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
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