Re: [Jmol-users] Jmol application w/ command line options
Sure. The order of appearance on the line means nothing. There is also -j and -J that should be mentioned. The order of execution is: someFileName (implied load) -J some script commands here -s someScriptFileNameHere -j some script commands here Bob 2009/11/3 Angel Herráez angel.herr...@uah.es Sorry to insist, but I'd like to clear this up in the Wiki: Bob, can we say that these options are all possible? 1) Jmol.jar molFileName 2) Jmol.jar scriptFileName 3) Jmol.jar -s scriptFileName 4) Jmol.jar -s scriptFileName molFileName 5) Jmol.jar molFileName -s scriptFileName -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Two applets initialized with different scripts
Eran kindly provided me with his test files that demonstrate what appears to us to possibly be a bug in Jmol 11.8.7 and later versions that precludes getting the correct initial display when 2 jmols are on one page. I have adapted Eran's demo and put it here http://www.umass.edu/molvis/tests/Jmolx2_version_test/ There you can test a very simple page with 2 Jmols, with 3 different versions of Jmol. When one of the Jmols gives the wrong display (and reports loading the wrong PDB file in its menu), if you open its console and re-execute its one-line history, the display comes out correct! The 2 jmols are running state scripts generated by Jmols versions 11.5.41 and 11.5.42. Could this be part of the problem -- using state scripts from earlier versions of Jmol? If so, it is a significant problem for Proteopedia.Org which has hundreds of state scripts saved with earlier Jmols being run in later Jmols. Proteopedia is currently using Jmol 11.6.14. When we tried to upgrade it to 11.8.7, the problem demonstrated above became apparent. Ideally we would like to use the existing state scripts (from older versions) in newer Jmols. At the main page at the above URL you can download the entire fileset in one zip file, for local testing and editing. Thanks for your help! -Eric -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Getting list of protein secondary structures fromJmolViewer
you should just have to say: select strucno=3 --Bob On Tue, Nov 3, 2009 at 12:12 PM, Charles Shubert cshub...@mit.edu wrote: Hi Bob, I'm having a little difficulty controlling the rendering of specific secondary structures. show structure for Jmol 11.8.7 returns the list below and I want to select an arbitrary structure from this list and render it as a cartoon. Suppose that I selected the following from the list below: HELIX5 5 TYR B 90 THR B 102 strucno= 8 ### Note that the strucno is the modelInfo structure index + 1 What would be the preferred way of showing this Helix in the viewer window? I'd like to use the scripting language, but this is not critical. Thanks, --Chuck HELIX1 1 LEU A 22 GLU A 35 strucno= 1 HELIX2 2 LEU A 43 THR A 49 strucno= 3 HELIX3 3 LYS A 55 ILE A 68 strucno= 4 HELIX4 4 GLY B 70 LYS B 85 strucno= 7 HELIX5 5 TYR B 90 THR B 102 strucno= 8 HELIX6 6 ALA B 109 ASP B 111 strucno= 9 HELIX7 7 ALA B 113 ALA B 132 strucno= 10 SHEET1 A 3 VAL A 40 ASP A 42 strucno= 2 SHEET3 A 3 ILE A 71 SER A 75 strucno= 5 SHEET2 A 3 SER A 78 TRP A 81 strucno= 6 On Aug 11, 2009, at 6:48 PM, Charles Shubert wrote: Thanks, Bob. I'll parse the header from the pdb files that I load in the JmolViewer. If you decide to make a change in the way Jmol handles this, I'll be happy to change my code to take advantage of it and test it for you. --Chuck - Original Message - *From:* Robert Hanson hans...@stolaf.edu *To:* Charles Shubert cshub...@mit.edu ; jmol-users@lists.sourceforge.net *Sent:* Tuesday, August 11, 2009 3:16 PM *Subject:* Re: [Jmol-users] Getting list of protein secondary structures fromJmolViewer Charles, the information from show structure isn't exactly what is in the header. For example, for 1a6g we have: SHEET1 A 3 GLU A 2 LEU A 5 0 SHEET2 A 3 GLU A 26 ASN A 31 1 N VAL A 28 O VAL A 3 SHEET3 A 3 THR A 69 THR A 73 -1 N VAL A 72 O ILE A 27 SHEET1 B 3 ASP A 18 VAL A 21 0 SHEET2 B 3 VAL A 93 VAL A 98 1 N LYS A 95 O PHE A 19 SHEET3 B 3 GLY A 78 TYR A 83 -1 N PHE A 82 O GLY A 94 in the header and SHEET1 S1 2 GLU A 2 LEU A 5 SHEET2 S2 2 ASP A 18 VAL A 21 SHEET3 S3 2 GLU A 26 ASN A 31 SHEET4 S4 2 THR A 69 THR A 73 SHEET5 S5 2 GLY A 78 TYR A 83 SHEET6 S6 2 VAL A 93 VAL A 98 for show structure. You will find the information in the header itself more useful, I think. Actually, this has never been implemented well. What's really happening is that Jmol is arbitrarily filling in the first four columns. They really don't mean anything. But I could fix that Bob On Tue, Aug 11, 2009 at 11:13 AM, Charles Shubert cshub...@mit.edu wrote: Thanks, Bob. I would like to confirm that my interpretation of the string returned from scriptWait(show structure;) is correct for SHEETS. i.e. SHEET1 S1 2 VAL A 40 ASP A 42 SHEET2 S2 2 ILE A 71 SER A 75 SHEET3 S3 2 SER A 78 TRP A 81 - There is only 1 sheet and the sheet id is 2. There are 3 SHEET strands with ids S1, S2, S3. Thanks, --Chuck - Original Message - *From:* Robert Hanson hans...@stolaf.edu *To:* jmol-users@lists.sourceforge.net *Sent:* Tuesday, August 11, 2009 10:37 AM *Subject:* Re: [Jmol-users] Getting list of protein secondary structures fromJmolViewer Sure, so in your case you want to process the header yourself and not rely upon Jmol's processing. On Mon, Aug 10, 2009 at 2:41 PM, Charles Shubert cshub...@mit.edu wrote: Hi Bob, In looking at the return from viewer.getProperty(null, PolymerInfo, *) I see that the structureId: for helices and sheets is sequential and bears no particular relationship to the ids defined in the pdb file. I'm seeing only structureIds and sheets are really just sheet strands. I'm finding no way to identify a sheet as a set of sheet strands. Would that be a correct interpretation of the PolymerInfo data structure? In looking at the secondary structure definition in 1CF7.pdb I see: HELIX1 1 LEU A 22 GLU A 35 1 14 HELIX2 2 LEU A 43 THR A 49 1 7 HELIX3 3 LYS A 55 ILE A 68 5 14 HELIX4 4 GLY B 70 LYS B 85 1 16 HELIX5 5 TYR B 90 THR B 102 1 13 HELIX6 6 ALA B 109 ASP B 111 5 3 HELIX7 7 ALA B 113 ALA B 132 1 20 SHEET1 A 3 VAL A 40 ASP A 42 0 SHEET2 A 3 SER A 78 TRP A 81 -1 N ILE A 79 O LEU A 41 SHEET3 A 3 ILE A 71 SER A 75 -1 N SER A 75 O SER A 78 In looking at the string that is return from scriptWait(show structure;); I see: HELIX1 H1 LEU A 22 GLU A 35 HELIX2 H2 LEU A 43 THR A 49 HELIX3 H3 LYS A 55 ILE A 68 HELIX4 H4 GLY B 70 LYS B 85 HELIX
Re: [Jmol-users] Two applets initialized with different scripts
Thank you very much for that careful assessment. Oy, my bad. In Jmol 11.7.45 I mistakenly turned all functions starting with _ global (shared between applets). Prior to that it was the other way around -- that functions NOT starting with _ were shared. But the reason those were NOT global was that state scripts use that _ prefix. It was a poor choice all around. I've now set both Jmol 11.8.8 and Jmol 11.9.7 to consider all functions to be local functions unless they explicitly start with global_. My VPN is down or I would upload these files tonight; they will have to wait until tomorrow. Bob On Tue, Nov 3, 2009 at 8:06 PM, Eric Martz ema...@microbio.umass.eduwrote: Eran kindly provided me with his test files that demonstrate what appears to us to possibly be a bug in Jmol 11.8.7 and later versions that precludes getting the correct initial display when 2 jmols are on one page. I have adapted Eran's demo and put it here http://www.umass.edu/molvis/tests/Jmolx2_version_test/ There you can test a very simple page with 2 Jmols, with 3 different versions of Jmol. When one of the Jmols gives the wrong display (and reports loading the wrong PDB file in its menu), if you open its console and re-execute its one-line history, the display comes out correct! The 2 jmols are running state scripts generated by Jmols versions 11.5.41 and 11.5.42. Could this be part of the problem -- using state scripts from earlier versions of Jmol? If so, it is a significant problem for Proteopedia.Org which has hundreds of state scripts saved with earlier Jmols being run in later Jmols. Proteopedia is currently using Jmol 11.6.14. When we tried to upgrade it to 11.8.7, the problem demonstrated above became apparent. Ideally we would like to use the existing state scripts (from older versions) in newer Jmols. At the main page at the above URL you can download the entire fileset in one zip file, for local testing and editing. Thanks for your help! -Eric -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Two applets initialized with different scripts
According to Robert Hanson hans...@stolaf.edu: state scripts use that _ prefix. It was a poor choice all around. I've now set both Jmol 11.8.8 and Jmol 11.9.7 to consider all functions to be local functions unless they explicitly start with global_. Dear Bob, Thank you for a prompt action, and for choosing the clear 'global_' label to avoid further confusions. Best regards, Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
