OK, ignore me.
That's fixed for 12.0.42 and 12.1.45. See
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
On Thu, Apr 28, 2011 at 9:42 AM, Robert Hanson <[email protected]> wrote:
> Brian, how did you create sucrose2.spt? It is that white space -- if the
> first is from saving the script, what is the second, with the white space,
> from? You can't expect Jmol to read data statements correctly with random
> white space. That's asking too much.
>
> Bob
>
>
> On Thu, Apr 28, 2011 at 9:36 AM, Robert Hanson <[email protected]> wrote:
>
>> 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
>>> except 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
>>
>
>
>
> --
> 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
>
--
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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The most intuitive, comprehensive, and cost-effective network
management toolset available today. Delivers lowest initial
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http://p.sf.net/sfu/whatsupgold-sd
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