Eric, you can't go doing this in a script and expect it to run:
#if (loadedfileprev != "64de27ae08d6baa2e9e1f5c22db739ae");
# load
/*file*/"/cgi-bin/getfrozenstructure?64de27ae08d6baa2e9e1f5c22db739ae";
# loadedfileprev = "64de27ae08d6baa2e9e1f5c22db739ae";
# reloadfile = true;
#endif;
That's just asking for trouble -- which is exactly what you got. State
scripts are designed to run ONLY as written, not adapted. In this case you
are running the script on a file that has fewer atoms than the original file
the state script was designed for. So one of the structure commands is
failing.
True, it's not a graceful exit, but you just have to be more careful if you
are going to run state scripts.
Sorry I can't be of more help to you.
Bob
On Thu, Jul 7, 2011 at 9:41 PM, Eric Martz <[email protected]>wrote:
> Dear Bob:
>
> With Jmol 12.0.47 application, I drag 16models.pdb.gz and drop it
> into Jmol. The molecule appears, all is OK. Then I drag 2.spt and
> drop it into Jmol. Jmol freezes. These files are downloadable here:
> www.umass.edu/molvis/tmp/CrashesJmol12.0.47.zip
>
> Noticing the hbond calculation preceding the crash, I commented out
> the line "calculate hbonds" in 2.spt. The pseudo-hbond calculation
> line no longer appears in the Java Console, but the crash is
> identical. (That line is NOT commented out in the downloadable 2.spt file.)
>
> Now that I can open the Java Console for the Jmol Application, I can
> see the following:
>
> FileManager opening file:/Users/emartz/Desktop/Luis for MP/2.spt
> ColorManager: color "roygb" range 0.0 0.0
> RasMol pseudo-hbond calculation
> Exception in thread "QueueThread0"
> java.lang.ArrayIndexOutOfBoundsException: 111328
> at org.jmol.modelset.ModelCollection.setProteinType(Unknown Source)
> at org.jmol.viewer.Viewer.setProteinType(Unknown Source)
> at org.jmol.script.ScriptEvaluator.structure(Unknown Source)
> at org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown
> Source)
> at org.jmol.script.ScriptEvaluator.runFunction(Unknown Source)
> at org.jmol.script.ScriptEvaluator.runFunction(Unknown Source)
> at org.jmol.script.ScriptEvaluator.function(Unknown Source)
> at org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown
> Source)
> at org.jmol.script.ScriptEvaluator.runFunction(Unknown Source)
> at org.jmol.script.ScriptEvaluator.runFunction(Unknown Source)
> at org.jmol.script.ScriptEvaluator.function(Unknown Source)
> at org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown
> Source)
> at org.jmol.script.ScriptEvaluator.script(Unknown Source)
> at org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown
> Source)
> at org.jmol.script.ScriptEvaluator.evaluateCompiledScript(Unknown
> Source)
> at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source)
> at
> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown Source)
> at
> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown
> Source)
> at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown
> Source)
> at java.lang.Thread.run(Thread.java:655)
>
>
> Thanks, -Eric
>
>
>
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
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> _______________________________________________
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--
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
------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
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