Re: [Jmol-users] Jmol application w/ command line options

[Matt K. <mku...@ma...>]

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