Re: [Jmol-users] How to save to JVXL both surface and structure
According to Robert Hanson hans...@stolaf.edu: write xxx.zip Thanks, 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) -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] jmolScript() show spin bug?
Hello, I am trying to update the Jmol in my Jmol Tutorial Authoring Template (JTAT, http://www.bioinformatics.org/jmol-tutorials/) from 11.6.RC12 to 12.0.8. I appear to be observing the following anomaly: When I type show spin into Jmol's console, the report ends with spin on when spinning is on, and spin on is simply omitted when spinning is off. This is what I expect, and my code uses it to toggle spinning in up to 4 concurrent jmols. However, when jmolScript(exit; spin on;, 1) is executed, the report never ends with spin on even when spinning is on. (Thus my existing code never toggles spinning off.) Is this a bug? The report is correct in 11.6.RC12 but not in 12.0.8. Thanks very much, -Eric -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] show isosurface
Thanks Bob! Eran __ From Robert Hanson hans...@stolaf.edu Sent Sat 8/21/2010 5:45 AM To jmol-users@lists.sourceforge.net Subject Re: [Jmol-users] show isosurface Oh, cool! print getproperty(modelinfo.models.name (http://modelinfo.models.name)) [list of names] print getproperty(modelinfo.models.modelProperties.frequency) [list of frequencies] Why didn't I think of this before?? Bob On Fri, Aug 20, 2010 at 9:37 PM, Robert Hanson hans...@stolaf.edu (mailto:hans...@stolaf.edu) wrote: Just added to Jmol 12.1.8: print getProperty(shapeInfo.isosurface.ID (http://shapeInfo.isosurface.ID)) isosurface1 s2 surface3 That is, if a property happens to be a list of associative arrays (a very common thing), then whereas normally you would think you would have to do this: print getProperty(shapeInfo.isosurface[1].ID) print getProperty(shapeInfo.isosurface[2].ID) print getProperty(shapeInfo.isosurface[3].ID) since Jmol knows isosurface is a list, and .ID only refers to associative arrays, we can assume you want the list of IDs of all the isosurfaces. 10 lines of code! :) Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr (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 __ -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev (http://p.sf.net/sfu/RIM-dev2dev) __ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net (mailto:Jmol-users@lists.sourceforge.net) https://lists.sourceforge.net/lists/listinfo/jmol-users (https://lists.sourceforge.net/lists/listinfo/jmol-users) -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] jmolScript() show spin bug?
On Sun, Aug 22, 2010 at 5:32 PM, Eric Martz ema...@microbio.umass.eduwrote: Hello, I am trying to update the Jmol in my Jmol Tutorial Authoring Template (JTAT, http://www.bioinformatics.org/jmol-tutorials/) from 11.6.RC12 to 12.0.8. I appear to be observing the following anomaly: When I type show spin into Jmol's console, the report ends with spin on when spinning is on, and spin on is simply omitted when spinning is off. correct. This is what I expect, and my code uses it to toggle spinning in up to 4 concurrent jmols. However, when jmolScript(exit; spin on;, 1) is executed, the report never ends with spin on even when spinning is on. (Thus my existing code never toggles spinning off.) what report is that? Sometimes after the script command is given? Maybe you need jmolScriptWait(exit; spin on) so that Jmol doesn't just cache the script. I bet that's what is happening. Is this a bug? The report is correct in 11.6.RC12 but not in 12.0.8. Hmm. But then why the version difference. Be more specific about the sequence of events. Thanks very much, -Eric -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ 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 -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
