11.8.4 (Running on Mac OS X 10.5.8)
On 11/2/09 8:17 PM, "Robert Hanson" <[email protected]> wrote:
> Version of Jmol?
>
> On Mon, Nov 2, 2009 at 4:46 PM, Matt Kubasik <[email protected]>
> wrote:
>> Thanks for your comments, Angel. See below.
>>
>>> > I just tested
>>> > it and it works if you do
>>> >
>>> > Jmol -ionxs myscript.spt molecule.pdb
>>> >
>>> > (note the added "s")
>>> >
>>> >
>>
>> Yes, I tried this ( Jmol -ionxs myscript.spt molecule.pdb), and I receive
>> the following list of errors:
>>
>> Exception in thread "QueueThread0" java.lang.NullPointerException
>> at
>> org.openscience.jmol.app.jmolpanel.JmolPanel$MyStatusListener.notifyCallback
>> (JmolPanel.java:1390)
>> at
>> org.jmol.viewer.StatusManager.setStatusMeasuring(StatusManager.java:406)
>> at org.jmol.viewer.Viewer.setStatusMeasuring(Viewer.java:4527)
>> at org.jmol.shape.Measures.define(Measures.java:416)
>> at org.jmol.shape.Measures.nextMeasure(Measures.java:445)
>> at org.jmol.shape.Measures.nextMeasure(Measures.java:470)
>> at org.jmol.shape.Measures.nextMeasure(Measures.java:470)
>> at org.jmol.shape.Measures.define(Measures.java:357)
>> at org.jmol.shape.Measures.setProperty(Measures.java:181)
>> at org.jmol.modelset.ModelSet.setShapeProperty(ModelSet.java:301)
>> at org.jmol.viewer.Viewer.setShapeProperty(Viewer.java:4081)
>> at org.jmol.viewer.Viewer.defineMeasurement(Viewer.java:3031)
>> at org.jmol.viewer.ScriptEvaluator.monitor(ScriptEvaluator.java:6957)
>> at
>> org.jmol.viewer.ScriptEvaluator.instructionDispatchLoop(ScriptEvaluator.java
>> :4403)
>> at
>> org.jmol.viewer.ScriptEvaluator.evaluateCompiledScript(ScriptEvaluator.java:
>> 224)
>> at org.jmol.viewer.Viewer.evalStringWaitStatus(Viewer.java:3862)
>> at
>> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(ScriptManager.ja
>> va:222)
>> at
>> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(ScriptManage
>> r.java:210)
>> at
>> org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(ScriptManager.java:172
>> )
>> at java.lang.Thread.run(Thread.java:613)
>>
>>
>>>> >> #Place measurement in variable dist
>>>> >> dist=script("show measurements")
>>>> >> then, dist14.txt is created, but is empty except for "Show
>>>> measurements."
>>> >
>>> > I'm not sure this should work. Do you have any doc supporting this
>>> script()
>>> > syntax?
>>> >
>>> >
>>
>> This script works when I invoke it from an open Jmol application and a
>> molecule is loaded. It is suggsted on the Jmol Interactive Script
>> Documentation Page, http://chemapps.stolaf.edu/jmol/docs/?ver=11.8#functions
>> (See x= script("..."))
>>
>> I think I came across this on the Jmol-users list, too, somewhere.
>>
>> I was surprised to find that while
>>
>> z =script("show measurements")
>>
>> puts a nice string of measurements into z,
>>
>> z = script("measure (atomno=10) (atomno=15)")
>>
>> puts nothing into z.
>>
>> Perhaps it is a mismatch of data types?
>>
>>
>>>> >> I suspect that Jmol is not loading the pdb file specified in the command
>>>> >> $Jmol -ionx myscript.spt molecule.pdb
>>> >
>>> > Yes, so it seems. Try
>>> > Jmol myscript.spt molecule.pdb
>>> > and you will see that the pdb is indeed not loaded.
>>> >
>>> >
>>>> >> What am I doing wrong? Do these command line options work on the Mac?
>>> >
>>> > It's not a Mac issue. I have the same in Windows
>>> >
>>> >
>>>> >> PS Using
>>>> >> $ jmol -s myscript.spt molecule.pdb
>>>> >> provides the requested results, but it leaves Jmol open.
>>> >
>>> > This is the clue: as I said, add "s" to "-ionx"
>>> >
>>
>> Perhaps the errors the Mac offers (above) will provide a hint. Thank you
>> for your ideas and suggestions.
>>
>> Matt
>>
>>
>>
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