Re: [Jmol-users] State Problem
Bob,
OK, this is reproducible, I think!
If I hammer AJAX save state to my server and check each saved file, all seems
OK. I'm getting state with:
Jmol.getPropertyAsString(jmolApplet0, stateInfo)
If I restore one of these files, it restores, but the next save shows:
set defaultlattice {NaN NaN NaN};
under _setVaribaleState.
Save again, and the NaN damage is extended to set defaultLattice under
_setFileState()
With this damage done, the model will not load from state. To restore state,
I'm using:
var scpt = 'st1=load(temp/' + kitid +
'.txt);st1=st1.replace(!AMP!,);script INLINE @st1;';
Jmol.script(jmolApplet0, scpt);
I have to do this because I need to load from a variable that has been
corrected (replace above) for the Windows server nonsense.
Here's the crazy part. I'm pretty sure once the set defaultlattice {NaN NaN
NaN} under _setVariableState damage is done, I'm skunked even if I load a new
model. In other words, if a go through phase 1 with butane (one save load
cycle), but load ethanol before going through the second save load, ethanol's
save load fails.
It looks to me like the guilty party here is my method of restoring. That this
carries over to a new load seems strange, however.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
On Dec 9, 2013, at 9:25 PM, Otis Rothenberger osrot...@chemagic.com wrote:
Bob,
With our multi-user feature, I'm attempting to go back to state as the
approach to save/load. I've got the Windows server issue fixed, but I'l
running into a random problem. After a series of model save and load cycles
for simple modes, I'm ending up with the following line in the state file:
set defaultLattice {NaN NaN NaN};
It is the act of simply loading a model that breaks this line. There in no
pattern - completely random.
This is Mac Chrome with 14.0.1_2013.12.04.
Otis
--
Otis Rothenberger
o...@chemagic.com
http://chemagic.com
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[Jmol-users] map on pointillist broken?
Bob, It appears that mapping on pointillist representation of atomic orbitals is broken. It works in v, 12,2 but not in v 13 on 14 of Jmol. For example: isosurface atomicOrbital 1 0 0 1 points 5000 2 map atomicOrbital 1 0 0 1 does not work (no errors in script console). PM -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] PHP server
I am a naïve user who takes the sample pages and modifies them to my purposes with only minimal understanding of what is actually involved under the hood. While note necessary for pages where I just show some structures (e. g. this page I made: http://www.mcb.ucdavis.edu/courses/jsmol/aapages/Aliphatic.html), all pages that I construct that include scripts that alter structures only work if I include a call to jmol.php. Unfortunately, I do not have a PHP server I can use at my location. I saw that pages at multiple locations made use of http://chemapps.stolaf.edu/jmol/jsmol/jsmol.php;. So I copied this and have been using this in my pages that have selectable scripts (e. g. http://www.mcb.ucdavis.edu/courses/jsmol/Nucleosomejs.htm ). I am not sure that using this site is appropriate. So first I ask Robert if it is okay for me to have my pages access this site that he setup at his institution. Second I ask about the persistence of this site as all of my pages with scripts will break if this site changes its name or evaporates. Finally am I wrong? Can scripts be done without making use of the PHP code? I am having a great time with JSmol and am recruiting others to make additional useful pages. Thanks for your help! Chuck Gasser == Charles S. Gasser Professor Dept. of Molecular and Cellular Biology University of California, Davis 1 Shields Ave. Davis, CA 95616 104 Briggs Hall 530 752-1013 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] PHP server
Dear Charles, You are welcome to create and host your pages at http://proteopedia.org We have material from several courses and also provide environment for students to do their practices and prepare their own work. Some examples at http://proteopedia.org/w/Student_Projects . Proteopedia includes a friendly scene editor that might help you in preparing your interactive pages. Pages you may want to browse are http://proteopedia.org/w/Teaching_Scenes%2C_Tutorials%2C_and_Educators%27_Pages , http://proteopedia.org/w/Help:Contents , http://proteopedia.org/w/Teaching_Strategies_Using_Proteopedia Please feel free to write if you have questions or need any help. Regards, Jaim __ Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel mail: jaime.prilu...@weizmann.ac.il tel: 972-8-9344959 fax: 972-8-9344113 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) On Dec 11, 2013, at 6:59 AM, Charles Gasser csgas...@ucdavis.edu wrote: I am a naïve user who takes the sample pages and modifies them to my purposes with only minimal understanding of what is actually involved under the hood. While note necessary for pages where I just show some structures (e. g. this page I made: http://www.mcb.ucdavis.edu/courses/jsmol/aapages/Aliphatic.html), all pages that I construct that include scripts that alter structures only work if I include a call to jmol.php. Unfortunately, I do not have a PHP server I can use at my location. I saw that pages at multiple locations made use of http://chemapps.stolaf.edu/jmol/jsmol/jsmol.php;. So I copied this and have been using this in my pages that have selectable scripts (e. g. http://www.mcb.ucdavis.edu/courses/jsmol/Nucleosomejs.htm ). I am not sure that using this site is appropriate. So first I ask Robert if it is okay for me to have my pages access this site that he setup at his institution. Second I ask about the persistence of this site as all of my pages with scripts will break if this site changes its name or evaporates. Finally am I wrong? Can scripts be done without making use of the PHP code? I am having a great time with JSmol and am recruiting others to make additional useful pages. Thanks for your help! Chuck Gasser == Charles S. Gasser Professor Dept. of Molecular and Cellular Biology University of California, Davis 1 Shields Ave. Davis, CA 95616 104 Briggs Hall 530 752-1013 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
