thanks. Blank line in the data statement. I will track that down.
On Thu, Apr 28, 2011 at 8:56 AM, Brian McMahon <[email protected]> wrote:
> There is an apparent bug, or at least over-sensitivity in the way Jmol
> reads in a state script for a small molecule which contains calculated
> hydrogen bonds. I attach two scripts derived from Bob's sucrose example
> ("load sucrose.cif {1 1 1}; hbonds calculate;"). The first is as written
> out
> by the signed applet with "Save script with state"; the second is identical
> excepte for some white-space changes (most notably the inclusion of a blank
> line within the data "connect_atoms" block).
>
> The first loads and renders fine; the second causes the applet to crash
> and the Java console shows the following error trace:
>
> Exception in thread "QueueThread0"
> java.lang.ArrayIndexOutOfBoundsException: 0
> at org.jmol.modelset.ModelSet.connect(Unknown Source)
> at org.jmol.viewer.Viewer.connect(Unknown Source)
> at org.jmol.script.ScriptEvaluator.data(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.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(Unknown Source
>
> Can this be easily fixed? (The IUCr enhanced figure toolkit saves scripts
> is a manner that is not guaranteed to preserve whitespace.)
>
> The problem appears to have been present since at least Jmol 12.0.10, but
> is
> still present in 12.1.44.
>
> Thanks
> Brian
>
>
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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
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