OK, that's fixed for Jmol 11.8.8:
jmol -ionxs with a script that includes measurement was trying to update a
nonexistant measurementTable
If you try 11.9 you shouldn't see this problem, and as soon as 11.8.8 is
released, you shouldn't see it there, either.
The temporary workaround for now is to leave off the -n option. You will see
the flash of the application window, but it will close and there will be no
error.
Bob
On Mon, Nov 2, 2009 at 6:12 PM, Matt Kubasik <[email protected]>wrote:
> 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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--
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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