 17:08:21 +0000 To: rasmol@lists.umass.edu I've been following this thread with interest. It seems to me that there is a general consensus arising, aptly summarized by Todd Carlson. First, we want to give the user any information they need to recreate and/or test the scientific aspects of our work. This would certainly include calculation algorithms. Second, we want to give credit for any intellectual properties that inspired or allowed the work to succeed. And, as Frank said, it would be good for the field as a whole to let the authors know when we're making use of their product. Such feedback is courteous, gratifying and may help future funding. As a newbie, this information comes to me at a good time-- I'll start routinely putting such info in my sites. If a client gives me a real hard time, maybe I'll put it as a header comment on the index page. I usually look there for copyright information, anyway. Thanks to all, Pat O'Hern Todd Carlson wrote: >referencing a molecular modeling program used to generate an mol >file >would be wise as it is a tool that would be needed to repeat >the work. If >using someone else's javascript, that would be >referenced as someone's >idea. Patricia A. O'Hern, Ph.D. CyberScience Design 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 _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: Cindy Klevickis Subject: Re: referencing software (was CHIMEd Web Sites as Scholarly Works) Date: Sat, 27 Oct 2001 13:43:59 -0400 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_APUgAT/xDuClTk1D5mP8RA) boundary="Boundary_(ID_LgtpqT9nIfwf44qwjYCYiw)" --Boundary_(ID_LgtpqT9nIfwf44qwjYCYiw) For my students' project pages, they use the following example as a template for reference citations. I ask them to include the reference citation within the caption of any figure created using RasMol, as an echo command in a RasMol script or as a caption for a Chime model. I am interested in any feedback any of you might have. I think I should probably add an item in the template about the PDB main page as the source for the pdb file? "The figure shown on the right is a model of human deoxyhemoglobin. It was created in RasMol version 2.6 by Roger Sayle using the pdb coordinates from the pdb file 4hhb. The 3D coordinates were determined using x-ray crystallography by Fermi, G., Perutz, M. F., Shaanan, B., Fourme, R.: "The crystal structure of human deoxyhaemoglobin at 1.74 Angstroms resolution. J Mol Biol 175 pp. 159 (1984)"" Pat O'Hern wrote: > I've been following this thread with interest. It seems to me that there is > a general consensus arising, aptly summarized by Todd Carlson. First, we > want to give the user any information they need to recreate and/or test the > scientific aspects of our work. This would certainly include calculation > algorithms. Second, we want to give credit for any intellectual properties > that inspired or allowed the work to succeed. And, as Frank said, it would > be good for the field as a whole to let the authors know when we're making > use of their product. Such feedback is courteous, gratifying and may help > future funding. As a newbie, this information comes to me at a good time-- > I'll start routinely putting such info in my sites. If a client gives me a > real hard time, maybe I'll put it as a header comment on the index page. I > usually look there for copyright information, anyway. > Thanks to all, > Pat O'Hern > > Todd Carlson wrote: > >referencing a molecular modeling program used to generate an mol >file > >would be wise as it is a tool that would be needed to repeat >the work. If > >using someone else's javascript, that would be >referenced as someone's > >idea. > Patricia A. O'Hern, Ph.D. > CyberScience Design > 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 > > _________________________________________________________________ > Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp > --Boundary_(ID_LgtpqT9nIfwf44qwjYCYiw) For my students' project pages, they use the following example as a template for reference citations.  I ask them to include the reference citation within the caption of any figure created using RasMol, as an echo command in a RasMol script or as a caption for a Chime model. I am interested in any feedback any of you might have.  I think I should probably add an item in the template about the PDB main page as the source for the pdb file? 

"The figure shown on the right is a model of human deoxyhemoglobin.  It was created in RasMol version 2.6 by Roger Sayle using the pdb coordinates from the pdb file 4hhb.  The 3D coordinates were determined using x-ray crystallography by Fermi, G., Perutz, M. F., Shaanan, B., Fourme, R.: "The crystal structure of human deoxyhaemoglobin at 1.74 Angstroms  resolution. J Mol Biol 175 pp. 159 (1984)""
 
 
 
 
 
 

Pat O'Hern wrote:

I've been following this thread with interest. It seems to me that there is
a general consensus arising, aptly summarized by Todd Carlson. First, we
want to give the user any information they need to recreate and/or test the
scientific aspects of our work. This would certainly include calculation
algorithms. Second, we want to give credit for any intellectual properties
that inspired or allowed the work to succeed. And, as Frank said, it would
be good for the field as a whole to let the authors know when we're making
use of their product. Such feedback is courteous, gratifying and may help
future funding. As a newbie, this information comes to me at a good time--
I'll start routinely putting such info in my sites. If a client gives me a
real hard time, maybe I'll put it as a header comment on the index page. I
usually look there for copyright information, anyway.
Thanks to all,
Pat O'Hern

Todd Carlson wrote:
>referencing a molecular modeling program used to generate an mol >file
>would be wise as it is a tool that would be needed to repeat >the work.  If
>using someone else's javascript, that would be >referenced as someone's
>idea.
Patricia A. O'Hern, Ph.D.
CyberScience Design
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

_________________________________________________________________
Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp --Boundary_(ID_LgtpqT9nIfwf44qwjYCYiw)-- --Boundary_(ID_APUgAT/xDuClTk1D5mP8RA) Content-description: Card for Cindy Klevickis Content-disposition: attachment; filename=klevicca.vcf begin:vcard n:Klevickis;Cindy tel;home:office phone: 540-568-2726 tel;work:James Madison University x-mozilla-html:FALSE adr:;;;;;; version:2.1 email;internet:klevicca@jmu.edu x-mozilla-cpt:;-22192 fn:Cindy Klevickis end:vcard --Boundary_(ID_APUgAT/xDuClTk1D5mP8RA)-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: Re: referencing software Date: Sat, 27 Oct 2001 13:43:31 -0400 To: rasmol@lists.umass.edu hi todd, On 10.26.01 at 10:58 AM, carlsont@gvsu.edu (Todd Carlson) wrote: > In other words, ideas progress from cutting edge to routine with many grey areas > in between. This influences references in research papers. We reference > other's ideas that we may have used. However, when the idea has been around > long enough, it becomes more of a tool. However we do reference the tools we > have used if it is necessary information for someone trying to repeat our > results. Eventually tools become so familiar and routine that references become > irrelevant (have you ever referenced your NaCl supplier?). > an excellent point, and well-phrased. in fact, I *have* seen journal articles that reference their chemical suppliers - and sometimes this has proven essential to repeating an experimental protocol (personal experience). does that justify a citation in the paper itself, however mundane it may seem? maybe...but I digress. of course, I have also seen papers that neglect to acknowledge contributors based on political reasons. obviously this is not ethical, but one person's good reason is another's backroom politics, eh? I digress again. > So by analogy, it seems that referencing a molecular modeling program used to > generate an mol file would be wise as it is a tool that would be needed to > repeat the work. If using someone else's javascript, that would be referenced > as someone's idea. But the points at which an idea becomes a tool and when a > tool becomes irrelevant seem to be a grey area, in some cases. > I heartily agree with your assessment - this is a gray area - and your analogy is a decent one, I think. so I wonder how do we go about applying the "scientific journal" model to CHIMEd Web Sites as a standard? this is not meant to be rhetorical; I'm honestly unsure. (I'll have to add this disclaimer to all of my questions to this list from now on, I guess.) best, 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: timothy driscoll Subject: RE: referencing software (was CHIMEd Web Sites as Scholarly Works ) Date: Sat, 27 Oct 2001 14:23:40 -0400 To: rasmol@lists.umass.edu On 10.26.01 at 9:14 AM, FGORGA@bridgew.edu (Gorga, Frank) wrote: > With commercial software the situation is somewhat more complicated... if > all you are doing is using the software to make a graphic, I tend to agree > with Tim. Your payment for the software is enough credit. > > However, if you use the software to perform any sort of calculations (e.g. > to determine a minimized structure, or other property), you should cite both > the software used and the type of calculation you did. This is simply a > matter of intellectual (scholarly) rigor, after all not all calculations > will result in the same answer and different programs implement the > algorithms in slightly different ways. > a good point - but I would argue that it depends on your ultimate goal. at the risk of being tarred and feathered by the more academically-minded, let me introduce a theoretical scenario: let's say I am asked to produce a print figure for a science textbook based on the crystal structure of a macromolecule. I find the structure in the PDB, open the file in WebLab Viewer, render and save it out as a VRML. Then I open it in Strata 3D, tweak the render and output in very high quality, and it is printed in the textbook. now, I submit that referencing the original author of the structure is a must. if I altered the structure in any way (i.e., mutated a residue or minimized the structure), I would also ref that b/c it is crucial to the information being conveyed. and the fact that it is present in the PDB also merits acknowledgement, since that implies some sense of validity (i.e., it has been checked by the RCSB). however, I don't necessarily want to reveal my creative process for others to duplicate, so I do not feel obliged to ref WLV or Strata3D, nor do I mention my protocol at all. I have no qualms about this, despite the freeware issue, b/c knowledge of the rendering/converting software is not important for the end product - they are just the tools that I use. I'm curious; do you agree with the above logic? my main question is to try and define, with some specificity, when a software program is a tool and when it is information. I think most would agree that knowing what browser I used to visit the PDB and download the file is superfluous information. when do programs such as WLV cross the line? your email (and todd's email) paint a fairly clear picture, at least IMO, and you summarized it exceptionally well: > The point of all of this is not to provide software makers free > advertisements, but to provide the information necessary to evaluate the > rigor of a site and the validity of the claims being made. > With regard to Tim's point about screen "real estate"... this sort of > citation does not require significant space on the "main screen"... In my > view a small link to a "footnote" on another page is all that is required... > one can collect all of the "footnotes" on a separate page where the > information is available for those who wish to view it. > well, define significant? while I agree whole-heartedly with you, I suspect many of my clients might disagree. ;-) (REQUISITE DISCLAIMER: this is an attempt at light humor, and does not imply in any way that ethics should take a back seat to commercialism.) best, 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: timothy driscoll Subject: Re: referencing software (was CHIMEd Web Sites as Scholarly Works) Date: Sat, 27 Oct 2001 17:19:37 -0400 To: rasmol@lists.umass.edu hmm. against my better judgement, but since this seems to be pointed at me, I'll respond. On 10.26.01 at 9:10 AM, yaya@bernstein-plus-sons.com (Herbert J. Bernstein) wrote: > Dear Collleagues, > > I vigorously disagree with the concept that one should not cite software simply > because it is a "commercial product." As scholars, we are obliged by long > academic > tradition to give credit where credit is due. How can we teach our students to > be honest in their submisssions to us if we are not scrupulously open and > honest in > our publications about the sources of what we present? > this was not the point of my email, and since you obliquely imply by quoting me that I am neither scrupulous nor honest, let me make this *abundantly* clear. I know of not a single person, in or out of academia, that would omit citation to an information source, especially if it involved a direct quote. I certainly would reference Dante if I quoted him in a piece of writing, but I wouldn't cite Bic simply b/c I used their pen to write it. It is somewhat disturbing to think that you would take my statements to such a ridiculous conclusion. > Timithy Driscoll asks, "when a user signs/accepts a licence agreement to use > a copy of a software program, does that mean the copy is "owned" by the user?" > The answer to that question depends, of course, on the terms of the particular > license, but in most cases the entire purpose of having a license is to grant > to the user only certain rights to use the software for certain intended > purposes and to retain for the grantor of the license most or all of the rights > of "ownership". > I've never found a clause in a licensing agreement that says I am obligated to cite the software manufacturer in the work I do with that software. I do recognize the ethical obligation to cite software in the interests of reproducing/validatiing scientific research. (Todd and Frank both explained this more eloquently than I can, so I point you to their messages.) I do appreciate the irony of you attempting to cite me above, but misspelling my name. please cite your spell-checking software, since I now have some obvious concerns about its validity :-P > Would anyone seriously claim that when they buy a book at the bookstore they > become the "owner" of the intellectual property contained in the > book and need not give credit when to the ideas they use from that book? > By using a program in the way in which it is intended to be used, but not referencing it, I'm hardly stealing the intellectual property of the manufacturer. if I decompiled, modified, recompiled and resold their code as my own program, that would constitute theft of ip. > Buying a book is a highly commercial transaction, but we drum students out of > school for using words or ideas from books without credit. Let us adhere > to the > same high scholarly standard when dealing with software. > not exactly. we "drum students out of school" for passing off the language, ideas, or creations of another author as their own original work (paraphrased from Webster's Unabridged English Dictionary, to be intellectually honest). I doubt you could expel a student if, when stating his belief that we are all created equal, he neglects to cite the US Constitution for giving him the idea. a more apt analogy might be if a student learned to read english from Dr. Suess' "One Fish Two Fish, Red Fish, Blue Fish" but didn't cite that book every time he read another. the book was his tool; he didn't steal its content by learning to read, he used it for its intended purpose. somehow, I don't think the author would feel slighted, since I imagine his motivation for writing the book was to teach young children to read, not to see his name cited all over the place. > The argument that giving credit takes space and bandwidth is unsound. It > is very easy to have a clearly identified bibliography or references page > and to include cites as simple "[nnn]" anotations or hyperlinks. > for my part, I was not making an argument but stating a fact: bandwidth, download time, and screen elements are all important considerations to many publishers, who must target users with slow modems and small screens. again, you draw your own faulty conclusions from my statements and pass them off as my own. as I have said, I agree with the need for annotating legitimate sources of information. on the other hand, if I have to cite every tool that I used in production not only would it take up more space, it would detract from legitimate references by jacking up the noise-to-signal ratio. and in my experience, one doesn't try to explain something to a client/employer by calling them "unsound." I suspect that you and I work in different worlds. > The creation of visualization tutorials is a valuable scholarly effort. The > same standards we apply in writing textbooks and journal articles should be > applied to creating tutorials. > don't try to put a square peg in a round hole. Web-based material is vastly different from print material and those differences need to be addressed. the concept of "giving credit where credit is due" is morally unassailable; however, we need to be certain that our methods of applying that concept do it appropriate justice. I think we can and need to do it better. 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: <9F5E83E17008D31193DD0090274E75050663346D@mailhost.bridgew.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Jim Perkins Subject: RE: referencing software (was CHIMEd Web Sites as Scholarly Works ) Date: Sun, 28 Oct 2001 02:36:42 -0500 To: rasmol@lists.umass.edu Timothy Driscoll said: >however, I don't necessarily want to reveal my creative process for others to >duplicate, so I do not feel obliged to ref WLV or Strata3D, nor do I >mention my >protocol at all. I have no qualms about this, despite the freeware issue, b/c >knowledge of the rendering/converting software is not important for the end >product - they are just the tools that I use. > >I'm curious; do you agree with the above logic? I normally lurk on this list but I feel compelled to come out in support of Mr. Driscoll's comments. The software that I use to manipulate and render molecular images is a tool - no different from a pen, paintbrush, or any piece of graphics software. When I create digital artwork, I certainly don't reference all of the Adobe or Macromedia products that I use. Nor would I reference WebLab Viewer, Strata, or any of the other programs I use to make molecular images. My $.02. By the way, Tim, it's nice to make the acquaintance of someone else who employs this method. Molecular graphics is something of a sideline for me, but I've enjoyed dabbling in it for a few years. I tried POV for a while but have been using Strata almost exclusively for over ayear. I also take screen shots of CHIME displays and use them as templates which I render in Illustrator. Jim ___________________________________________________________ James A. Perkins, MS, MFA Assistant Professor of Medical Illustration College of Imaging Arts and Sciences Rochester Institute of Technology 73 Lomb Memorial Drive Rochester, NY 14623 716-475-2443 fax: 716-475-6447 japfaa@rit.edu ___________________________________________________________ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-WebMail-UserID: fmargoli X-EXP32-SerialNo: 00003544 ++++------+------+------+------+------+------+------+------+------+------+ From: fmargoli Subject: RE: referencing software (was CHIMEd Web Sites as Scholarly Works) Date: Sun, 28 Oct 2001 12:21:36 -0500 To: rasmol@lists.umass.edu Against my better judgement I am also adding my 2p worth. Maybe I do not understand the essence of the dispute but it is common usage to cite that DNA sequences were determined on a particular manufacturer's instrument or to indicate sources of reagents. Anatomists frequently indicate how images were obtained and (not) manipulated in the generation of the final figures? I am as guilty as the next one but why should software be different if it played a significant role in the production or analysis of the data? Frank >===== Original Message From rasmol@lists.umass.edu ===== >hmm. against my better judgement, but since this seems to be pointed at me, >I'll respond. > > >On 10.26.01 at 9:10 AM, yaya@bernstein-plus-sons.com (Herbert J. Bernstein) >wrote: > >> Dear Collleagues, >> >> I vigorously disagree with the concept that one should not cite software >simply >> because it is a "commercial product." As scholars, we are obliged by long >> academic >> tradition to give credit where credit is due. How can we teach our students >to >> be honest in their submisssions to us if we are not scrupulously open and >> honest in >> our publications about the sources of what we present? >> >this was not the point of my email, and since you obliquely imply by quoting me >that I am neither scrupulous nor honest, let me make this *abundantly* clear. I >know of not a single person, in or out of academia, that would omit citation to >an information source, especially if it involved a direct quote. I certainly >would reference Dante if I quoted him in a piece of writing, but I wouldn't cite >Bic simply b/c I used their pen to write it. It is somewhat disturbing to think >that you would take my statements to such a ridiculous conclusion. > > >> Timithy Driscoll asks, "when a user signs/accepts a licence agreement to use >> a copy of a software program, does that mean the copy is "owned" by the user?" >> The answer to that question depends, of course, on the terms of the particular >> license, but in most cases the entire purpose of having a license is to grant >> to the user only certain rights to use the software for certain intended >> purposes and to retain for the grantor of the license most or all of the >rights >> of "ownership". >> >I've never found a clause in a licensing agreement that says I am obligated to >cite the software manufacturer in the work I do with that software. I do >recognize the ethical obligation to cite software in the interests of >reproducing/validatiing scientific research. (Todd and Frank both explained >this more eloquently than I can, so I point you to their messages.) > >I do appreciate the irony of you attempting to cite me above, but misspelling my >name. please cite your spell-checking software, since I now have some obvious >concerns about its validity :-P > > >> Would anyone seriously claim that when they buy a book at the bookstore they >> become the "owner" of the intellectual property contained in the >> book and need not give credit when to the ideas they use from that book? >> >By using a program in the way in which it is intended to be used, but not >referencing it, I'm hardly stealing the intellectual property of the >manufacturer. if I decompiled, modified, recompiled and resold their code as my >own program, that would constitute theft of ip. > > >> Buying a book is a highly commercial transaction, but we drum students out of >> school for using words or ideas from books without credit. Let us adhere >> to the >> same high scholarly standard when dealing with software. >> >not exactly. we "drum students out of school" for passing off the language, >ideas, or creations of another author as their own original work (paraphrased >from Webster's Unabridged English Dictionary, to be intellectually honest). I >doubt you could expel a student if, when stating his belief that we are all >created equal, he neglects to cite the US Constitution for giving him the idea. > >a more apt analogy might be if a student learned to read english from Dr. Suess' >"One Fish Two Fish, Red Fish, Blue Fish" but didn't cite that book every time he >read another. the book was his tool; he didn't steal its content by learning to >read, he used it for its intended purpose. somehow, I don't think the author >would feel slighted, since I imagine his motivation for writing the book was to >teach young children to read, not to see his name cited all over the place. > > >> The argument that giving credit takes space and bandwidth is unsound. It >> is very easy to have a clearly identified bibliography or references page >> and to include cites as simple "[nnn]" anotations or hyperlinks. >> >for my part, I was not making an argument but stating a fact: bandwidth, >download time, and screen elements are all important considerations to many >publishers, who must target users with slow modems and small screens. again, >you draw your own faulty conclusions from my statements and pass them off as my >own. as I have said, I agree with the need for annotating legitimate sources of >information. on the other hand, if I have to cite every tool that I used in >production not only would it take up more space, it would detract from >legitimate references by jacking up the noise-to-signal ratio. > >and in my experience, one doesn't try to explain something to a client/employer >by calling them "unsound." I suspect that you and I work in different worlds. > > >> The creation of visualization tutorials is a valuable scholarly effort. The >> same standards we apply in writing textbooks and journal articles should be >> applied to creating tutorials. >> >don't try to put a square peg in a round hole. Web-based material is vastly >different from print material and those differences need to be addressed. the >concept of "giving credit where credit is due" is morally unassailable; however, >we need to be certain that our methods of applying that concept do it >appropriate justice. I think we can and need to do it better. > > >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 > > Frank L. Margolis Ph.D. Professor Department of Anatomy and Neurobiology University of Maryland School of Medicine HSF 222 685 West Baltimore Street Baltimore MD 21201 phone 410-706-8913/4 fax 410-706-2512 fmargoli@umaryland.edu http://neurobiology.umaryland.edu/ http://neuroscience.umaryland.edu/ "Any sufficiently advanced technology is indistinguishable from magic" Arthur C. Clarke ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: referencing software (was CHIMEd Web Sites as Scholarly Works) Date: Sun, 28 Oct 2001 07:44:47 -0500 (EST) To: rasmol@lists.umass.edu Dear Colleagues, My apologies to one and all if the strength of my feelings about and important issue of the methodology of science came across as an personal attack on Timothy Driscoll. My disagreement is with some ideas. No offense intended. In the sciences we adhere to rigorous standards of scholarly citation for at least at two purposes that have been mentioned in this discussion: 1. Giving credit where credit is due 2. Helping others to have sufficient information to reporpoduce our results The concept has been raised that some items we use are simply common tools to which neither the first nor the second case apply. Certainly, there are such cases. For example, one might fairly argue that the particular choice of word processing program did not in any way influence the intellectual content of the result, and need not be cited. I would argue, however, that, in most cases, the choice of molecular graphics program is a significant contributor to the intellectual content of papers, books, tutorials and other publications. The images produced by each program are likely to differ in significant ways that influence the reader's comprehension of the science being discussed. Some choose one way to, say, present sheets, turns and helices. Some choose other approaches. Decades of effort by hundreds of people have gone into exploring different approaches to rendering. Giving credit for the method or methods chosen for use in a particular publication helps others to evaluate the best choices for their own work, helps others to reproduce your work, and most importantly gives credit for the intellectual content that is being used. Since the issue of the PDB was raised, let me also mention that there is significant intellectual effort involved in the curation of the PDB entries, and urge those who make use of the PDB or to include literature citations for the PDB in their publications. Regards, Herbert J. Bernstein ===================================================== **** BERNSTEIN + SONS * * INFORMATION SYSTEMS CONSULTANTS **** P.O. BOX 177, BELLPORT, NY 11713-0177 * * *** **** * Herbert J. Bernstein * *** yaya@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Sat, 27 Oct 2001, timothy driscoll wrote: > hmm. against my better judgement, but since this seems to be pointed at me, > I'll respond. > > > On 10.26.01 at 9:10 AM, yaya@bernstein-plus-sons.com (Herbert J. Bernstein) > wrote: > > > Dear Collleagues, > > > > I vigorously disagree with the concept that one should not cite software > simply > > because it is a "commercial product." As scholars, we are obliged by long > > academic > > tradition to give credit where credit is due. How can we teach our students > to > > be honest in their submisssions to us if we are not scrupulously open and > > honest in > > our publications about the sources of what we present? > > > this was not the point of my email, and since you obliquely imply by quoting me > that I am neither scrupulous nor honest, let me make this *abundantly* clear. I > know of not a single person, in or out of academia, that would omit citation to > an information source, especially if it involved a direct quote. I certainly > would reference Dante if I quoted him in a piece of writing, but I wouldn't cite > Bic simply b/c I used their pen to write it. It is somewhat disturbing to think > that you would take my statements to such a ridiculous conclusion. > ... > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: Need links to molecules for high-school classes Date: Sun, 28 Oct 2001 14:03:23 -0500 To: Kirk and/or Deb Mateer Cc: rasmol@lists.umass.edu Dear Kirk: I'm glad you're considering using Protein Explorer in your high school classes! At 10/28/2001, you wrote: >Dear Dr. Martz, > > Hello, I am a high school biology and biotechnology teacher outside >of Baltimore, MD. I am very interested in the new protein explorer >program. I have used the RasMol viewer before on a limited basis. > I have two questions for you about the program which I am just >learning to use. > > 1) where is the site to download the protein explorer program so I >need not run it from the internet? I have already downloaded the latest >version of CHIME and I was able to go into the quick session and view a >macromolecule without any problems. Go to http://proteinexplorer.org and look at the right gray panel About PE, click on Download. > 2) Is there a site where I can download simple macromolecules for >use by high school students? (the basic carbohydrates, simple proteins >and enzymes, lipids, and of course DNA models for use by my >biotechnology students) Go to http://molvisindex.org, click on the section Molecules, and go from there. For macromolecules, I recommend PDB At A Glance, and for small bio-molecules, KLOTHO. For DNA, try http://www.umass.edu/microbio/chime/dna/index.htm or other sites under DNA at molvisindex. Whenever you see a molecule in Chime, at any website, you can save it to your disk. Click on MDL to open Chime's menu, then on File, Save Molecule As. Be sure to give the file a useful name ending in ".pdb", and put it where you can find it. You can then open the saved PDB file in Protein Explorer: from the FrontDoor, start Bare Explorer, and use the Browse button to find your molecule. Next time you start Bare Explorer, it will be on the menu of 'Recently loaded' molecules (on the Load Molecule page). In a SEPA course for high school teachers this summer (in Milwaukee, http://www.rpc.msoe.edu/sepa/), we agreed that we need a short list, with example molecules readily at hand that mesh with the major biology class topics (physiology, photosynthesis, evolution, etc. etc.). I don't know of such a list -- I'm copying this to the Molecular Visualization Freeware email list in case someone can point one out to me. Such a list should be indexed under K12 resources at molvisindex.org, but you'll see the K12 category is nearly empty at this time. VISITORS TO THE SITE CAN INDEX ADDITIONAL ON-LINE RESOURCES BY FILLING OUT A SHORT FORM -- NO PASSWORD NEEDED. JUST CLICK ON THE LINK "Submit a new ..." in the category in question. A short list of some of my favorite molecules is at the VERY BOTTOM of this page: http://www.umass.edu/molvis/workshop/umass01.htm -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en References: <20011027171937-r01010800-6100793b-0910-010c@192.168.1.3> ++++------+------+------+------+------+------+------+------+------+------+ From: Dr Nicholas Keep Subject: Re: referencing software (was CHIMEd Web Sites as Scholarly Works) Date: Mon, 29 Oct 2001 10:16:11 +0000 To: rasmol@lists.umass.edu A couple of points from over the Atlantic. I must admit I have not read every mailing in detail and may have missed this point being made. We should encourage the students to differentiate between peer-reviewed and non-peer reviewed material and between primary sources and reviews. (This I guess is more about the earlier part of the discussion). Timothy Driscoll says >I've never found a clause in a licensing agreement that says I am obligated to >cite the software manufacturer in the work I do with that software. The license agreements for MOLSCRIPT and CCP4 suite -probably the most used pieces of software by X-ray crystallographers (at least on this side of the Atlantic) make precisely this demand. They are however free to academics and are constructed on an academic and not a businees model. They have both accumulated huge numbers of citations and rightly so. I would favour all software being referenced and disclosed- particularly as this allows you to find out whether the figure has been drawn by the author (student) or nicked from the internet/scanned in. I would describe drawing a figure as part of the scientific process rather than as a creative process and in an ideal world the instructions to duplicate it should be given. -- Dr Nicholas H. Keep School of Crystallography, Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.keep@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room 1083 Office) 020-7631-6868 (Rosalind Franklin Laboratory) 020-7631-6800 (Department Office) Fax 020-7631-6803 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-PMrqc: 1 ++++------+------+------+------+------+------+------+------+------+------+ From: Diona Koerner Subject: Re: Lab exercises using web materials Date: Mon, 29 Oct 2001 16:05:21 -0500 To: rasmol@lists.umass.edu I'd also be interested in seeing your materials for lab execrcises using the web Date sent: Thu, 25 Oct 2001 17:13:40 -0400 Send reply to: rasmol@lists.umass.edu From: Marlene Kayne Subject: Lab exercises using web materials To: Frieda Texter > Dear Dr. Texter, > I would be very happy to share the exercises I have put together. As I > wrote to Judy Voet, I have used materials from the Web and placed them > together into a fairly reasonable package. I would be happy to send > them to you. > Regards, > Marlene Kayne > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed ++++------+------+------+------+------+------+------+------+------+------+ From: "Gorga, Frank" Subject: RE: referencing software (was CHIMEd Web Sites as Scholarly Works ) Date: Mon, 29 Oct 2001 13:17:27 -0500 To: "'rasmol@lists.umass.edu'" Colleagues, I think that Herbert Bernstein summarized the issues succinctly when he stated: >In the sciences we adhere to rigorous standards of scholarly citation >for at least at two purposes that have been mentioned in this discussion: > > 1. Giving credit where credit is due > 2. Helping others to have sufficient information to >reporpoduce our results I think that we need to, in part, distinguish the "simple" preparation of a graphic, where "#1" above is the main issue in my view and the more computational aspects of some work where structures are actually calculated, where both #1 and #2 are clearly involved. I also think that the "credit" issue is distinctly different in the case of commercial software vs. non-commercial software. In the case of commercial software we users "vote with our pocketbooks"... if the program is good and useful to us, we will buy it and continue to pay for updates. In my view this is enough compensation for the authors and no citation is needed, unless point # 2 (see above) is involved. However, in the case of non-commercial software (including RasMol and Protein Explorer to name two random examples!) things are different. A large part of the authors "compensation" is derived from having the use of their software publicly acknowledged. Additionally, in the case of software that is written with grant support, public acknowledgement of the usefulness of the software is generally critical for continued support and development. Thus, in my view, the obligation to cite the use of a particular program is much increased when the software in not a commercial product. Also, since Tim Driscoll asked directly for my thoughts at one point, I would like to respond: Tim wrote (in part)... >let's say I am asked to produce a print figure for a science textbook based on >the crystal structure of a macromolecule. I find the structure in the PDB, open >the file in WebLab Viewer, render and save it out as a VRML. Then I open it in >Strata 3D, tweak the render and output in very high quality, and it is printed >in the textbook. >now, I submit that referencing the original author of the structure is a must. >if I altered the structure in any way (i.e., mutated a residue or minimized the >structure), I would also ref that b/c it is crucial to the information being >conveyed. and the fact that it is present in the PDB also merits >acknowledgement, since that implies some sense of validity (i.e., it has been >checked by the RCSB). >I'm curious; do you agree with the above logic? my main question is to try and >define, with some specificity, when a software program is a tool and when it is I tend to agree with most of what you say... I think that there is a large difference between "simply" preparing an image and calculating a structure. To use your example, if you are taking a pdb file and making a picture, I would agree that a simple citation of the pdb entry is probably sufficient. However, if I used non-commercial software I would also mention the software (see above). However, if you now make changes in a structure (i.e. the mutation in your example), or prepare your own structures, now the requirements for documentation (/citation) go way up... I would want to know if you simply made the substitution (using a random conformation for the new atoms) and did no further calculations; I would want to know that the structure being shown is complete fiction! If you took the mutated structure and minimized the new structure, I would want to know the details of the calculation and the program used to perform the calculation. Likewise, for small molecules, I would want to know if the structure was drawn with standard bond lengths and angles, or if it is the result of some more sophisticated calculation. If the latter is true then additional citation of the details is in order. >> With regard to Tim's point about screen "real estate"... this sort of >> citation does not require significant space on the "main screen"... In my >> view a small link to a "footnote" on another page is all that is required... >> one can collect all of the "footnotes" on a separate page where the >> information is available for those who wish to view it. >> >well, define significant? while I agree whole-heartedly with you, I suspect >many of my clients might disagree. ;-) Not knowing anything about your clients, this might be dangerous! But, I think that this is a matter of education and making your clients aware of the issues. Most companies are very aware of intellectual property rights and thus need to see this issue in those terms. In fact, some of the best referenced CHIMEd websites are those associated with textbooks; I suspect this is because publishers are sensitized to the issues. I would expect that companies (pharmaceutical, biotech, etc.) whose livelihood depend on patents can be educated on these issues. But enough surmising about the nature of your clients! ;-) In a second message, Tim wrote: >I heartily agree with your assessment - this is a gray area - and your analogy >is a decent one, I think. so I wonder how do we go about applying the >"scientific journal" model to CHIMEd Web Sites as a standard? this is not meant >to be rhetorical; I'm honestly unsure. (I'll have to add this disclaimer to all >of my questions to this list from now on, I guess.) This is a HARD question... and I do not have all of (any?) the answers, but, in my view, there are two issues tied up in this question: The first issue is "trusting of information"... can you gain enough information about how a presentation (i.e. CHIMEd web site) was put together that you can evaluate the claims being made. Of course this can be done at many levels... for non-experts it may not happen at all, or they may simply rely on the reputation of the "publisher". The "expert" will want to see "footnotes" citing the type of information alluded to above. The second issue, related to the first, but applying to those of us academic types is getting credit for scholarly work (towards tenure and promotion) by preparing CHIMEd websites. Both issues can be partially solved by a peer review system organized and supported by a "known" publisher (a commercial or scientific society)... I.e. the "scientific journal" model. This is not a perfect solution, nor, the only solution, but it is, perhaps the easiest solution. The biggest downside to this model, is that publishers usually want to restrict the access of material they publish to paying subscribers. In the case of web-based material this has the effect of reducing the availability of the material... what was presumably available on the open web is now stuck behind a "password protected" site for subscribers only. Compare this situation with traditional print, where the effect of submitting an article to a journal results in wider distribution of material, rather than narrower! And you can see one of the major downsides to this model. This model is, in fact, in active use by a number of entities (the Journal of Chemical Education, comes to mind, but I do not mean to single them out). I have, thus far, refused to submit my sites to any on these publishers, because of this major (in my view) downside. Another possible solution is an model based very loosely on the "open source" software idea. A group of experts would agree to review sites and, once a site passes muster, to either publish the site on a freely available server, or to maintain a link to the site on the author's server in a "table of contents". Neither of these sub-models is ideal. The first model (a central server) takes control of the material (for updates, etc.) away from the author, but allows the reviewers to insure that the pubic ally available site is indeed the site that was reviewed. The second model ( links from a table of contents to author's sites) allows the author to make changes to the site, at will, but the reviewers lose a significant amount of control. Personally, I would favor the central server model. As always, I welcome hearing other's ideas about these issues. --- Frank ---------------------------------------------------------------------------- - Frank R. Gorga, Ph.D., Chair Department of Chemical Sciences Bridgewater State College Bridgewater, MA 02325 508-531-2827 / 508-531-1785 (fax) fgorga@bridgew.edu webhost.bridgew.edu/fgorga ---------------------------------------------------------------------------- Comfort the troubled; trouble the comfortable. -- Dietrich Bonhoeffer, 1906-1945 http://www.dbonhoeffer.org/who-was-db2.htm ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-WebMail-UserID: cxhedg X-EXP32-SerialNo: 00002882 ++++------+------+------+------+------+------+------+------+------+------+ From: cxhedg Subject: RCPT: RE: Lab exercises using web materials Date: Tue, 30 Oct 2001 08:53:14 -0600 To: rasmol@lists.umass.edu *** Confirmation of Registered Mail *** Your message sent to cxhedg has been read. Return Receipt Notification --------------------------- I'd also be interested in seeing your materials for lab execrcises using the web Date sent: Thu, 25 Oct 2001 17:13:40 -0400 Send reply to: rasmol@lists.umass.edu From: Marlene Kayne Subject: Lab exercises using web materials To: Frieda Texter ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: If your email breaks, you'll be unsubscribed Date: Tue, 30 Oct 2001 12:52:03 -0500 To: rasmol@lists.umass.edu Dear subscribers to the Molecular Visualization Freeware email list: Please be aware that if your email stops working for as little as one day, you may be unsubscribed from this list. Since your email would not be working, you won't get the usual notification -- you'll just stop getting the list broadcasts once your email is repaired. The list management software has an option to delete automatically all returned messages, but I have that disabled. Most returned messages are simply because a server is unreachable for a few hours. To avoid automatically unsubscribing all these people, I examine each error message manually. I only unsubscribe addresses that are returned 'user unknown', 'invalid server domain', or those that could not be delivered for at least 24 hours. It used to be that the 'undeliverable' messages tried for 5 days. Then some began returning messages after 3 days, and now some return them after only 1 day. The problem is that if I don't unsubscribe these addresses, I keep getting a flood of error messages day after day. So, you'll be unsubscribed if your mail is returned as undeliverable for 1 or more days. Sorry, but there are now over 600 subscribers to this list, and maintenance takes significant time on a daily basis. Sincerely, -Eric - - - Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 01003-5720 Molecular Visualization Freeware EMail Discussion List TO SUBSCRIBE, UNSUBSCRIBE, CHANGE YOUR ADDRESS, GO TO ABOVE URL. History -- all messages sent to this list are searchable at ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- <429FEE3FD9597E4788D82B2966AD8F7C07DC1F@ils099.uopnet.plymouth.ac.uk> X-MIMEOLE: Produced By Microsoft Exchange V6.0.4712.0 Thread-Topic: Displaying double bonds Thread-Index: AcFh+caRVl5S283iEdWHHABQ2kZrVQ== content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: ++++------+------+------+------+------+------+------+------+------+------+ From: Anthony Lewis Subject: Displaying double bonds Date: Wed, 31 Oct 2001 10:51:04 +0000 To: rasmol@lists.umass.edu Hello, I'm sure the answer to this is obvious... I've just realised that many of the pdb (and mol) files I've been seeing using Chime show double bonds (and there's an option to show/not show them under the options menu). However, all the pdb files I've ever created do not show double bonds and the relevant option in Chime is always greyed out... I've always assumed that is the way it is (daft assumption really) and accepted the situation. So, how do I make pdb files that enable double bonds to be displayed in wireframe models? I tend to make the pdb files by drawing the structure in ChemDraw, transferring it to Chem3d, doing a bit of simple minimisation and the saving as a pdb file. I have a hunch this may be the problem... Many thanks for any comments, Anthony Lewis C. Anthony Lewis Petroleum & Environmental Geochemistry Group, Department of Environmental Sciences, University of Plymouth, Plymouth, Devon PL4 8AA, U.K. tel: +44 (0)1752 233000 ext. 2988 FAX: +44 (0)1752 233035 e-mail: calewis@plymouth.ac.uk ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <3BD88084.40C3156D@tcnj.edu> X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id f9VC6vW06969 ++++------+------+------+------+------+------+------+------+------+------+ From: Vito De Pinto Subject: Re: Lab exercises using web materials Date: Wed, 31 Oct 2001 13:05:53 -0800 To: rasmol@lists.umass.edu >Dear Dr. Texter, > I would be very happy to share the exercises I have put together. As I >wrote to Judy Voet, I have used materials from the Web and placed them >together into a fairly reasonable package. I would be happy to send >them to you. > Regards, > Marlene Kayne Dear dr. Kayne, i would be glad to have a look to your material and to try to use it in my course. Best regerds Vito De Pinto -- prof. Vito De Pinto - Università di Catania Dip. Scienze Chimiche, lab. di Biochimica e Biologia Molecolare viale A. Doria, 6 - CATANIA 95125 ITALIA tel: 095-7384244 lab: 095-7384092 fax: 095-337036 e-mail: vdpbiofa@mbox.unict.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-- uth.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Displaying double bonds Date: Wed, 31 Oct 2001 12:21:14 -0500 To: rasmol@lists.umass.edu Anthony Lewis inquired about double bonds in RasMol. At the (old) RasMol Home Page, http://www.umass.edu/microbio/rasmol/index2.htm click on FAQ, Martz's, Double Bonds, or go directly to http://www.umass.edu/microbio/rasmol/faq_em.htm#doublebonds N.B. it appears that display of double bonds had been disabled in RasMol 2.7 (see http://openrasmol.org/FAQ.html#nobonds) but it works in 2.6beta2a still available (http://www.umass.edu/microbio/rasmol/getras.htm). In general, the UMass (old) RasMol site emphasizes help and documentation but is frozen at RasMol version 2.6, while the (new) OpenRasMol site (http://openrasmol.org) emphasizes development of the RasMol 2.7 program, and offers it with the latest new features (including non-English versions), an updated reference manual and new FAQ, but lacks the extensive documentation I developed for RasMol 2.6 during 1995-1999. So go to the old site for the Quick-Start, gallery, old FAQ (original Sayle FAQ + Martz FAQ), numerous tutorials, a systematic introduction to selection commands, an introduction to colors listing RasMol's built-in RGB values (http://www.umass.edu/microbio/rasmol/rascolor.htm), history of RasMol and of molecular visualization, PDB file modification documentation and tools, this email list and its entire history, etc. Most of the tutorials are listed at http://www.umass.edu/microbio/rasmol/rastut.htm -- if there's something you can't find, feel free to ask. I am not expanding the old site because I now concentrate my efforts on Chime and Protein Explorer. However the documention on the old site is still the most detailed and extensive available, is 100% applicable to RasMol 2.6beta2a, and very largely applicable to RasMol 2.7. Those of you working with >>macromolecular<< visualization (as distinct from small organic or inorganic compounds) on Windows, Macintosh, or linux* systems may wish to try Protein Explorer as an alternative to RasMol. Protein Explorer is much easier to use and much more powerful (http://molvis.sdsc.edu/protexpl/pe_v_ras.htm). It was designed to address the ease of use problems I observed when teaching college faculty to use RasMol in their teaching. Notably, you don't have to learn a single RasMol-style command to go way beyond basic visualizations in Protein Explorer. It works largely from menus, buttons and form slots, offers color keys automatically for all color schemes, and detailed help and troubleshooting for most operations. However, for those of you who have learned the RasMol command language, Protein Explorer accepts nearly all RasMol and Chime commands in its command entry slot, and from that persective, can be seen as "RasMol in a Web Page". To get a feel for it, look at the snapshots (http://molvis.sdsc.edu/protexpl/preview.htm), and then try the 1-hour QuickTour prominently linked at the main page (http://proteinexplorer.org). -Eric *linux presently requires a Windows subsystem -- see http://molvis.sdsc.edu/protexpl/platform.htm /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: Displaying double bonds Date: Wed, 31 Oct 2001 13:38:11 -0500 (EST) To: rasmol@lists.umass.edu Eric is quite right when he says that the new RasMol site, www.OpenRasMol.org, focuses on the current releases. We are happy to accept contributions of documentation and suggestions for documentation appropriate to those versions. Eric is also right when he says that we disabled the double bond option for early releases of the RasMol 2.7 series. The version of the code for multiple bonds used in the versions of RasMol predating RasMol 2.7 did not conform to the PDB format specification and could cause validly formatted files to display incorrect bond orders. Newer RasMol 2.7 releases have an alternate means of specifying bond order with the Bond command. We expect to be able to restore support for RasMol 2.6 style double bonds as an option in the RasMol 2.7.3 release scheduled for February 2002. That release is also expected to provide optional Japanese and Chinese messages in addition to the English, Spanish, Italian and French messages now available. If Chime and Protein Explorer are ever released as Open Source programs (with, say, GNU-like licenses), we will be happy to include Chime and PE and documentation for them on the OpenRasMol site. Unfortunately, in order to avoid the possibilities of claims that new features added to RasMol result from reverse engineering of features MDLI _might_ contend are proprietary parts of Chime, under the present Chime licenses it is not appropriate for certain Open Source RasMol developers to make significant use of Chime or Protein Explorer. Ordinary users (and Open Source RasMol developers who are working on RasMol features not derived from Chime extensions to RasMol) are free to use any or all of these programs without such concerns. One can only hope that the licensing for CHIME will change eventually to remove this impediment. -- 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 Wed, 31 Oct 2001, Eric Martz wrote: > Anthony Lewis inquired about double bonds in RasMol. > > At the (old) RasMol Home Page, http://www.umass.edu/microbio/rasmol/index2.htm > click on FAQ, Martz's, Double Bonds, or go directly to > > http://www.umass.edu/microbio/rasmol/faq_em.htm#doublebonds > > N.B. it appears that display of double bonds had been disabled in RasMol 2.7 > (see http://openrasmol.org/FAQ.html#nobonds) > but it works in 2.6beta2a still available > (http://www.umass.edu/microbio/rasmol/getras.htm). > > In general, the UMass (old) RasMol site emphasizes help and documentation > but is frozen at RasMol version 2.6, while the (new) OpenRasMol site > (http://openrasmol.org) emphasizes development of the RasMol 2.7 program, > and offers it with the latest new features (including non-English > versions), an updated reference manual and new FAQ, but lacks the extensive > documentation I developed for RasMol 2.6 during 1995-1999. So go to the old > site for the Quick-Start, gallery, old FAQ (original Sayle FAQ + Martz > FAQ), numerous tutorials, a systematic introduction to selection commands, > an introduction to colors listing RasMol's built-in RGB values > (http://www.umass.edu/microbio/rasmol/rascolor.htm), history of RasMol and > of molecular visualization, PDB file modification documentation and tools, > this email list and its entire history, etc. Most of the tutorials are > listed at http://www.umass.edu/microbio/rasmol/rastut.htm -- if there's > something you can't find, feel free to ask. > > I am not expanding the old site because I now concentrate my efforts on > Chime and Protein Explorer. However the documention on the old site is > still the most detailed and extensive available, is 100% applicable to > RasMol 2.6beta2a, and very largely applicable to RasMol 2.7. > > Those of you working with >>macromolecular<< visualization (as distinct > from small organic or inorganic compounds) on Windows, Macintosh, or linux* > systems may wish to try Protein Explorer as an alternative to RasMol. > Protein Explorer is much easier to use and much more powerful > (http://molvis.sdsc.edu/protexpl/pe_v_ras.htm). It was designed to address > the ease of use problems I observed when teaching college faculty to use > RasMol in their teaching. Notably, you don't have to learn a single > RasMol-style command to go way beyond basic visualizations in Protein > Explorer. It works largely from menus, buttons and form slots, offers color > keys automatically for all color schemes, and detailed help and > troubleshooting for most operations. However, for those of you who have > learned the RasMol command language, Protein Explorer accepts nearly all > RasMol and Chime commands in its command entry slot, and from that > persective, can be seen as "RasMol in a Web Page". To get a feel for it, > look at the snapshots (http://molvis.sdsc.edu/protexpl/preview.htm), and > then try the 1-hour QuickTour prominently linked at the main page > (http://proteinexplorer.org). > > -Eric > > > *linux presently requires a Windows subsystem -- see > http://molvis.sdsc.edu/protexpl/platform.htm > > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > The Protein Explorer: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org > PDB Lite molecule finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor (Immunology), Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 ++++------+------+------+------+------+------+------+------+------+------+ From: Meng-Juei Hsieh Subject: Re: Displaying double bonds Date: Wed, 31 Oct 2001 11:25:33 -0800 To: rasmol@lists.umass.edu Perhaps openrasmol can do something on netscape/mozilla plugin feature, it would be a good start to attract people's contribution. I agree that Chime is a great, but I still feel pain when I can't use it on other platforms. I think it would be okay, if RasMol includes some similar features. Meng-Juei Hsieh on 10/31/2001 10:38 AM, Herbert J. Bernstein at yaya@bernstein-plus-sons.com wrote: > If Chime and Protein Explorer are ever released as Open > Source programs (with, say, GNU-like licenses), we will be > happy to include Chime and PE and documentation for them > on the OpenRasMol site. Unfortunately, in order to avoid the > possibilities of claims that new features added to RasMol > result from reverse engineering of features MDLI _might_ > contend are proprietary parts of Chime, under the > present Chime licenses it is not appropriate for certain > Open Source RasMol developers to make significant use of > Chime or Protein Explorer. Ordinary users (and Open Source > RasMol developers who are working on RasMol features not > derived from Chime extensions to RasMol) are free to use > any or all of these programs without such concerns. One > can only hope that the licensing for CHIME will change > eventually to remove this impediment. > -- H. J. Bernstein ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- (by way of Eric Martz ) ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: Displaying double bonds Date: Wed, 31 Oct 2001 16:32:09 -0500 To: rasmol@lists.umass.edu Hi Herbert, > Eric is also right when he says that we disabled the > double bond option for early releases of the RasMol 2.7 > series. The version of the code for multiple bonds used > in the versions of RasMol predating RasMol 2.7 did not > conform to the PDB format specification and could cause > validly formatted files to display incorrect bond orders. This is the classic philosophical difference over file formats that separates data providers from users of that data. On the one hand, the people that define file formats wish that the community should precisely adhere to a possibly ambiguous file format specification and in writing parsers for checking programs, should issue error messages for the smallest discrepancy. The user community, on the other hand, exists in a world where a diversity of file formats variants exist, and rather than be bombarded with error messages, would hope that software should make the best effort to interpret as many indiscretions as possible. For example, believing that they understood the intricasies of the MDL .mol file format, MDL switched to using their own internal .mol file readers in Chime rather than the implementation in RasMol. As a result, this mailing list has since had numerous postings about files that RasMol can read but the Chime cannot. Similarly, well intentioned as it is, Herbert Bernstein's switch to using an "validating" parser creates numerous problems for the RasMol community. RasMol v2.7 cannot correctly read PDB files generated by the programs Concord and Corina that places elements in the wrong columns, or Cambridgesoft's Chem3D that have the wrong coordinate precision, or XPLOR and CNS generated files that place pseudo atoms at (9999.000,9999.000,9999.000) or Raster3D COLOR records, or Midas/MidasPlus USER records, etc... I appreciate that Herbert and Frances Bernstein were instrumental in defining the original PDB file for Brookhaven National Laboratories nearly 30 years ago. However even Brookhaven/RCSB validated PDB files contain numerous problems and poorly conform to the published specification. A truly strict conformance to the PDB standard, as published, would render the format almost useless in practice (for example refusing files without a MASTER record that correctly reflects the record counts of the file, or the incompatability of current recent PDB standards with earlier ones that require sequential record numbers). For a recent exposition of additional issues with the PDB file format, you're welcome to read my talk entitled "PDB: Cruft to Content" that was presented at a meeting earlier this year, which is available online at "http://www.daylight.com/meetings/mug01/Sayle/". The "interpretation" of repeated CONECT records is neither prescribed nor prohibited by the PDB standard, and as such is an ambiguity that may be exploited to encode bond orders. Whilst it is possible that a hypothetical program could mistakenly use repeated CONECT records without intending to imply bond orders, to my knowledge this has never occured in the tens of thousands of PDB files I've processed from numerous sources or been reported as an issue by the hundreds of thousands of RasMol/Chime users. Instead, the multiple CONECT convention is supported by numerous packages including DGEOM, Rubicon, Midas, MidasPlus, Chimera, etc... I'll leave it to this forum to argue the finer pros and cons. 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) 505-438-3470 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: Displaying double bonds Date: Wed, 31 Oct 2001 17:40:26 -0500 (EST) To: rasmol@lists.umass.edu The _only_ feature I have removed from RasMol was the presentation of bond orders by multiple conect records. I removed that feature because I was dealing with valid PDB entries that did not display correctly with the feature in place. I believe I can restore the feature as an option in the next release. The focus of my changes has been to incorporate useful features contributed by the community and to fix bugs. As to the other problems reported, this is the _first_ I have heard of them, and I will be happy to receive either suggested fixes, or to have some test cases and attempt to fix them myself. Regards, Herbert ===================================================== **** 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 Wed, 31 Oct 2001, Roger Sayle wrote: > Hi Herbert, > > Eric is also right when he says that we disabled the > > double bond option for early releases of the RasMol 2.7 > > series. The version of the code for multiple bonds used > > in the versions of RasMol predating RasMol 2.7 did not > > conform to the PDB format specification and could cause > > validly formatted files to display incorrect bond orders. > > This is the classic philosophical difference over file formats > that separates data providers from users of that data. > > On the one hand, the people that define file formats wish that > the community should precisely adhere to a possibly ambiguous > file format specification and in writing parsers for checking > programs, should issue error messages for the smallest discrepancy. > > The user community, on the other hand, exists in a world where > a diversity of file formats variants exist, and rather than be > bombarded with error messages, would hope that software should > make the best effort to interpret as many indiscretions as > possible. > > For example, believing that they understood the intricasies of > the MDL .mol file format, MDL switched to using their own internal > .mol file readers in Chime rather than the implementation in > RasMol. As a result, this mailing list has since had numerous > postings about files that RasMol can read but the Chime cannot. > > Similarly, well intentioned as it is, Herbert Bernstein's switch > to using an "validating" parser creates numerous problems for the > RasMol community. RasMol v2.7 cannot correctly read PDB files > generated by the programs Concord and Corina that places elements > in the wrong columns, or Cambridgesoft's Chem3D that have the wrong > coordinate precision, or XPLOR and CNS generated files that place > pseudo atoms at (9999.000,9999.000,9999.000) or Raster3D COLOR > records, or Midas/MidasPlus USER records, etc... > > I appreciate that Herbert and Frances Bernstein were instrumental > in defining the original PDB file for Brookhaven National Laboratories > nearly 30 years ago. However even Brookhaven/RCSB validated PDB > files contain numerous problems and poorly conform to the published > specification. A truly strict conformance to the PDB standard, as > published, would render the format almost useless in practice (for > example refusing files without a MASTER record that correctly reflects > the record counts of the file, or the incompatability of current > recent PDB standards with earlier ones that require sequential > record numbers). > > For a recent exposition of additional issues with the PDB file format, > you're welcome to read my talk entitled "PDB: Cruft to Content" that > was presented at a meeting earlier this year, which is available online > at "http://www.daylight.com/meetings/mug01/Sayle/". > > The "interpretation" of repeated CONECT records is neither prescribed > nor prohibited by the PDB standard, and as such is an ambiguity that > may be exploited to encode bond orders. Whilst it is possible that > a hypothetical program could mistakenly use repeated CONECT records > without intending to imply bond orders, to my knowledge this has never > occured in the tens of thousands of PDB files I've processed from numerous > sources or been reported as an issue by the hundreds of thousands of > > RasMol/Chime users. Instead, the multiple CONECT convention is supported > by numerous packages including DGEOM, Rubicon, Midas, MidasPlus, Chimera, > etc... > > > I'll leave it to this forum to argue the finer pros and cons. > > 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) 505-438-3470 > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: referencing software (was CHIMEd Web Sites as Scholarly Works ) Date: Wed, 31 Oct 2001 20:13:13 -0500 To: rasmol@lists.umass.edu thanks for your input, Frank; your comments make a lot of sense. thanks to you and others on this list, I've been able to craft a feasible policy for handling citations, and I feel comfortable explaining to clients the need for easy and obvious access to these citations from within my products. regarding the review system for mol vis sites, in the spirit of full disclosure, my perspective is from the intersection of academia and commercial multimedia development. as such, I'm fairly certain that I have a different viewpoint on this issue then do many list members. however, I believe it is important to remember that there are a growing number of mol vis sites developed outside of the university systems, by independent producers like myself. a fair peer-review should take into account such "commercial" sites, especially since many are freely available on the web. (of course, nothing in your comments lead me to believe otherwise, but I feel it is an important point to raise.) thanks for your insights, tim On 10.29.01 at 1:17 PM, FGORGA@bridgew.edu (Gorga, Frank) wrote: > Colleagues, > > > I think that Herbert Bernstein summarized the issues succinctly when he > stated: > > >In the sciences we adhere to rigorous standards of scholarly citation > >for at least at two purposes that have been mentioned in this discussion: > > > > 1. Giving credit where credit is due > > 2. Helping others to have sufficient information to > >reporpoduce our results > > I think that we need to, in part, distinguish the "simple" preparation of a > graphic, where "#1" above is the main issue in my view and the more > computational aspects of some work where structures are actually calculated, > where both #1 and #2 are clearly involved. > > I also think that the "credit" issue is distinctly different in the case of > commercial software vs. non-commercial software. In the case of commercial > software we users "vote with our pocketbooks"... if the program is good and > useful to us, we will buy it and continue to pay for updates. In my view > this is enough compensation for the authors and no citation is needed, > unless point # 2 (see above) is involved. > > However, in the case of non-commercial software (including RasMol and > Protein Explorer to name two random examples!) things are different. A large > part of the authors "compensation" is derived from having the use of their > software publicly acknowledged. Additionally, in the case of software that > is written with grant support, public acknowledgement of the usefulness of > the software is generally critical for continued support and development. > > Thus, in my view, the obligation to cite the use of a particular program is > much increased when the software in not a commercial product. > > Also, since Tim Driscoll asked directly for my thoughts at one point, I > would like to respond: > > Tim wrote (in part)... > > >let's say I am asked to produce a print figure for a science textbook based > on > >the crystal structure of a macromolecule. I find the structure in the PDB, > open > >the file in WebLab Viewer, render and save it out as a VRML. Then I open it > in > >Strata 3D, tweak the render and output in very high quality, and it is > printed > >in the textbook. > > >now, I submit that referencing the original author of the structure is a > must. > >if I altered the structure in any way (i.e., mutated a residue or minimized > the > >structure), I would also ref that b/c it is crucial to the information > being > >conveyed. and the fact that it is present in the PDB also merits > >acknowledgement, since that implies some sense of validity (i.e., it has > been > >checked by the RCSB). > > >I'm curious; do you agree with the above logic? my main question is to try > and > >define, with some specificity, when a software program is a tool and when > it is > > > I tend to agree with most of what you say... I think that there is a large > difference between "simply" preparing an image and calculating a structure. > > To use your example, if you are taking a pdb file and making a picture, I > would agree that a simple citation of the pdb entry is probably sufficient. > However, if I used non-commercial software I would also mention the software > (see above). > > However, if you now make changes in a structure (i.e. the mutation in your > example), or prepare your own structures, now the requirements for > documentation (/citation) go way up... I would want to know if you simply > made the substitution (using a random conformation for the new atoms) and > did no further calculations; I would want to know that the structure being > shown is complete fiction! If you took the mutated structure and minimized > the new structure, I would want to know the details of the calculation and > the program used to perform the calculation. Likewise, for small molecules, > I would want to know if the structure was drawn with standard bond lengths > and angles, or if it is the result of some more sophisticated calculation. > If the latter is true then additional citation of the details is in order. > > >> With regard to Tim's point about screen "real estate"... this sort of > >> citation does not require significant space on the "main screen"... In my > >> view a small link to a "footnote" on another page is all that is > required... > >> one can collect all of the "footnotes" on a separate page where the > >> information is available for those who wish to view it. > >> > >well, define significant? while I agree whole-heartedly with you, I > suspect > >many of my clients might disagree. ;-) > > Not knowing anything about your clients, this might be dangerous! But, I > think that this is a matter of education and making your clients aware of > the issues. Most companies are very aware of intellectual property rights > and thus need to see this issue in those terms. In fact, some of the best > referenced CHIMEd websites are those associated with textbooks; I suspect > this is because publishers are sensitized to the issues. I would expect that > companies (pharmaceutical, biotech, etc.) whose livelihood depend on patents > can be educated on these issues. But enough surmising about the nature of > your clients! ;-) > > In a second message, Tim wrote: > > >I heartily agree with your assessment - this is a gray area - and your > analogy > >is a decent one, I think. so I wonder how do we go about applying the > >"scientific journal" model to CHIMEd Web Sites as a standard? this is not > meant > >to be rhetorical; I'm honestly unsure. (I'll have to add this disclaimer to > all > >of my questions to this list from now on, I guess.) > > This is a HARD question... and I do not have all of (any?) the answers, but, > in my view, there are two issues tied up in this question: > > The first issue is "trusting of information"... can you gain enough > information about how a presentation (i.e. CHIMEd web site) was put together > that you can evaluate the claims being made. Of course this can be done at > many levels... for non-experts it may not happen at all, or they may simply > rely on the reputation of the "publisher". The "expert" will want to see > "footnotes" citing the type of information alluded to above. > > The second issue, related to the first, but applying to those of us academic > types is getting credit for scholarly work (towards tenure and promotion) by > preparing CHIMEd websites. > > Both issues can be partially solved by a peer review system organized and > supported by a "known" publisher (a commercial or scientific society)... > I.e. the "scientific journal" model. This is not a perfect solution, nor, > the only solution, but it is, perhaps the easiest solution. > > The biggest downside to this model, is that publishers usually want to > restrict the access of material they publish to paying subscribers. In the > case of web-based material this has the effect of reducing the availability > of the material... what was presumably available on the open web is now > stuck behind a "password protected" site for subscribers only. Compare this > situation with traditional print, where the effect of submitting an article > to a journal results in wider distribution of material, rather than > narrower! And you can see one of the major downsides to this model. This > model is, in fact, in active use by a number of entities (the Journal of > Chemical Education, comes to mind, but I do not mean to single them out). I > have, thus far, refused to submit my sites to any on these publishers, > because of this major (in my view) downside. > > Another possible solution is an model based very loosely on the "open > source" software idea. A group of experts would agree to review sites and, > once a site passes muster, to either publish the site on a freely available > server, or to maintain a link to the site on the author's server in a "table > of contents". > > Neither of these sub-models is ideal. The first model (a central server) > takes control of the material (for updates, etc.) away from the author, but > allows the reviewers to insure that the pubic ally available site is indeed > the site that was reviewed. The second model ( links from a table of > contents to author's sites) allows the author to make changes to the site, > at will, but the reviewers lose a significant amount of control. Personally, > I would favor the central server model. > > As always, I welcome hearing other's ideas about these issues. > > --- Frank > > ---------------------------------------------------------------------------- > - > Frank R. Gorga, Ph.D., Chair > Department of Chemical Sciences > Bridgewater State College > Bridgewater, MA 02325 > 508-531-2827 / 508-531-1785 (fax) > fgorga@bridgew.edu > webhost.bridgew.edu/fgorga > ---------------------------------------------------------------------------- > Comfort the troubled; trouble the comfortable. > -- Dietrich Bonhoeffer, 1906-1945 > http://www.dbonhoeffer.org/who-was-db2.htm > > > > _________________________________________ 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: timothy driscoll Subject: Re: referencing software (was CHIMEd Web Sites as Scholarly Works) Date: Wed, 31 Oct 2001 20:35:39 -0500 To: rasmol@lists.umass.edu On 10.29.01 at 10:16 AM, n.keep@mail.cryst.bbk.ac.uk (Dr Nicholas Keep) wrote: > > Timothy Driscoll says > >I've never found a clause in a licensing agreement that says I am obligated to > >cite the software manufacturer in the work I do with that software. > > The license agreements for MOLSCRIPT and CCP4 suite -probably the most > used pieces of software by X-ray crystallographers (at least on this > side of the Atlantic) make precisely this demand. They are however > free to academics and are constructed on an academic and not a businees > model. > well, I stand by my statement, since I've never used those two programs ;-) seriously, there appears to be total agreement on this list that freeware deserves citation regardless of the situation. > so. I would favour all software being referenced and disclosed- > particularly as this allows you to find out whether the figure has been > drawn by the author (student) or nicked from the internet/scanned in. > this is a good point - using citations to combat plagiarism. although, I would argue that if I were dishonest enough to steal a figure, faking a citation wouldn't slow me down much. not to belabor the point (too late, right?) but let's face it - at some point it does boil down to personal ethics. I produce multimedia for a living - I don't have grant funding or a university position. if I tell everyone how I do what I do, I'll find myself out of a job rather promptly. part of being a successful competitor in a free market is covering your own butt, pardon the indelicacy, esp when you're a little fish in a big pond. to be fair, I will admit that my perspective is outside of mainstream academia. I like to think I have a perspective from both sides of the fence, though I suppose it is possible that I just need to find a new list to haunt ;-) > I > would describe drawing a figure as part of the scientific process rather > than as a creative process and in an ideal world the instructions to > duplicate it should be given. > I would disagree most heartily, but since this is strictly a matter of personal opinion, I'm willing to leave it at that :-) best, 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: "Herbert J. Bernstein" Subject: Re: Displaying double bonds Date: Thu, 01 Nov 2001 09:53:43 -0500 (EST) To: rasmol@lists.umass.edu Would someone be kind enough to send me a test case of RASTER3D COLOUR records that works with RasMol 2.6 and does not work with RasMol 2.7. The cases I have tried after seeing Roger's message seem to work properly with the RasMol 2.7 series. -- HJB ===================================================== **** 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 Wed, 31 Oct 2001, Roger Sayle wrote: > ... or Raster3D COLOR > records, ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: Displaying double bonds Date: Thu, 01 Nov 2001 10:07:10 -0500 (EST) To: rasmol@lists.umass.edu Could anyone who has cases that don't work with the RasMol 2.7 series but did work with the RasMol 2.6 series where the cases are of the following types: 1. PDB files generated by the programs Concord and Corina that places elements in the wrong columns 2. Cambridgesoft's Chem3D that have the wrong coordinate precision 3. XPLOR and CNS generated files that place pseudo atoms at (9999.000,9999.000,9999.000) 4. Midas/MidasPlus USER records please send me some examples. Thanks. -- HJB ===================================================== **** 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 Wed, 31 Oct 2001, Roger Sayle wrote: > Similarly, well intentioned as it is, Herbert Bernstein's switch > to using an "validating" parser creates numerous problems for the > RasMol community. RasMol v2.7 cannot correctly read PDB files > generated by the programs Concord and Corina that places elements > in the wrong columns, or Cambridgesoft's Chem3D that have the wrong > coordinate precision, or XPLOR and CNS generated files that place > pseudo atoms at (9999.000,9999.000,9999.000) or Raster3D COLOR > records, or Midas/MidasPlus USER records, 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,es-ES ++++------+------+------+------+------+------+------+------+------+------+ From: shalpine@earthlink.net Subject: Web graphics - an essential skill for biochemistry Date: Thu, 01 Nov 2001 12:26:28 -0800 To: rasmol@lists.umass.edu Hello Gale, Judy: I applaud your comments on including web graphics with introductory biochem instruction. I'm a long time proponent of using art to teach science, especially biochemistry. In 1994, as Biochemist at the National Gallery of Art, I was asked by the Smithsonian to give a workshop for K-6 teachers on integrating art into science education. More recently I emphasized the importance of interactive Web animation in my presentation at this Spring's ACS meeting in San Diego, in an article published in IEEE MultiMedia, and in a review of Science Visualization at SIGGRAPH 2001 for Animation World Magazine, due out next week ( and , respectively). As a developer of educational animations, I've given workshops on Flash animation at science communication conferences, and was recently asked to teach Macromedia Flash to HS and college chemistry teachers in the LA area. I've also developed the STArt! teaching Science Through Art program for grades K-12. Through this program I've successfully introduced molecular visualization to third graders to help them meet the new CA Science Standards. I am putting together a website on educational animation resources for teachers and students. The response I get from K-12 students is that they are eager to used multimedia for homework assignments. I'd love to discuss this topic with you both and anyone else interested in an interdisciplinary approach to science education. Best regards, Susana Susana Maria Halpine Artist Biochemist Candle Light Productions 8640 Gulana Ave., J-1016 Playa del Rey, CA 90293 (310) 306-8399 shalpine@earthlink.net http://home.earthlink.net/~shalpine Women Chemists Committee Chair, American Chemical Society Los Angeles Section ______ > Hi! > > I recently posted a web article on molecular graphics as an essential skill > for students in introductory biochemistry. To many of you, this might be > coals to Newcastle, but if you're looking for some why and how, and perhaps > some ammunition for convincing colleagues, see > > http://www.usm.maine.edu/~rhodes/Manifesto/index.html > > I will appreciate your comments. > > Cheers! > > Gale Rhodes > Professor of Chemistry > University of Southern Maine > PO Box 9300 > Portland, Maine 04104-9300 > 207-780-4736 > http://www.usm.maine.edu/~rhodes ________ > From: Judy Voet > CC: bgordon@asbmb.faseb.org, voet@sas.upenn.edu > > Dear Rasmolers, > > Frank Gorga's note is extremely timely. Next spring, the ASBMB, > IUBMB and the journal Biochemistry and Molecular Biology Education > (BAMBED) will begin constructing a digital library of peer-reviewed, > web-based educational materials. We will start planning soon and > would like as much input as possible on the best way to do it. If > you would like to participate in this planning, please contact me. > Best regards, > Judy Voet, Co-Editor-in-chief, BAMBED ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: Displaying double bonds Date: Thu, 01 Nov 2001 22:24:38 +0100 To: rasmol@lists.umass.edu The new release of Mol2Mol 4.0 from Compuchem (www.compuchem.com/mol2mol) (within a few weeks) will have support for generating pdb files with 1-2-3 bonds in Rasmol/Chime style. It interconverts a number of file formats, bond orders can be assigned, hydrogens can be added in pH dependent mode, and finally pdb files can be saved optionally in the "official" style or PDBQ or Rasmol/Chime formats. Tamas E. Gunda --------------------------------------- Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Academy of Sciences University of Debrecen, POBox 36 H-4010 Debrecen Hungary ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: Displaying double bonds Date: Thu, 01 Nov 2001 15:26:03 -0700 (MST) To: rasmol@lists.umass.edu My sincere apologies to Herbert Bernstein. From his previous messages I had been lead to believe that RasMol's PDB file reader had been completely replaced in v2.7 with an implementation that ensured stricter adherence with the published PDB standard. I now appreciate he has just selectively disabled features considered troublesome, and continues to read the remaining non-standard variants. My remarks should not be considered as listing the failings of RasMol v2.7, but instead of the potential pitfalls a hypothetical PDB file reader based solely on the standards and not the common usage of the format. Once again my apologies, 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) 505-438-3470 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-WebMail-UserID: cxhedg X-EXP32-SerialNo: 00002882 ++++------+------+------+------+------+------+------+------+------+------+ From: cxhedg Subject: RE: Web graphics - an essential skill for biochemistry Date: Fri, 02 Nov 2001 09:00:49 -0600 To: rasmol@lists.umass.edu Susana Maria Halpine I wonder if you could give a more complete reference to the "reading" at www.awn.com - I can't find anything directly relevant among the numerous topics. >===== Original Message From rasmol@lists.umass.edu ===== >Hello Gale, Judy: > >I applaud your comments on including web graphics with introductory biochem >instruction. I'm a long time proponent of using art to teach science, >especially biochemistry. In 1994, as Biochemist at the National Gallery >of Art, I was asked by the Smithsonian to give a workshop for K-6 >teachers on integrating art into science education. More recently I >emphasized the importance of interactive Web animation in my >presentation at this Spring's ACS meeting in San Diego, in an article >published in IEEE >MultiMedia, and in a review of Science Visualization at SIGGRAPH 2001 >for Animation World Magazine, due out next week >( and >, respectively). > >As a developer of educational animations, I've given workshops on Flash >animation at science communication conferences, and was recently asked >to teach Macromedia Flash to HS and college chemistry teachers in the LA >area. > >I've also developed the STArt! teaching Science Through Art program >for grades K-12. Through this program I've successfully introduced molecular >visualization to third graders to help them meet the new CA Science Standards. > >I am putting together a website on educational animation resources for >teachers and students. The response I get from K-12 students is that >they are eager to used multimedia for homework assignments. I'd love to >discuss this topic with you both and anyone else interested in an >interdisciplinary approach to science education. > >Best regards, > >Susana > > >Susana Maria Halpine >Artist Biochemist >Candle Light Productions >8640 Gulana Ave., J-1016 >Playa del Rey, CA 90293 >(310) 306-8399 >shalpine@earthlink.net >http://home.earthlink.net/~shalpine > >Women Chemists Committee Chair, American Chemical Society Los Angeles Section > >______ > >> Hi! >> >> I recently posted a web article on molecular graphics as an essential skill >> for students in introductory biochemistry. To many of you, this might be >> coals to Newcastle, but if you're looking for some why and how, and perhaps >> some ammunition for convincing colleagues, see >> >> http://www.usm.maine.edu/~rhodes/Manifesto/index.html >> >> I will appreciate your comments. >> >> Cheers! >> > >> Gale Rhodes >> Professor of Chemistry >> University of Southern Maine >> PO Box 9300 >> Portland, Maine 04104-9300 >> 207-780-4736 >> http://www.usm.maine.edu/~rhodes > >________ > > >> From: Judy Voet >> CC: bgordon@asbmb.faseb.org, voet@sas.upenn.edu >> >> Dear Rasmolers, >> >> Frank Gorga's note is extremely timely. Next spring, the ASBMB, >> IUBMB and the journal Biochemistry and Molecular Biology Education >> (BAMBED) will begin constructing a digital library of peer-reviewed, >> web-based educational materials. We will start planning soon and >> would like as much input as possible on the best way to do it. If >> you would like to participate in this planning, please contact me. >> Best regards, >> Judy Voet, Co-Editor-in-chief, BAMBED > Charles Hedgcoth Phone: 785-532-6121 Fax: 785-532-7278 Professor and Head Department of Biochemistry 103 Willard Hall Kansas State University Manhattan, Kansas 66506-3702 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en,es-ES ++++------+------+------+------+------+------+------+------+------+------+ From: shalpine@earthlink.net Subject: Re: Web graphics - an essential skill for biochemistry Date: Sun, 04 Nov 2001 07:49:08 -0800 To: rasmol@lists.umass.edu, cxhedg Hello Charles: > I wonder if you could give a more complete reference to the "reading" at > www.awn.com The review of science visualization at SIGGRAPH 2001 is expected out next week. I'll post a more direct link when it becomes available. Susana Susana Maria Halpine Artist-Biochemist Candle Light Productions 8640 Gulana Ave., J-1016 Playa del Rey, CA 90293 (310) 306-8399 shalpine@earthlink.net http://home.earthlink.net/~shalpine Women Chemists Committee Chair, American Chemical Society Los Angeles Section >===== Original Message From rasmol@lists.umass.edu ===== >Hello Gale, Judy: > >I applaud your comments on including web graphics with introductory biochem >instruction. I'm a long time proponent of using art to teach science, >especially biochemistry. In 1994, as Biochemist at the National Gallery >of Art, I was asked by the Smithsonian to give a workshop for K-6 >teachers on integrating art into science education. More recently I >emphasized the importance of interactive Web animation in my >presentation at this Spring's ACS meeting in San Diego, in an article >published in IEEE >MultiMedia, and in a review of Science Visualization at SIGGRAPH 2001 >for Animation World Magazine, due out next week >( and >, respectively). > >As a developer of educational animations, I've given workshops on Flash >animation at science communication conferences, and was recently asked >to teach Macromedia Flash to HS and college chemistry teachers in the LA >area. > >I've also developed the STArt! teaching Science Through Art program >for grades K-12. Through this program I've successfully introduced molecular >visualization to third graders to help them meet the new CA Science Standards. > >I am putting together a website on educational animation resources for >teachers and students. The response I get from K-12 students is that >they are eager to used multimedia for homework assignments. I'd love to >discuss this topic with you both and anyone else interested in an >interdisciplinary approach to science education. > >Best regards, > >Susana > > >Susana Maria Halpine >Artist Biochemist >Candle Light Productions >8640 Gulana Ave., J-1016 >Playa del Rey, CA 90293 >(310) 306-8399 >shalpine@earthlink.net >http://home.earthlink.net/~shalpine > >Women Chemists Committee Chair, American Chemical Society Los Angeles Section > >______ > >> Hi! >> >> I recently posted a web article on molecular graphics as an essential skill >> for students in introductory biochemistry. To many of you, this might be >> coals to Newcastle, but if you're looking for some why and how, and perhaps >> some ammunition for convincing colleagues, see >> >> http://www.usm.maine.edu/~rhodes/Manifesto/index.html >> >> I will appreciate your comments. >> >> Cheers! >> > >> Gale Rhodes >> Professor of Chemistry >> University of Southern Maine >> PO Box 9300 >> Portland, Maine 04104-9300 >> 207-780-4736 >> http://www.usm.maine.edu/~rhodes > >________ > > >> From: Judy Voet >> CC: bgordon@asbmb.faseb.org, voet@sas.upenn.edu >> >> Dear Rasmolers, >> >> Frank Gorga's note is extremely timely. Next spring, the ASBMB, >> IUBMB and the journal Biochemistry and Molecular Biology Education >> (BAMBED) will begin constructing a digital library of peer-reviewed, >> web-based educational materials. We will start planning soon and >> would like as much input as possible on the best way to do it. If >> you would like to participate in this planning, please contact me. >> Best regards, >> Judy Voet, Co-Editor-in-chief, BAMBED > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en,es-ES ++++------+------+------+------+------+------+------+------+------+------+ From: shalpine@earthlink.net Subject: Electronic watermarks for referencing science images Date: Sun, 04 Nov 2001 17:47:38 -0800 To: rasmol@lists.umass.edu I've followed with great interest the discussion regarding proper references for scientific images and Web graphics. (I get the weekly digest, so I apologize for the delayed response.) This topic was discussed several times at the Image and Meaning Conference held at MIT this Spring. The use of commercial software such as Adobe Photoshop can have very important implications in viewing photographic images, to site an obvious example. Similarly, using another familiar instance, the color maps for NASA interplanetary images are often omitted because it's thought that the general public will not be interested. As graphic images become increasingly critical for our understanding and proper discussion of science, this very issue of referencing images must be addressed by artists, scientists and publishers alike. My suggestion for graphic images that are to be considered on the par with science publications is to include an electronic watermark, link, or other device that documents the history of the image, much like a textual reference. And, just like their textual counterpart, these references no doubt will range from in-depth and helpful, to sketchy and less helpful. Images without proper documentation will simply carry less weight. For the record, in the past I've included PDB file numbers in educational animations that were then removed by the editorial staff. Susana Susana Maria Halpine Artist-Biochemist Candle Light Productions 8640 Gulana Ave., J-1016 Playa del Rey, CA 90293 (310) 306-8399 shalpine@earthlink.net http://home.earthlink.net/~shalpine Women Chemists Committee Chair, American Chemical Society Los Angeles Section ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- boundary="Boundary_(ID_X7EF0i45rtaqKmLJRc2uPA)" X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: Lettice AuYeung Subject: CRIDALA 2002 in Hong Kong - Call for papers: Reminder Date: Tue, 06 Nov 2001 09:40:43 +0800 To: rasmol@lists.umass.edu Cc: cridala@ouhk.edu.hk --Boundary_(ID_X7EF0i45rtaqKmLJRc2uPA) Dear Colleagues, The Centre for Research in Distance and Adult Learning (CRIDAL) of the Open University of Hong Kong is hosting the Second Conference on Research in Distance and Adult Learning in Asia (CRIDALA 2002) from June 5-7 2002 in Hong Kong. The theme of this Conference is WWW.Research.ODL. The Conference will allow researchers in ODL in particular, and education in general, to engage in discussion about the best ways of enhancing and advancing the use of technology in researching open distance and adult learning. Specific topics to be covered include: * Researching ODL online * Teaching and learning online * Developing databases on and for ODL research * Culture, community building and ODL research The conference will provide a unique blend of pre- and post-conference electronic discussions, with face-to-face plenary addresses, symposia and round-table discussions. Could I please invite you, and through you all your interested colleagues, to join us in what promises to be an interesting and important event in distance and adult learning research in Hong Kong. Important Dates * November 30, 2001 -- Paper submission deadline * January 25, 2002 -- Notification of accepted papers * February 28, 2002 -- Early-bird registration deadline * February 28, 2002 -- Last day for submission of revised papers * April 26, 2002 -- Last day of registration * April 29, 2002 -- Pre-conference electronic discussion * June 5, 2002 -- Conference Opening * June 21, 2002 -- Post-conference electronic discussion For guidelines for submitting papers and further information about the Conference and registration, please visit the Conference official Website at: http://www.ouhk.edu.hk/cridal/cridala2002 In the meantime, you may indicate your interest in the Conference by completing the Reply Form available at the conference Website: http://www.ouhk.edu.hk/cridal/cridala02/form02_2.htm You may return the form simply via the Internet. We look forward to the receipt of your paper and to meeting you at CRIDALA 2002. David Murphy For CRIDALA 2002 Organising Committee **************************************************** David Murphy, PhD Acting Director & Associate Professor Centre for Research in Distance & Adult Learning The Open University of Hong Kong 30 Good Shepherd Street, Homatin, Kowloon HONG KONG Tel: +852 2768 6700 Fax: +852 2715 9042 E-mail: dmurphy@ouhk.edu.hk URL: http://www.ouhk.edu.hk/cridal/staff/dmurphy --Boundary_(ID_X7EF0i45rtaqKmLJRc2uPA) Dear Colleagues,

The Centre for Research in Distance and Adult Learning (CRIDAL) of the Open University of Hong Kong is hosting the Second Conference on Research in Distance and Adult Learning in Asia (CRIDALA 2002) from June 5-7 2002 in Hong Kong.

The theme of this Conference is WWW.Research.ODL. The Conference will allow researchers in ODL in particular, and education in general, to engage in discussion about the best ways of enhancing and advancing the use of technology in researching open distance and adult learning. Specific topics to be covered include:

  • Researching ODL online
  • Teaching and learning online
  • Developing databases on and for ODL research
  • Culture, community building and ODL research


The conference will provide a unique blend of pre- and post-conference electronic discussions, with face-to-face plenary addresses, symposia and round-table discussions.

Could I please invite you, and through you all your interested colleagues, to join us in what promises to be an interesting and important event in distance and adult learning research in Hong Kong.
 

Important Dates

  • November 30, 2001 -- Paper submission deadline
  • January 25, 2002 -- Notification of accepted papers
  • February 28, 2002 -- Early-bird registration deadline
  • February 28, 2002 -- Last day for submission of revised papers
  • April 26, 2002 -- Last day of registration
  • April 29, 2002 -- Pre-conference electronic discussion
  • June 5, 2002 -- Conference Opening
  • June 21, 2002 -- Post-conference electronic discussion


For guidelines for submitting papers and further information about the Conference and registration, please visit the Conference official Website at:
    http://www.ouhk.edu.hk/cridal/cridala2002

In the meantime, you may indicate your interest in the Conference by completing the Reply Form available at the conference Website: http://www.ouhk.edu.hk/cridal/cridala02/form02_2.htm

You may return the form simply via the Internet.

We look forward to the receipt of your paper and to meeting you at CRIDALA 2002.

David Murphy
For CRIDALA 2002 Organising Committee

****************************************************
David Murphy, PhD
Acting Director & Associate Professor
Centre for Research in Distance & Adult  Learning
The Open University of Hong Kong
30 Good Shepherd Street, Homatin, Kowloon
HONG KONG

Tel:  +852 2768 6700
Fax: +852 2715 9042
E-mail: dmurphy@ouhk.edu.hk
URL: http://www.ouhk.edu.hk/cridal/staff/dmurphy
 
  --Boundary_(ID_X7EF0i45rtaqKmLJRc2uPA)-- X-Accept-Language: en References: <9F5E83E17008D31193DD0090274E75050663345F@mailhost.bridgew.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Joan Slonczewski Subject: Help with Chime Date: Sat, 10 Nov 2001 15:24:48 -0500 To: rasmol@lists.umass.edu My students are writing a molecular tutorial on phosphoglucose isomerase using this PDB: http://www2.kenyon.edu/depts/biology/courses/biol63/PGIchime.pdb We tried to call the FGP molecule and color it etc., but neither Chime nor the script file seems to work on this piece. Any help as to which command to use? Joan Slonczewski http://www2.kenyon.edu/depts/biology/BMB/chime.htm ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Margaret Wong Subject: Re: Help with Chime Date: Sun, 11 Nov 2001 07:45:57 -0800 To: rasmol@lists.umass.edu Dear Joan > My students are writing a molecular tutorial on phosphoglucose > isomerase using this PDB: > http://www2.kenyon.edu/depts/biology/courses/biol63/PGIchime.pdb Edit all the instances of F6P (the middle character is a six) in the pdb file to something such as FGP then in rasmol/chime load PGIchime.pdb select FGP color yellow wireframe 150 and you will see FGP > > We tried to call the FGP molecule and color it etc., but neither Chime > nor the script file seems to work on this piece. Any help as to which > command to use? > > Joan Slonczewski > http://www2.kenyon.edu/depts/biology/BMB/chime.htm > > regards Margaret _ Dr Margaret Wong v marg@freon.chem.swin.edu.au _-_|\ \_ (_)o Chemistry Dept ) ( mgw@swin.edu.au / \ Subject: Re: Help with Chime Date: Sat, 10 Nov 2001 23:02:51 +0000 To: rasmol@lists.umass.edu Joan- If you prefer, instead of editing the pdb file (which would be an excellent exercise for the students) you could have them select "hetero and not HOH" (i.e., select the heterologous molecules and not the water molecules). Then apply spacefill or whatever. Patricia A. O'Hern, Ph.D. CyberScience Design 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 >From: Joan Slonczewski >Reply-To: rasmol@lists.umass.edu >To: rasmol@lists.umass.edu >Subject: Help with Chime >Date: Sat, 10 Nov 2001 15:24:48 -0500 > >My students are writing a molecular tutorial on phosphoglucose isomerase >using >this PDB: >http://www2.kenyon.edu/depts/biology/courses/biol63/PGIchime.pdb > >We tried to call the FGP molecule and color it etc., but neither Chime nor >the >script file seems to work on this piece. Any help as to which command to >use? > >Joan Slonczewski >http://www2.kenyon.edu/depts/biology/BMB/chime.htm > > > > > _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <3BED8D10.CFA51B13@kenyon.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Help with Chime Date: Sun, 11 Nov 2001 12:20:58 -0500 To: rasmol@lists.umass.edu Joan Slonczewski's snag probably results from the numeral in the hetero name F6P. Please see "Select Commands in Chime and RasMol" http://www.umass.edu/microbio/rasmol/seleccmd.htm Look under "Group/Residue names": Some residue names may contain digits, such as SO3 or PO4. These must be enclosed in square brackets in order to be recognized in select commands, for example "select [so3]". This trick is so obscure that even Chime's internal menu fails on this molecule (1HOX): Select, Residue, F6P selects 0 atoms, while "select [f6p]" selects 32 atoms. I have added a note about this in Protein Explorer's automatic help for SELECT Residue (for the next release). -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 X-MSMail-priority: Normal X-Lboro-Filtered: mailer2.lut.ac.uk, Mon, 12 Nov 2001 18:05:22 +0000 References: <004101c154d9$308e40b0$0200a8c0@cthulhu> <000701c154fc$5392b5a0$b3d8fac1@fti36qrh9z> <3BCA4479.DB7B676B@sympatico.ca> ++++------+------+------+------+------+------+------+------+------+------+ From: Vickie Mckee Subject: connect records Date: Mon, 12 Nov 2001 18:03:02 +0000 To: rasmol@lists.umass.edu I am teaching inorganic chemistry (sorry folks), so I would like to show the metal binding in metalloproteins. I have tried to to this by adding CONECT records to the pdb files but with limited success: OK for proximal histidine in Mb but not for Cu-His bonds in SOD. Am I missing something obvious? Thanks in advance. ***************************************************** Vickie McKee Chemistry Department Loughborough University Loughborough Leics LE11 3TU email: v.mckee@lboro.ac.uk http://www-staff.lboro.ac.uk/~cmvm Phone: +44 (0)1509 222565 Fax (Dept): +44 (0)1509 223925 ***************************************************** ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: <004101c154d9$308e40b0$0200a8c0@cthulhu> <000701c154fc$5392b5a0$b3d8fac1@fti36qrh9z> <3BCA4479.DB7B676B@sympatico.ca> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: connect records Date: Mon, 12 Nov 2001 17:55:28 -0500 To: rasmol@lists.umass.edu Have you consulted http://www.umass.edu/microbio/rasmol/rasbonds.htm? Are you doing this in RasMol or Chime (they can behave differently). If that doesn't solve it, please attach an example of a problematic PDB file to me (NOT TO THE LIST -- REPEAT -- DO NOT ATTACH ANY FILES TO THE 600 SUBSCRIBERS OF THIS LIST PLEASE!). -Eric At 11/12/2001, you wrote: >I am teaching inorganic chemistry (sorry folks), so I would like to show the >metal binding in metalloproteins. I have tried to to this by adding CONECT >records to the pdb files but with limited success: OK for proximal histidine >in Mb but not for Cu-His bonds in SOD. Am I missing something obvious? >Thanks in advance. > >***************************************************** >Vickie McKee >Chemistry Department >Loughborough University /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <004101c154d9$308e40b0$0200a8c0@cthulhu> <000701c154fc$5392b5a0$b3d8fac1@fti36qrh9z> <3BCA4479.DB7B676B@sympatico.ca> <200111122252.fACMqLW24826@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Showing a bond between Cu and N in SOD Date: Tue, 13 Nov 2001 16:27:15 -0500 To: Vickie Mckee , rasmol@lists.umass.edu At 11/13/2001, Vickie Mckee wrote: >Eric, > I am woking in chime. I had seen something about initscript but I guess >I'm not applying it properly. I've attached a html and the accompanying pdb >file for SOD. I have tried to join the copper to the histidines but have >only succeeded in linking it to water. (I have pruned most of the water out >of the pdb). Dear Vickie: Here comes blessed relief! For future reference, in the Martz FAQ http://www.umass.edu/microbio/rasmol/faq_em.htm you'll see "how can bonds be added?" linking you to http://www.umass.edu/microbio/rasmol/rasbonds.htm A careful reading of this in the section "Adding Arbitrary Bonds", reveals a critical statement in boldface: RasMol and Chime, in fact, ignore all CONECT-specified bonds in which the serial number of the second atom is less than the serial number of the first. Your embed tag uses initscript="set connect save" correctly. Your edited CONECT Records (in file 1B4L.PDB) were: CONECT 413 1059 CONECT 1059 413 CONECT 1108 1155 351 452 880 CONECT 1108 330 CONECT 1109 449 521 589 610 As you note, these fail to show a bond between e.g. copper 1108 and nitrogen 351. Following the advice above, change those involving copper 1108 to: CONECT 330 1108 CONECT 351 1108 CONECT 452 1108 CONECT 880 1108 CONECT 1108 1155 Voila! A similar strategy will work for zinc 1109. You inherited these CONECT 413 1059 CONECT 1059 413 from the original PDB file. These specify a single bond between sulfurs of a Cystine using correct "both ways, redundant" PDB format. They do not produce a double bond in RasMol/Chime. As explained in the above document, RasMol and Chime ignore the second line. Were you to want a double bond between these atoms (which you don't, but just to finish the CONECT story), you could get it with CONECT 413 1059 1059 See http://www.umass.edu/microbio/rasmol/faq_em.htm#doublebonds for more on this. -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Anthrax PA toxin and heptamer Date: Tue, 13 Nov 2001 19:28:43 -0500 To: rasmol@lists.umass.edu Dear Chimerials: There is an excellent review of Anthrax (Annu. Rev. Microbiol. 2001. 55:647-71) from which I learned about structural studies of the Protective Antigen (PA), the portion of the toxin responsible for getting the lethal factor or edema factor through the membrane of the target cell. PA is 1ACC.PDB (2.1A resolution). The full length 735 AA chain, PA83, is cleaved to form the active fragment PA63, which forms heptamers. Although the heptamer was not deposited in the PDB, Robert Liddington was kind enough to send me the PDB file (a model based on a 4.5A resolution crystal) with permission to share it publically for educational purposes. So if anyone is interested in making a Chime presentation on anthrax toxin (I have no plans to make a toxin presentation myself), or sharing this PDB file with their students, you can display it in Chime (from a gzipped 0.6 megabyte copy) at http://molvis.sdsc.edu/pdb/1acchept.pdb This link will fire up Protein Explorer and show it: http://molvis.sdsc.edu/protexpl/pe.htm?id=http://molvis.sdsc.edu/pdb/1acche pt.pdb The structural reference for both the monomer and heptamer is Petosa C, Collier RJ, Klimpel KR, Leppla SH, Liddington RC. Crystal structure of the anthrax toxin protective antigen. Nature 1997 Feb 27;385(6619):833-8 pubmed 9039918 (I haven't been able to get a copy of this paper to read, yet.) -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: Shelley Gaudia Subject: Re: Anthrax PA toxin and heptamer Date: Tue, 13 Nov 2001 16:34:01 -0800 To: rasmol@lists.umass.edu a prepublication of the paper (and others) is available at http://www.nature.com/nature/anthrax/ Shelley Gaudia Science Division Lane Community College 4000 E 30th Ave Eugene, OR 97405 phone: 541-747-4501 x2227 fax 541-744-3961 email: gaudias@lanecc.edu ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2615.200 boundary="Boundary_(ID_5Mpe5cCjeFf3mT5RVtqOtw)" X-MSMail-priority: Normal X-Authentication-warning: dep.chem.rug.nl: Host biof18.chem.rug.nl [129.125.35.193] claimed to be biof18 ++++------+------+------+------+------+------+------+------+------+------+ From: Tjaard Pijning Subject: Resetting dashed bonds Date: Wed, 14 Nov 2001 11:17:46 +0100 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_5Mpe5cCjeFf3mT5RVtqOtw) Hello, I am preparing a Chime-based web presentation using script buttons (embed objects). I want different script buttons to display different coordinations for the active center. As ar as I know, when I use the command monitor ##### ##### (where ##### are the two atomnumbers to be linked by a dashed bond) in a script button, the only way to turn them off for the next script button is by giving that same command again. If there are many dashed bonds to be displayed they all have to be treated this way. My question is : is there another way to "reset" and un-display all previously displayed dashed bonds ? Thanks in advance for any help, kind regards, Ing. Tjaard Pijning -------------------------------------------------------------------------- Protein Crystallography Group Dept. of Chemistry, RU Groningen Nijenborgh 4 9747 AG Groningen The Netherlands tel. (31)(0)50 3634385 email t.pijning@chem.rug.nl --Boundary_(ID_5Mpe5cCjeFf3mT5RVtqOtw)

Hello,
 
I am preparing a Chime-based web presentation using
script buttons (embed objects).
I want different script buttons to display different
coordinations for the active center. As ar as I know,
when I use the command
 
monitor ##### #####
 
(where ##### are the two atomnumbers to be linked by a
dashed bond)
in a script button, the only way to turn them off for
the next script button is by giving that same command
again. If there are many dashed bonds to be displayed they
all have to be treated this way.
My question is : is there another way to "reset" and un-display
all previously displayed dashed bonds ?
Thanks in advance for any help,
kind regards,
 
 

 Ing. Tjaard Pijning

Protein Crystallography Group
Dept. of Chemistry, RU Groningen
Nijenborgh 4  9747 AG Groningen
The Netherlands
tel. (31)(0)50 3634385
email t.pijning@chem.rug.nl

 

--Boundary_(ID_5Mpe5cCjeFf3mT5RVtqOtw)-- X-Accept-Language: en References: <002e01c16cf5$9c214d20$c1237d81@chem.rug.nl> ++++------+------+------+------+------+------+------+------+------+------+ From: Hens Borkent Subject: Re: Resetting dashed bonds Date: Wed, 14 Nov 2001 11:57:25 +0100 To: rasmol@lists.umass.edu Cc: Tjaard Pijning Dear Tjaard and others, About the monitor dashed bonds in Chime we had a discussion last week on the chemweb-mailing list. The Rasmol manual is the obvious source of information for this script-command, but one always has to check how it is interpreted by Chime. Let me try to summarize: Monitors are defined by monitor at1 at2 and show a distance label by default. This label can be toggled with set monitor on/off Repeating the monitor at1 at2 command will switch it off selectively, while monitor on/off will remove all monitors. At least, this is what I concluded from my experiments with this command. (see http://www.cmbi.kun.nl/wetche/organic/sharpless/index.html the 'spiro type of transition state' button near the bottom, which toggles just the lines, no labels shown) Regards, Hens -- Dr. J.H. (Hens) Borkent, CMBI, University of Nijmegen P.O. Box 9010, 6500 GL Nijmegen, The Netherlands Tel 0031 24 3652137 Fax 0031 24 3652977 http://www.cmbi.kun.nl/ Centre for Molecular and Biomolecular Informatics ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- charset=us-ascii X-Accept-Language: en,fr-FR X-Apparently-From: SydnyShll@aol.com References: ++++------+------+------+------+------+------+------+------+------+------+ From: "Dr. Sydney Shall" Subject: Re: Anthrax PA toxin and heptamer Date: Thu, 15 Nov 2001 13:52:30 +0000 To: rasmol@lists.umass.edu It is published in this week's Nature. Sydney Shall Shelley Gaudia wrote: > a prepublication of the paper (and others) is available at > > http://www.nature.com/nature/anthrax/ > > Shelley Gaudia > Science Division > Lane Community College > 4000 E 30th Ave > Eugene, OR 97405 > phone: 541-747-4501 x2227 > fax 541-744-3961 > email: gaudias@lanecc.edu > -- Dr. Sydney Shall, Department of Molecular Medicine, GKT School of Medicine, The Rayne Institute, 123 Coldharbour Lane, LONDON, SE5 9NU, ENGLAND. TEL: 020 7848 5901; FAX: 020 7733 3877 E-Mail: sydney.shall@kcl.ac.uk ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <66B7554F5B@usm.maine.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: Molecular dynamics trajectories Date: Thu, 15 Nov 2001 09:55:30 -0500 To: rasmol@lists.umass.edu >On Tue, 13 Nov 2001, I wrote: > >> Please see also Visual Molecular Dynamics (VMD). I have added a subject >> indexing term for it under "molecular dynamics" at http://molvisindex.org. Two subscribers to this list (thanks Gary and Nicolas) reported to me that they could not access the above URL. This occurred Nov 14 9:00-10:00 US Eastern time. Every time I have tried it, it works. I suspect there was a brief temporary configuration error at the domain service provider. Please try again if you had any problem, and if you continue to have problems, please let me know! I have used buydomains.com for about 9 months for several domain names and their service has been very reliable in general. Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Originator-info: login-token=Mulberry:01ubJvuDAfnyjLIPc+ADOfFUwS6uVE5ugmJ50d7zI=; token_authority=postmaster@andrew.cmu.edu Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: wm0p Subject: Re: Anthrax PA toxin and heptamer Date: Thu, 15 Nov 2001 12:52:40 -0500 To: rasmol@lists.umass.edu I had a freshman seminar course scheduled to discuss Anthrax topics this week. So the heptamer structure of PA63 fit nicely into our Chime viewing. A link to the Chime display (CA atoms, only) is on: http://www.bio.cmu.edu/Courses/BiochemMols/FYSF01/FYSLinks. html There is also a link to a display of Anthrax Lethal Factor. Thanks for posting the heptamer file. -Will McClure --On Tue, Nov 13, 2001 7:28 PM -0500 Eric Martz wrote: > Dear Chimerials: > > There is an excellent review of Anthrax (Annu. Rev. > Microbiol. 2001. 55:647-71) from which I learned about > structural studies of the Protective Antigen (PA), the > portion of the toxin responsible for getting the lethal > factor or edema factor through the membrane of the target > cell. PA is 1ACC.PDB (2.1A resolution). The full length > 735 AA chain, PA83, is cleaved to form the active > fragment PA63, which forms heptamers. Although the > heptamer was not deposited in the PDB, Robert Liddington > was kind enough to send me the PDB file (a model based on > a 4.5A resolution crystal) with permission to share it > publically for educational purposes. So if anyone is > interested in making a Chime presentation on anthrax > toxin (I have no plans to make a toxin presentation > myself), or sharing this PDB file with their students, > you can display it in Chime (from a gzipped 0.6 megabyte > copy) at > > > http://molvis.sdsc.edu/pdb/1acchept.pdb > > This link will fire up Protein Explorer and show it: > > http://molvis.sdsc.edu/protexpl/pe.htm?id=http://molvis.s > dsc.edu/pdb/1acche pt.pdb > > The structural reference for both the monomer and > heptamer is Petosa C, Collier RJ, Klimpel KR, Leppla SH, > Liddington RC. Crystal structure of the anthrax toxin > protective antigen. Nature 1997 Feb 27;385(6619):833-8 > pubmed 9039918 > > (I haven't been able to get a copy of this paper to read, > yet.) -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-- > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-Accept-Language: en,es-ES ++++------+------+------+------+------+------+------+------+------+------+ From: shalpine@earthlink.net Subject: Science Visualization at SIGGRAPH 2001 Date: Fri, 16 Nov 2001 09:13:45 -0800 To: cxhedg@ksu.edu, rasmol@lists.umass.edu Hello Charles: The article on Science Visualization at SIGGRAPH 2001 has gotten top billing in the recent issue of Animation World Magazine: http://www.awn.com/ The direct link is at: http://mag.awn.com/index.php3?ltype=pageone&article_no=855 Susana Susana Maria Halpine Artist-Biochemist Candle Light Productions 8640 Gulana Ave., J-1016 Playa del Rey, CA 90293 (310) 306-8399 shalpine@earthlink.net http://home.earthlink.net/~shalpine Women Chemists Committee Chair, American Chemical Society Los Angeles Section > I wonder if you could give a more complete reference to the "reading" at > www.awn.com > Charles Hedgcoth Phone: 785-532-6121 Fax: 785-532-7278 > Professor and Head > Department of Biochemistry > 103 Willard Hall > Kansas State University > Manhattan, Kansas 66506-3702 > >===== Original Message From rasmol@lists.umass.edu ===== >Hello Gale, Judy: > >I applaud your comments on including web graphics with introductory biochem >instruction. I'm a long time proponent of using art to teach science, >especially biochemistry. In 1994, as Biochemist at the National Gallery >of Art, I was asked by the Smithsonian to give a workshop for K-6 >teachers on integrating art into science education. More recently I >emphasized the importance of interactive Web animation in my >presentation at this Spring's ACS meeting in San Diego, in an article >published in IEEE >MultiMedia, and in a review of Science Visualization at SIGGRAPH 2001 >for Animation World Magazine, due out next week >( and >, respectively). > >As a developer of educational animations, I've given workshops on Flash >animation at science communication conferences, and was recently asked >to teach Macromedia Flash to HS and college chemistry teachers in the LA >area. > >I've also developed the STArt! teaching Science Through Art program >for grades K-12. Through this program I've successfully introduced molecular >visualization to third graders to help them meet the new CA Science Standards. > >I am putting together a website on educational animation resources for >teachers and students. The response I get from K-12 students is that >they are eager to used multimedia for homework assignments. I'd love to >discuss this topic with you both and anyone else interested in an >interdisciplinary approach to science education. > >Best regards, > >Susana > > >Susana Maria Halpine >Artist Biochemist >Candle Light Productions >8640 Gulana Ave., J-1016 >Playa del Rey, CA 90293 >(310) 306-8399 >shalpine@earthlink.net >http://home.earthlink.net/~shalpine > >Women Chemists Committee Chair, American Chemical Society Los Angeles Section > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIME-Autoconverted: from quoted-printable to 8bit by marlin.bio.umass.edu id fANGDOL14396 ++++------+------+------+------+------+------+------+------+------+------+ From: Jean Richelle Subject: RasMol under Mac OS X ? Date: Fri, 23 Nov 2001 17:11:32 +0100 To: rasmol@lists.umass.edu Hello, Is there any plan to port RasMol under Mac OS X ? Regards Jean _____________________________________________________________________________ Jean Richelle Service de Conformation des Macromolécules Biologiques Tel: +32 02 650 3587 et de Bioinformatique - Université libre de Bruxelles FAX: +32 02 648 8954 av. F.D. Roosevelt 50 - CP160/16, B-1050 Bruxelles, Belgium _____________________________________________________________________________ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- FCB X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by marlin.bio.umass.edu id fANGwCL15216 ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: RasMol under Mac OS X ? Date: Fri, 23 Nov 2001 11:56:18 -0500 (EST) To: Jean Richelle , rasmol@lists.umass.edu Cc: "Herbert J. Bernstein" , I assume you are referring to a Mac OS X - native version, rather than the current mac version which run in a Mac OS 9.1 window under Mac OS X. I would be happy to work with someone who has Mac OS X to get a ported binary out, but there are no explicit plans right now for the port. -- HJB ===================================================== **** 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 Fri, 23 Nov 2001, Jean Richelle wrote: > Hello, > > Is there any plan to port RasMol under Mac OS X ? > > Regards > > Jean > _____________________________________________________________________________ > Jean Richelle > Service de Conformation des Macromolécules Biologiques Tel: +32 02 650 3587 > et de Bioinformatique - Université libre de Bruxelles FAX: +32 02 648 8954 > av. F.D. Roosevelt 50 - CP160/16, B-1050 Bruxelles, Belgium > _____________________________________________________________________________ > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- yaya@bernstein-plus-sons.com on Fri, Nov 23, 2001 at 11:56:18AM -0500 Content-disposition: inline User-Agent: Mutt/1.2.5i References: ++++------+------+------+------+------+------+------+------+------+------+ From: Chen-hsiung Chan Subject: Re: RasMol under Mac OS X ? Date: Sat, 24 Nov 2001 11:59:38 +0800 To: rasmol@lists.umass.edu On Fri, Nov 23, 2001 at 11:56:18AM -0500, Herbert J. Bernstein wrote: > I assume you are referring to a Mac OS X - native version, rather than the > current mac version which run in a Mac OS 9.1 window under Mac OS X. I > would be happy to work with someone who has Mac OS X to get a ported > binary out, but there are no explicit plans right now for the port. Max OS X can utilize FreeBSD ports system, which has a Rasmol port there. Someone might want to try out whether it works. However, this version requires X and not native corbon app. -- Chen-Hsiung Chan [¸âÂíºµ](BIG5) Department of Life Science http://waru.life.nthu.edu.tw/~frankch/ National Tsing Hua University email: frankch@waru.life.nthu.edu.tw Taiwan ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: "Francis M.J. Hsieh" Subject: Re: RasMol under Mac OS X ? Date: Mon, 26 Nov 2001 13:24:35 +0800 To: rasmol@lists.umass.edu --Boundary_(ID_LOOFb7mLohULT6uKbYQlbw) Content-description: Main Text on 11/23/2001 7:59 PM, bearscorp at frankch@waru.life.nthu.edu.tw wrote: > Max OS X can utilize FreeBSD ports system, which has a Rasmol > port there. > Someone might want to try out whether it works. > However, this version requires X and not native corbon app. I didn't use the ports system, but I did compile RasMol on my MacOS X 10.1 with XFree86/XonX/OroborOSXv0.75a3. It works fine. But it would be still great if somebody can build one without X window. :-) I am new to the OS X except BSD part. 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kWb/AKrY8Ef532LxS7nfVdY/6uFn/wBIs3/VbHgj/O+xeKXc76rrH/Vws/8ApFm/ 6rY8Ef532LxS7nfVdY/6uFn/ANIs3/VbHgj/ADvsXil3O+q6x/1cLP8A6RZv+q2P BH+d9i8Uu531XWP+rhZ/9Is3/VbHgj/O+xeKXc76rrH/AFcLP/pFm/6rY8Ef532L xS7nfVdZ/wCrhZ/9Is3/AFXx4IfzvsXil3KtohFrI97Krag8E3CNUKRovE1C1L/v ONOfxt/kfBl+ERHI2WvIZdeT/9k= --Boundary_(ID_LOOFb7mLohULT6uKbYQlbw)-- X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Tamas Gunda Subject: Mol2mol 4.0 Date: Mon, 26 Nov 2001 10:41:38 +0100 To: rasmol@lists.umass.edu Dear List Members, The new 4.0 version of the molecule file conversion, manipulation and utility program Mol2Mol is now available from CompuChem Ltd. The current version of Mol2Mol recognizes, and interconverts about 40 different file formats (including subtypes). Contrary to the previous versions, there is no limit in the number of inputted atoms (apart from memory limitations). It can slice multiple structural files to single ones (such as PDB models or MDL SD files to single ones) and vice versa in several variations. Support for PDB Chime subformat (with 1-2-3 bonds). It contains a simple graphical display module to inspect the currently loaded molecule. It possesses chemical intelligence for recognizing detailed atom types, hybridization and chemical environments, which is necessary for converting simpler formats (like X-ray crystallographic files) to more advanced ones, or when hydrogen atoms are automatically to be added. Calculation of pyramidalities, ring puckerings, checking for mistakes in protein backbones. Mol2Mol is a very handy tool for everybody dealing with molecular modelling. It is impossible to write here all of the features of Mol2Mol, but have a look to the following links: A very brief summary for those who don't like reading too much: http://dragon.klte.hu/~gundat/m2m/mol2mol-sum.htm For more info see: http://www.compuchem.com/mol2mol.htm and/or http://dragon.klte.hu/~gundat/mol2mola.htm POV-Ray users may also have a look at: http://dragon.klte.hu/~gundat/povraya.htm Demo and normal versions are available from CompuChem. http://www.compuchem.com ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Meng-Juei Hsieh Subject: Re: RasMol under Mac OS X ? Date: Tue, 27 Nov 2001 10:20:01 -0800 To: Jean Richelle Cc: rasmol@lists.umass.edu Dear Jean, As I remembered, it seems that RasMol didn't use hardware acceleration like OpenGL, I will check it later. I am using G4-400(powerbook) and my X server is XFree86 (OroborOSX is a window manager). I have no idea about the smoothness of the rotation. What PDB file did you use to test? I am not familiar with the Cocoa/Carbon developmental environment, maybe we should ask someone else? Best, MJ On Tuesday, November 27, 2001, at 03:03 AM, Jean Richelle wrote: > Dear MJ / Francis, > Thank you very much. Your executable runs for me and display the > rasmol window in Xtools. NB I had, of course, to change the > permission of the rasmol file, and I have to launch rasmol from a > terminal window. Do you have any idea of how to launch it from the > MacOS X finder ? > Now I have to add that the Xtools rendering is not very good: it is > not smooth at all when e.g. rotating the model. Do you have nice move > rendering with Orobor (that's what you are using as X server, isn't > it ?) ? > Best regards, > 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-Sent: 7 Dec 2001 03:06:06 GMT X-Accept-Language: en ++++------+------+------+------+------+------+------+------+------+------+ From: James Meek Subject: CHIME viewer integrated with PDB/SCOP/PROSITE search tool Date: Thu, 06 Dec 2001 22:06:04 -0500 To: rasmol@lists.umass.edu CHIME and RASMOL users might find useful the site http://exlnt.com/search_pdb/index.htm This site offers search tools for data derived from PDB, the Structural Classification of Proteins (SCOP), the PROSITE database of patterns and annotations, and links to CHIME viewers. "Value added" features include: The data on PDB files is displayed organized by their SCOP PROSITE classification Links on individual PDB's connect to SCOP, the PDB server for header information, Eric Martz's Protein Explorer, and via EC numbers, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and WIT for metabolic pathway information. Sequences can be searched for exact sequence matches (e.g. the zinc binding motif HELGH) (with active links to PDB SCOP 1bkc d.92.1.10 YGKTILTKEADLVTTHELGHNFGAEHDPDGKAECAPNEDQ Tumor Necrosis Factor 1bqq d.92.1.11 RNEDLNGNDIFLVAVHELGHALGLEHSSDPSAIMAPFYQW Membrane-Type Matrix 1cgf d.92.1.11 WTNNFREYNLHRVAAHELGHSLGLSHSTDIGALMYPSYTF Fibroblast Collagenase (E.C. or using perl 'regular expressions' for complex patterns, e.g. the PROSITE pattern for zinc fingers: C.{2,4}C.{3}[LIVMFYWC].{8}H.{3,5}H . The matched residues can be highlighted directly in the viewer. Patterns from PROSITE are available as 'regular expressions' for searching and highlighting PDBs can be chosen based on name (e.g. transcriptase), presence or absence of hetero atoms (e.g. salts, substrates, inhibitors, cofactors, nucleotides), source (man, rat, bacteria, virus), date of entry, size, authors etc, etc, etc. So, for example you can search for: Kinases Kinases of human origin Kinases of human origin with bound nucleotide..... Reverse transcriptases Reverse transcriptases with bound inhibitor Reverse transcriptases with bound inhibitor with a mutation in the NNRTI site..... The site is multi-lingual, with pages completely or partially available in French, German, Spanish, Swedish and Russian. Corrections or additions are welcome (jlmeek@telocity.com). (If these pages are useful, would translation be a good extra-credit student exercise?) Please note that the site is on my home PC via a DSL broadband link It is occasionally unavailable if the link is down. I created the site because I thought it interesting to 1) search for enzymes containing a given conserved sequence, that 2) contained bound hetero atoms, 3) see what related and unrelated proteins contained that sequence, 4) visualize where on the enzymes the conserved residues were located, without knowing the residue numbering system on each protein, and 5) visualize the cavity surrounding the bound hetero atoms, 6) demonstrate amateur-created interfaces to large databases. While there are other programs that will allow carrying out these steps, I'm not aware of any that allow it to be done very easily. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Meng-Juei Hsieh Subject: rasmol preliminary port on MacOSX Date: Sat, 08 Dec 2001 05:59:01 -0800 To: rasmol@lists.umass.edu Dear folks This is a preliminary port I make on my MacOSX powerbook. I put it on http://rayl0.bio.uci.edu/~mjhsieh/RasMol_2.7.2.1.OSXbin.tgz Requirement: 0. MacOSX 1. X Server (XFree86 recommended) 2. root permission of your MacOSX Install You can put this tarball file in wherever you like. (for example: ~/) Use /Application/Utilities/Terminal.app to open a unix shell. Under the unix shell, use following commands; % cd / % sudo tar zxvf ~/RasMol_2.7.2.1.OSXbin.tgz Password: <---- Enter your password usr/local/bin/rasmol usr/local/lib/rasmol usr/local/lib/rasmol/1crn.pdb usr/local/lib/rasmol/3cro.pdb usr/local/lib/rasmol/rasmol usr/local/lib/rasmol/rasmol.hlp Please start your X server before you use this preliminary port. To use rasmol, enter following command % /usr/local/bin/rasmol You can modify the content of /usr/local/bin/rasmol to what ever you want. It's a script. I had already put my screenshot in the mailing list before. With Regards, MengJuei ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly 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: Setting up Protein Explorer for Spring Classes Date: Mon, 10 Dec 2001 10:05:27 -0500 To: anita.klein@unh.edu Cc: rasmol@lists.umass.edu, edmolvis@lists.umass.edu At 12/09/2001, Anita Klein wrote: >HI Eric, > >I'm back after sabbatic leave and need to update/upgrade my course >materials for the spring [ as well a migrate to a new computer on Monday >the 10th]. I can't figure out from the new PE web pages if I need to >download Protein Explorer or will need to use it via Netscape/Chime. If >so, will I be able to load in some of the pdb files I downloaded over the >years, which I used to directly open in rasmol. > >Thanks > >Anita Klein, Associate Professor and Chair >Biochemistry and Molecular Biology >46 College Road >University of New Hampshire >Durham NH 03824-2617 Greetings, Anita, Your questions are probably in the minds of many right about now, so I'm copying the answers to the lists. Regardless of whether you will be using Protein Explorer (PE) on-line or off-line, you use it in Netscape version 4.7x (not version 6), and PE looks and works just the same either way. For use in a student computer lab: 1. If you have a fast, reliable Internet connection, you really don't need to download PE. I routinely give workshops in computer labs around the country running it off the Internet. Alternatively, PE can be downloaded and installed on a local server, or every PC, for fastest and most reliable performance. 2. For Internet access, be sure to use http://proteinexplorer.org (not, for example, the UMass URL). This gets PE from San Diego, which is usually faster than from UMass. 3. For students, you can make a class web page with hyperlinks that will load the molecules of interest. Instructions are on the FrontDoor of PE. For example, for PDB ID 1bl8: http://molvis.sdsc.edu/protexpl/pe.htm?id=1bl8 (That fetches the PDB code via Internet from San Diego.) 4. Beginners should start with the QuickTour, linked to the FrontDoor. For use illustrating lectures: 1. Best to download a local copy of PE as well as your PDB files so you can be sure everything works optimally. Downloading give you the option to work entirely off-line. Downloading link is on FrontDoor of PE (gray box at right). 2A. If you open BARE Explorer (see links on FrontDoor) and use the BROWSE Button to pick up PDB files from your local hard disk, then when you return to BARE Explorer later, the last 10 loaded are on a 'previously loaded' pull-down menu and can be loaded instantly from there. Then you don't necessarily need 2B. 2B. If you wish, make an html file with links to PDB files on your hard disk. Each link will start a new PE session and automatically display the molecule. For example (for Windows), if your PE is in c:\chime\protexpl and the antibody PDB file 1igt.pdb is in c:\pdb\antibody, file:///C|/chime/protexpl/pe.htm?id=file%3A///c|/pdb/antibody/1igt.pdb (More detailed instructions are linked to the FrontDoor. Notice that the colons after the disk drive letters are replaced with vertical bars, and that the colon after 'file' is replaced with %3A.) Open the html file containing your bookmarks with Netscape's File menu, Open Page. Bookmark it. Now you're ready to go. Using the QuickViews menus in PE, it is easy to show the major features of a protein with a few menu clicks, live, in front of the class (no command scripts needed). Be sure to take a look at the new, visitor-maintained "World Index of Molecular Visualization Resources" at http://molvisindex.org. There you'll find, indexed by molecule name, tutorials on over 100 proteins. Let me know if I can be of further help, -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-- chemweb@ic.ac.uk X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Giulio Vistoli Subject: Post doctoral position Date: Fri, 14 Dec 2001 14:24:40 +0100 To: CCL , pdb-l@rcsb.org, rasmol@lists.umass.edu, Dear CCLers, We have an opening for a post-doctoral position (12 months) in the field of computational and experimental drug design. The position is at the Université de Lausanne, Institut de Chimie Thérapeutique (Prof. Bernard Testa and Dr. Pierre-Alain Carrupt) and will involve collaborative projects with the computational group of Dr. Giulio Vistoli (Dip. di Chimica Farmaceutica, Università di Milano). Keywords include: molecular fields, 3D-QSAR descriptors, physicochemical profiling by experimental and computational methods. The following skills are required: - PhD in pharmaceutical sciences or chemistry; - Very good background in drug design, particular molecular modelling and/or experimental physicochemical techniques; - Knowledge of the most popular molecular modelling packages. Interested persons should send a detailed CV (no attachement) to , with copy to Best regards Giulio Vistoli ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: MolUSc : a new chime-based visualization program Date: Fri, 14 Dec 2001 19:40:41 +0100 To: rasmol@lists.umass.edu Dear list members, I'm glad to announce you the creation of MolUSc. http://www.ac-orleans-tours.fr/svt/travaux/Visionneuse/pcindex.htm MolUSc is a Chime-based web resource in French (MolUSc is the French acronym for Molecules for Scholarly Use). It may be thought of as a simpler Protein Explorer. Its aim is to give students full access to Chime possibilities, without needing to know any RasMol script commands. In MolUSc all commands are available in easy-access menus. MolUSc allows surface displays, selections from sequences, comparing two molecules... MolUSc works with Netscape Navigator and even better in Internet Explorer. MolUSc can be downloaded and used freely for non commercial purposes. MolUSc is in french, but Eric Martz told me that he had several requests for a simpler version of PE. MolUSc could be a good answer to those requests, but i don't intend to make myself an english translation. But, I'm willing to help any volunteers interested in doing this translation. Just join me : paul.pillot@ac-orleans-tours.fr Paul Pillot ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Kristin Fox Subject: Spacefill display problems on a Mac Date: Wed, 19 Dec 2001 16:11:28 -0500 To: rasmol@lists.umass.edu Protein Explorer Folks, I am running the latest PE (1.901 beta) on a Mac with OS9, Netscape 4.7 and Chime 2.0a. Almost everything on it seems to be working well except that I cannot display molecules in spacefill mode. I load the molecule, then click on explore more. Then I select something (all, protein, helices, etc.) and choose spacefill from the display list, and then a color. There is no change in the shape of the molecule, only the color changes. All other display modes work. I have tried several molecules and each time I get the following Javascript error: file:///Macintosh%20HD/Applications/Chime%20Resources/shared/getselec.js, line 4: selectObj has no properties. I have tried clearing Netscape's cache, restarting the computer, wiping PE from the disk and redownloading. All to no avail, the problem persists. I went back to the older version of PE I had on another computer and it works fine (I was also able to do it on this machine yesterday before I installed the latest PE). Has anybody else encountered this? Any fixes? Kristin -- Kristin M. Fox Phone: (518)388-6250 Department of Chemistry FAX: (518)388-6795 Union College Email: foxk@union.edu Schenectady, NY 12308 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as 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: Jeffrey Atkinson Subject: Re: Spacefill display problems on a Mac Date: Wed, 19 Dec 2001 20:40:41 -0500 To: rasmol@lists.umass.edu To All; I had the same problem on a Mac (G4, OS 9.1, Netscape 4.76, and Chime 2.0a). It is also true that my older version of PE works, similar to Kristin. I'd also look forward to a solution. Sorry that was basically only moral support Kristin. I wasn't of any help. Jeffrey Kristin M. Fox wrote: >Protein Explorer Folks, > > I am running the latest PE (1.901 beta) on a Mac with OS9, >Netscape 4.7 and Chime 2.0a. Almost everything on it seems to be >working well except that I cannot display molecules in spacefill >mode. I load the molecule, then click on explore more. Then I >select something (all, protein, helices, etc.) and choose spacefill >from the display list, and then a color. There is no change in the >shape of the molecule, only the color changes. All other display >modes work. > I have tried several molecules and each time I get the >following Javascript error: > >file:///Macintosh%20HD/Applications/Chime%20Resources/shared/getselec.js, -- Dr. Jeffrey Atkinson Associate Professor Department of Chemistry Director, Centre for Biotechnology Brock University St. Catharines, Ontario Canada L2S 3A1 jatkin@spartan.ac.BrockU.ca http://chemiris.labs.brocku.ca/~chemweb/faculty/atkinson/ phone: 905 688-5550 ext 3967 fax: 905 682-9020 ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: ++++------+------+------+------+------+------+------+------+------+------+ From: Eric C Niederhoffer Subject: Re: Spacefill display problems on a Mac Date: Thu, 20 Dec 2001 10:33:21 -0600 To: rasmol@lists.umass.edu Protein Explorers: I have made some additional observations concerning PE 1.901 beta. My computer system is a PowerMac G3 (grey, 266 MHz) running OS 9.0.4 with 160 MB RAM. Although I observe the same behavior of not getting Spacefill to work when in the Explore More window, I can use the MDL pull-down menu within the molecule's window frame and change to display spacefill. More interesting is the observation that I find that the above behavior is not present when running PE 1.901 beta from the UMass internet site. In other words, if I launch PE over the internet (not my local copy), the Spacefill function within the Explore More window works. I have used a couple of different pdb files. Eric Niederhoffer >To All; > > I had the same problem on a Mac (G4, OS 9.1, Netscape 4.76, >and Chime 2.0a). It is also true that my older version of PE works, >similar to Kristin. I'd also look forward to a solution. > > Sorry that was basically only moral support Kristin. I >wasn't of any help. > > Jeffrey > >Kristin M. Fox wrote: > >>Protein Explorer Folks, >> >> I am running the latest PE (1.901 beta) on a Mac with OS9, >>Netscape 4.7 and Chime 2.0a. Almost everything on it seems to be >>working well except that I cannot display molecules in spacefill >>mode. I load the molecule, then click on explore more. Then I >>select something (all, protein, helices, etc.) and choose spacefill >>from the display list, and then a color. There is no change in the >>shape of the molecule, only the color changes. All other display >>modes work. >> I have tried several molecules and each time I get the >>following Javascript error: >> >>file:///Macintosh%20HD/Applications/Chime%20Resources/shared/getselec.js, > >-- > > >Dr. Jeffrey Atkinson >Associate Professor >Department of Chemistry >Director, Centre for Biotechnology >Brock University >St. Catharines, Ontario >Canada L2S 3A1 > >jatkin@spartan.ac.BrockU.ca >http://chemiris.labs.brocku.ca/~chemweb/faculty/atkinson/ >phone: 905 688-5550 ext 3967 >fax: 905 682-9020 > Eric C Niederhoffer, PhD Associate Professor Biochemistry & Molecular Biology, MC 4413 1245 Lincoln Drive, Rm 211 Southern Illinois University School of Medicine Carbondale, IL 62901-4413 eniederhoffer@siumed.edu 618.453.6467 (office) 618.453.6440 (fax) http://www.siu.edu/departments/biochem/faculty/Niederhoffer.html ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed boundary="Boundary_(ID_32SA0MPYmlpgFvHVCkXO+Q)" ++++------+------+------+------+------+------+------+------+------+------+ From: David Margulies Subject: RE: Spacefill display problems on a Mac Date: Thu, 20 Dec 2001 11:39:00 -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_32SA0MPYmlpgFvHVCkXO+Q) yes, i observe the same phenomenon as Eric using 1.90 beta on a G4 cube. The MDL menu works fine, as does the command line: select :a, cpk. but the menu pulldown from the explore more window doesn't. D > ---------- > From: Eric C Niederhoffer > Reply To: rasmol@lists.umass.edu > Sent: Thursday, December 20, 2001 11:33 AM > To: rasmol@lists.umass.edu > Subject: Re: Spacefill display problems on a Mac > > Protein Explorers: > > I have made some additional observations concerning PE 1.901 beta. > > My computer system is a PowerMac G3 (grey, 266 MHz) running OS 9.0.4 > with 160 MB RAM. > > Although I observe the same behavior of not getting Spacefill to work > when in the Explore More window, I can use the MDL pull-down menu > within the molecule's window frame and change to display spacefill. > > More interesting is the observation that I find that the above > behavior is not present when running PE 1.901 beta from the UMass > internet site. In other words, if I launch PE over the internet (not > my local copy), the Spacefill function within the Explore More window > works. I have used a couple of different pdb files. > > Eric Niederhoffer > > >To All; > > > > I had the same problem on a Mac (G4, OS 9.1, Netscape 4.76, > >and Chime 2.0a). It is also true that my older version of PE works, > >similar to Kristin. I'd also look forward to a solution. > > > > Sorry that was basically only moral support Kristin. I > >wasn't of any help. > > > > Jeffrey > > > >Kristin M. Fox wrote: > > > >>Protein Explorer Folks, > >> > >> I am running the latest PE (1.901 beta) on a Mac with OS9, > >>Netscape 4.7 and Chime 2.0a. Almost everything on it seems to be > >>working well except that I cannot display molecules in spacefill > >>mode. I load the molecule, then click on explore more. Then I > >>select something (all, protein, helices, etc.) and choose spacefill > >>from the display list, and then a color. There is no change in the > >>shape of the molecule, only the color changes. All other display > >>modes work. > >> I have tried several molecules and each time I get the > >>following Javascript error: > >> > >>file:///Macintosh%20HD/Applications/Chime%20Resources/shared/getselec.js > , > > > >-- > > > > > >Dr. Jeffrey Atkinson > >Associate Professor > >Department of Chemistry > >Director, Centre for Biotechnology > >Brock University > >St. Catharines, Ontario > >Canada L2S 3A1 > > > >jatkin@spartan.ac.BrockU.ca > >http://chemiris.labs.brocku.ca/~chemweb/faculty/atkinson/ > >phone: 905 688-5550 ext 3967 > >fax: 905 682-9020 > > > > Eric C Niederhoffer, PhD > Associate Professor > Biochemistry & Molecular Biology, MC 4413 > 1245 Lincoln Drive, Rm 211 > Southern Illinois University School of Medicine > Carbondale, IL 62901-4413 > > eniederhoffer@siumed.edu > 618.453.6467 (office) > 618.453.6440 (fax) > > http://www.siu.edu/departments/biochem/faculty/Niederhoffer.html > > > --Boundary_(ID_32SA0MPYmlpgFvHVCkXO+Q) RE: Spacefill display problems on a Mac

yes, i observe the same phenomenon as Eric using 1.90 beta on a G4 cube.  The MDL menu works fine, as does the command line:  select :a, cpk.  but the menu pulldown from the explore more window doesn't.

D

    ----------
    From:   Eric C Niederhoffer
    Reply To:       rasmol@lists.umass.edu
    Sent:   Thursday, December 20, 2001 11:33 AM
    To:     rasmol@lists.umass.edu
    Subject:        Re: Spacefill display problems on a Mac

    Protein Explorers:

    I have made some additional observations concerning PE 1.901 beta.

    My computer system is a PowerMac G3 (grey, 266 MHz) running OS 9.0.4
    with 160 MB RAM.

    Although I observe the same behavior of not getting Spacefill to work
    when in the Explore More window, I can use the MDL pull-down menu
    within the molecule's window frame and change to display spacefill.

    More interesting is the observation that I find that the above
    behavior is not present when running PE 1.901 beta from the UMass
    internet site.  In other words, if I launch PE over the internet (not
    my local copy), the Spacefill function within the Explore More window
    works.  I have used a couple of different pdb files.

    Eric Niederhoffer

    >To All;
    >
    >       I had the same problem  on a Mac (G4, OS 9.1, Netscape 4.76,
    >and Chime 2.0a).  It is also true that my older version of PE works,
    >similar to Kristin.  I'd also look forward to a solution.
    >
    >       Sorry that was basically only moral support Kristin.  I
    >wasn't of any help.
    >
    >       Jeffrey
    >
    >Kristin M. Fox wrote:
    >
    >>Protein Explorer Folks,
    >>
    >>      I am running the latest PE (1.901 beta) on a Mac with OS9,
    >>Netscape 4.7 and Chime 2.0a.  Almost everything on it seems to be
    >>working well except that I cannot display molecules in spacefill
    >>mode.  I load the molecule, then click on explore more.  Then I
    >>select something (all, protein, helices, etc.) and choose spacefill
    >>from the display list, and then a color.  There is no change in the
    >>shape of the molecule, only the color changes.  All other display
    >>modes work.
    >>      I have tried several molecules and each time I get the
    >>following Javascript error:
    >>
    >>file:///Macintosh%20HD/Applications/Chime%20Resources/shared/getselec.js,
    >
    >--
    >
    >
    >Dr. Jeffrey Atkinson
    >Associate Professor
    >Department of Chemistry
    >Director, Centre for Biotechnology
    >Brock University
    >St. Catharines, Ontario
    >Canada  L2S 3A1
    >
    >jatkin@spartan.ac.BrockU.ca
    >http://chemiris.labs.brocku.ca/~chemweb/faculty/atkinson/
    >phone:  905 688-5550 ext 3967
    >fax: 905 682-9020
    >

    Eric C Niederhoffer, PhD
    Associate Professor
    Biochemistry & Molecular Biology, MC 4413
    1245 Lincoln Drive, Rm 211
    Southern Illinois University School of Medicine
    Carbondale, IL 62901-4413

    eniederhoffer@siumed.edu
    618.453.6467 (office)
    618.453.6440 (fax)

    http://www.siu.edu/departments/biochem/faculty/Niederhoffer.html


--Boundary_(ID_32SA0MPYmlpgFvHVCkXO+Q)-- <913F8FBFBCDEAC439132B6C806C89FF0014E3A3E@niaid-mail2.niaid.nih.gov> ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: RE: Spacefill display problems on a Mac Date: Thu, 20 Dec 2001 12:42:12 -0500 To: rasmol@lists.umass.edu Thanks to everyone who confirmed Kristin's report and for pointing out that the Mac spacefill problem only happens with the downloaded copy, not on-line. That gives me one idea what might be the problem. I haven't had access to my Mac in the past few days so no opportunity to work on a fix (the problem doesn't occur on Windows). Meanwhile, what about just entering the alias 'sf' in the command entry slot? -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - The Protein Explorer: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org PDB Lite molecule finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor (Immunology), Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Protein Explorer 1.91A works in Internet Explorer Date: Thu, 20 Dec 2001 14:37:39 -0500 To: rasmol@lists.umass.edu This announcement is for Windows users only (not Macintosh): At http://www.umass.edu/microbio/chime/beta/pe_alpha/protexpl I have put a new version of Protein Explorer designed to work in both Microsoft Internet Explorer (Windows only) and Netscape (Windows or Macintosh). This is not a full beta release -- it is still under development and so is designated 1.91 alpha. It is presently only available from this one site (UMass) and you may find slow responses. If I receive enough complaints, I'll put a copy at the San Diego server. Also, you can download it from http://www.umass.edu/microbio/chime/beta/pe_alpha/download I will appreciate your feedback on any problems, and also knowing if everything you try works! Please send feedback to me, not to the list. If PE remains permanently busy and never shows the molecule, see troubleshooting, #4 below. This version works in IE5.5SP2 with Chime 2.6SP3. However, don't upgrade until you try it, and see if the messages you get are clear and helpful. I am aware that the following have not been dealt with: 1. Has not been tested on the Macintosh. (It is not designed to work in MacIE since MDL Chime doesn't support it, but it is supposed to still work in Mac Netscape. Sizing of the PE window will definitely need work!) 2. Has not been tested on IE6. I'm hoping this will work, but I'm afraid to install it in case it botches up my IE5.5 (like installing IE5.5 botched up IE5.0 and IE4.0!). 3. Most testing off-line; on-line testing very limited. 4. The Troubleshooting document has not been updated to incorporate IE. ** see below 5. The movies in the Tutorial have not been fixed to work in IE. Everything else that I've tested works, but PE is so big and complicated now that I'm sure I've missed some things. Also, I've revised the documentation to cover both Netscape and IE, so if you find a document that "doesn't know" about IE, point it out to me. I am greatly indebted to Paul Pillot and Jean-Philippe Demers each of whom made important contributions to this project as volunteers, and also to MDL's Chime Team for their quick response to Microsoft's unilateral removal of plugin support from IE last summer. Those of you who are interested in the details of getting Chime sites to work in IE will find a detailed account of what Jean-Philippe, Paul, and I have discovered. Despite having their work to start with, I have so far spent three full-time weeks on this (whew!). ** There are certain installations of IE5.5SP2/Chime 2.6SP3 that don't work, and I don't know why. I don't know how to fix these and any suggestions are welcome. I have two of them, one on Win98, and one on Win2K. In particular, on the Win98 system, reinstalling, and using Control Panel, Add/Remove Programs, MSIE, Add/Remove, Repair IE did NOT fix this problem. Here is a simple test to see if your IE has this problem. Go to http://www.umass.edu/microbio/chime/quizzer/ and start the Amino Acid Quizzer. You should see a wireframe protein in Chime. Enter a number, such as "1", in the slot and press Enter. If the wireframe image doesn't change, you have the problem. Luckily I have two Win98 systems that don't have this problem! Season's Greetings to all Chimeleons and Rasmolluscs, -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-- boundary="Boundary_(ID_UY+lPUKoJhAjr2VsAOzDEA)" X-Accept-Language: fr,en-US ++++------+------+------+------+------+------+------+------+------+------+ From: Jean-Philippe Demers Subject: A mechanism that makes chime pages work with Internet Explorer Date: Fri, 21 Dec 2001 00:13:12 -0500 To: rasmol@lists.umass.edu --Boundary_(ID_UY+lPUKoJhAjr2VsAOzDEA) Dear Chimeleons, Until now, because of some incompatibilities, it was impossible to have a Chime site which functions fully with Internet Explorer. However, I have just completed the construction of a mechanism that makes it possible to circumvent these incompatibilities. That means that any site using the functionalities of the Chemscape Chime plug-in could be viewed using Internet Explorer. That can make more accessible the biology and chemistry resources you created using Chime. You can download this mechanism on my personal website at www3.sympatico.ca/diane.demers/moi. You will also find, on this site, documentation and examples in connection with this new method. This mechanism also allows a better use of the Chemscape Chime plug-in. In addition to compatibility with Internet Explorer, this mechanism integrates message unscrambling in Netscape Communicator, making possible the creation of sites that query Chime extensively. The mechanism also allows the management of several plug-ins in a same page and ensures a better management of structure files downloads. Finally, communications with the plug-in are automated, which makes it possible to avoid programming problems. At the end, this mechanism will allow the Chime site creators to focus on the content of their site and not on the methods employed to interact with Chime. Thus, I invite you to visit my site at www3.simpatico.ca/diane.diane/moi and to give me your comments. And have great holidays... Jean-Philippe Demers --Boundary_(ID_UY+lPUKoJhAjr2VsAOzDEA) Dear Chimeleons,

Until now, because of some incompatibilities, it was impossible to have a Chime site which functions fully with Internet Explorer. However, I have just completed the construction of a mechanism that makes it possible to circumvent these incompatibilities. That means that any site using the functionalities of the Chemscape Chime plug-in could be viewed using Internet Explorer. That can make more accessible the biology and chemistry resources you created using Chime.

You can download this mechanism on my personal website at www3.sympatico.ca/diane.demers/moi. You will also find, on this site, documentation and examples in connection with this new method.

This mechanism also allows a better use of the Chemscape Chime plug-in. In addition to compatibility with Internet Explorer, this mechanism integrates message unscrambling in Netscape Communicator, making possible the creation of sites that query Chime extensively. The mechanism also allows the management of several plug-ins in a same page and ensures a better management of structure files downloads. Finally, communications with the plug-in are automated, which makes it possible to avoid programming problems.

At the end, this mechanism will allow the Chime site creators to focus on the content of their site and not on the methods employed to interact with Chime. Thus, I invite you to visit my site at www3.simpatico.ca/diane.diane/moi and to give me your comments.

And have great holidays...

Jean-Philippe Demers --Boundary_(ID_UY+lPUKoJhAjr2VsAOzDEA)-- Erratum boundary="Boundary_(ID_MQ4CkyYzjBoaFeJcfZjbkg)" X-Accept-Language: fr,en-US References: <3C22C4E8.8559107D@sympatico.ca> ++++------+------+------+------+------+------+------+------+------+------+ From: Jean-Philippe Demers Subject: A mechanism that makes chime pages work with Internet Explorer - Date: Fri, 21 Dec 2001 21:50:25 -0500 To: rasmol@lists.umass.edu --Boundary_(ID_MQ4CkyYzjBoaFeJcfZjbkg) Oops, As some of you have noticed, the address of my website was www3.sympatico.ca/diane.demers/moi and not www3.simpatico.ca/diane.demers/moi... Thanks for your comprehension... Jean-Philippe Demers > Dear Chimeleons, > > Until now, because of some incompatibilities, it was impossible to have a Chime site which functions fully with Internet Explorer. However, I have just completed the > construction of a mechanism that makes it possible to circumvent these incompatibilities. That means that any site using the functionalities of the Chemscape Chime > plug-in could be viewed using Internet Explorer. That can make more accessible the biology and chemistry resources you created using Chime. > > You can download this mechanism on my personal website at www3.sympatico.ca/diane.demers/moi. You will also find, on this site, documentation and examples > in connection with this new method. > > This mechanism also allows a better use of the Chemscape Chime plug-in. In addition to compatibility with Internet Explorer, this mechanism integrates message > unscrambling in Netscape Communicator, making possible the creation of sites that query Chime extensively. The mechanism also allows the management of several > plug-ins in a same page and ensures a better management of structure files downloads. Finally, communications with the plug-in are automated, which makes it > possible to avoid programming problems. > > At the end, this mechanism will allow the Chime site creators to focus on the content of their site and not on the methods employed to interact with Chime. Thus, I > invite you to visit my site at www3.simpatico.ca/diane.diane/moi and to give me your comments. > > And have great holidays... > > Jean-Philippe Demers > --Boundary_(ID_MQ4CkyYzjBoaFeJcfZjbkg) Oops,

As some of you have noticed, the address of my website was www3.sympatico.ca/diane.demers/moi and not www3.simpatico.ca/diane.demers/moi...

Thanks for your comprehension...

Jean-Philippe Demers
  

Dear Chimeleons, 

Until now, because of some incompatibilities, it was impossible to have a Chime site which functions fully with Internet Explorer. However, I have just completed the
construction of a mechanism that makes it possible to circumvent these incompatibilities. That means that any site using the functionalities of the Chemscape Chime
plug-in could be viewed using Internet Explorer. That can make more accessible the biology and chemistry resources you created using Chime. 

You can download this mechanism on my personal website at www3.sympatico.ca/diane.demers/moi. You will also find, on this site, documentation and examples
in connection with this new method. 

This mechanism also allows a better use of the Chemscape Chime plug-in. In addition to compatibility with Internet Explorer, this mechanism integrates message
unscrambling in Netscape Communicator, making possible the creation of sites that query Chime extensively. The mechanism also allows the management of several
plug-ins in a same page and ensures a better management of structure files downloads. Finally, communications with the plug-in are automated, which makes it
possible to avoid programming problems. 

At the end, this mechanism will allow the Chime site creators to focus on the content of their site and not on the methods employed to interact with Chime. Thus, I
invite you to visit my site at www3.simpatico.ca/diane.diane/moi and to give me your comments. 

And have great holidays... 

Jean-Philippe Demers
--Boundary_(ID_MQ4CkyYzjBoaFeJcfZjbkg)-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 boundary="Boundary_(ID_5tkwImkla1t734HH56iIZQ)" X-MSMail-priority: Normal References: <3C22C4E8.8559107D@sympatico.ca> <3C23F4F1.F14A7F9A@sympatico.ca> ++++------+------+------+------+------+------+------+------+------+------+ From: Paul Pillot Subject: reconnaissance d'IE6.0 Date: Sat, 22 Dec 2001 12:58:40 +0100 To: rasmol@lists.umass.edu This is a multi-part message in MIME format. --Boundary_(ID_5tkwImkla1t734HH56iIZQ) Jean Philippe, j'ai un peu parcouru ton script (beau travail de programmation), et j'ai = remarqu=E9 qu'avec IE6.0 j'aurais d=FB =EAtre =E9cart=E9, ce qui n'est = pas le cas. Il doit y-avoir une faille dans ton m=E9canisme de = d=E9tection du num=E9ro de version. Je pense qu'il faut que tu utilises = l'instruction parseFloat(), pour faire passer ta cha=EEne de = caract=E8res =E0 une valeur num=E9rique. Amicalement Paul PS : comme =E7a semble fonctionner avec IE6.0, ce n'est peut-=EAtre pas = la peine d'=E9carter ce navigateur ! ----- Original Message -----=20 From: Jean-Philippe Demers=20 To: rasmol@lists.umass.edu=20 Sent: Saturday, December 22, 2001 3:50 AM Subject: A mechanism that makes chime pages work with Internet = Explorer - Erratum Oops,=20 As some of you have noticed, the address of my website was = www3.sympatico.ca/diane.demers/moi and not = www3.simpatico.ca/diane.demers/moi...=20 Thanks for your comprehension...=20 Jean-Philippe Demers=20 =20 Dear Chimeleons,=20 Until now, because of some incompatibilities, it was impossible to have = a Chime site which functions fully with Internet Explorer. However, I = have just completed the construction of a mechanism that makes it possible to circumvent these = incompatibilities. That means that any site using the functionalities of = the Chemscape Chime plug-in could be viewed using Internet Explorer. That can make more = accessible the biology and chemistry resources you created using Chime.=20 You can download this mechanism on my personal website at = www3.sympatico.ca/diane.demers/moi. You will also find, on this site, = documentation and examples in connection with this new method.=20 This mechanism also allows a better use of the Chemscape Chime plug-in. = In addition to compatibility with Internet Explorer, this mechanism = integrates message unscrambling in Netscape Communicator, making possible the creation of = sites that query Chime extensively. The mechanism also allows the = management of several plug-ins in a same page and ensures a better management of structure = files downloads. Finally, communications with the plug-in are automated, = which makes it possible to avoid programming problems.=20 At the end, this mechanism will allow the Chime site creators to focus = on the content of their site and not on the methods employed to interact = with Chime. Thus, I invite you to visit my site at www3.simpatico.ca/diane.diane/moi and to = give me your comments.=20 And have great holidays...=20 Jean-Philippe Demers --Boundary_(ID_5tkwImkla1t734HH56iIZQ)
Jean Philippe,
 
j'ai un peu parcouru ton script (beau = travail de=20 programmation), et j'ai remarqu=E9 qu'avec IE6.0 j'aurais d=FB =EAtre = =E9cart=E9, ce qui=20 n'est pas le cas. Il doit y-avoir une faille dans ton m=E9canisme de = d=E9tection du=20 num=E9ro de version. Je pense qu'il faut que tu utilises l'instruction=20 parseFloat(), pour faire passer ta cha=EEne de = caract=E8res =E0 une=20 valeur num=E9rique.
Amicalement
Paul
 
PS : comme =E7a semble fonctionner avec = IE6.0, ce=20 n'est peut-=EAtre pas la peine d'=E9carter ce navigateur !
----- Original Message -----
From:=20 Jean-Philippe Demers =
Sent: Saturday, December 22, = 2001 3:50=20 AM
Subject: A mechanism that makes = chime=20 pages work with Internet Explorer - Erratum

Oops,=20

As some of you have noticed, the address of my website was www3.sympatico.ca/dia= ne.demers/moi=20 and not www3.simpatico.ca/diane.demers/moi...=20

Thanks for your comprehension...=20

Jean-Philippe Demers
 =20 

Dear Chimeleons, 

Until now, because of some incompatibilities, it was impossible to have =
a Chime site which functions fully with Internet Explorer. However, I =
have just completed the
construction of a mechanism that makes it possible to circumvent these =
incompatibilities. That means that any site using the functionalities of =
the Chemscape Chime
plug-in could be viewed using Internet Explorer. That can make more =
accessible the biology and chemistry resources you created using =
Chime. 

You can download this mechanism on my personal website at =
www3.sympatico.ca/diane.demers/moi. You will also find, on this site, =
documentation and examples
in connection with this new method. 

This mechanism also allows a better use of the Chemscape Chime plug-in. =
In addition to compatibility with Internet Explorer, this mechanism =
integrates message
unscrambling in Netscape Communicator, making possible the creation of =
sites that query Chime extensively. The mechanism also allows the =
management of several
plug-ins in a same page and ensures a better management of structure =
files downloads. Finally, communications with the plug-in are automated, =
which makes it
possible to avoid programming problems. 

At the end, this mechanism will allow the Chime site creators to focus =
on the content of their site and not on the methods employed to interact =
with Chime. Thus, I
invite you to visit my site at www3.simpatico.ca/diane.diane/moi and to =
give me your comments. 

And have great holidays... 

Jean-Philippe Demers
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