Re: [Jmol-users] Jmol 14.1.14 released
On Apr 26, 2014, at 6:58 AM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.1/Jmol%2014.1.14/ Was the release 14.1.14 removed from sourceforge.nethttp://sourceforge.net? The latest version I’m able to access is 14.1.13 Jaim -- Start Your Social Network Today - Download eXo Platform Build your Enterprise Intranet with eXo Platform Software Java Based Open Source Intranet - Social, Extensible, Cloud Ready Get Started Now And Turn Your Intranet Into A Collaboration Platform http://p.sf.net/sfu/ExoPlatform___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] once again, detecting Java TEST RESULTS
Eric, all tests must be done using http:// not file://. Local Java is a completely different story. So, for example, when I access http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=JAVA%20HTML5 after unchecking that box, it works fine in Firefox/Windows. But I do see that in Chrome that call fails with the yellow box, and yet RCSB works. So I will work on this a bit and see if I can glean what the PluginDetect module is doing. Can you please confirm that this link: http://www.rcsb.org/pdb/explore/jmol.do?structureId=1CRNbionumber=1 works for you in all your scenarios when the browser plug in is disabled? Thanks. Bob -- Start Your Social Network Today - Download eXo Platform Build your Enterprise Intranet with eXo Platform Software Java Based Open Source Intranet - Social, Extensible, Cloud Ready Get Started Now And Turn Your Intranet Into A Collaboration Platform http://p.sf.net/sfu/ExoPlatform___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] select chain=a broken in 14.1.14
Dear Bob, It appears to me that in 14.1.14, selecting chain=a (or any other chain name present in the model) always selects zero atoms. Still working is select :a. select chain=a works in 14.0.4. Regards, Eric -- Start Your Social Network Today - Download eXo Platform Build your Enterprise Intranet with eXo Platform Software Java Based Open Source Intranet - Social, Extensible, Cloud Ready Get Started Now And Turn Your Intranet Into A Collaboration Platform http://p.sf.net/sfu/ExoPlatform ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 14.1.14 released
yes, you have to be quick ;) The flexible fix problem turned out to be too serious, and then I've been delayed getting that back up. On Sun, Apr 27, 2014 at 1:08 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: On Apr 26, 2014, at 6:58 AM, Robert Hanson hans...@stolaf.edu wrote: http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.1/Jmol%2014.1.14/ Was the release 14.1.14 removed from sourceforge.net? The latest version I’m able to access is 14.1.13 Jaim -- Start Your Social Network Today - Download eXo Platform Build your Enterprise Intranet with eXo Platform Software Java Based Open Source Intranet - Social, Extensible, Cloud Ready Get Started Now And Turn Your Intranet Into A Collaboration Platform http://p.sf.net/sfu/ExoPlatform ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- Start Your Social Network Today - Download eXo Platform Build your Enterprise Intranet with eXo Platform Software Java Based Open Source Intranet - Social, Extensible, Cloud Ready Get Started Now And Turn Your Intranet Into A Collaboration Platform http://p.sf.net/sfu/ExoPlatform___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] select chain=a broken in 14.1.14
Found it. Thanks. There is an unfortunate nuance to this in that *select chain=a* selects a different thing if a is defined as a variable or not. I just realized that goes back to at least 11.8, so we will just leave it this way. $ load =1d66 TRANSCRIPTION/DNA 06-MAR-92 1D66 DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX found biomolecule 1: D, E, A, B $ select chain=a 483 atoms selected $ select chain=d 400 atoms selected $ a=X $ select chain=a 0 atoms selected $ a=D $ select chain=a 400 atoms selected $ reset a $ select chain=a 483 atoms selected To avoid this sort of surprise, use quotes with string-type comparisons. $ a=D $ select chain='a' // no substitution 483 atoms selected Bob On Sun, Apr 27, 2014 at 3:40 PM, Eric Martz ema...@microbio.umass.eduwrote: Dear Bob, It appears to me that in 14.1.14, selecting chain=a (or any other chain name present in the model) always selects zero atoms. Still working is select :a. select chain=a works in 14.0.4. Regards, Eric -- Start Your Social Network Today - Download eXo Platform Build your Enterprise Intranet with eXo Platform Software Java Based Open Source Intranet - Social, Extensible, Cloud Ready Get Started Now And Turn Your Intranet Into A Collaboration Platform http://p.sf.net/sfu/ExoPlatform ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- Start Your Social Network Today - Download eXo Platform Build your Enterprise Intranet with eXo Platform Software Java Based Open Source Intranet - Social, Extensible, Cloud Ready Get Started Now And Turn Your Intranet Into A Collaboration Platform http://p.sf.net/sfu/ExoPlatform___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] once again, detecting Java TEST RESULTS
OK, our goal here is to make *use:JAVA HTML5 *or *use:SIGNED HTML5 * smooth as can be. After studying PluginDetect, I found a simple fix for Chrome, and most likely Safari, but I will have to test that tomorrow. -- Well, you can try it at http://chemapps.stolaf.edu/jmol/jsmol/test2.htm and let me know if that's any different with Safari. When the setting is *use:JAVA* and Java is not available, that's got to be considered a design decision by the page developer. On Sun, Apr 27, 2014 at 12:21 PM, Robert Hanson hans...@stolaf.edu wrote: Eric, all tests must be done using http:// not file://. Local Java is a completely different story. So, for example, when I access http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm?_USE=JAVA%20HTML5 after unchecking that box, it works fine in Firefox/Windows. But I do see that in Chrome that call fails with the yellow box, and yet RCSB works. So I will work on this a bit and see if I can glean what the PluginDetect module is doing. Can you please confirm that this link: http://www.rcsb.org/pdb/explore/jmol.do?structureId=1CRNbionumber=1 works for you in all your scenarios when the browser plug in is disabled? Thanks. Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- Start Your Social Network Today - Download eXo Platform Build your Enterprise Intranet with eXo Platform Software Java Based Open Source Intranet - Social, Extensible, Cloud Ready Get Started Now And Turn Your Intranet Into A Collaboration Platform http://p.sf.net/sfu/ExoPlatform___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
