Yes, that's the bug if using append with trajectory. I'll look into it.



On Fri, Jul 27, 2012 at 4:49 AM, Andreas Truszkowski <atruszkowski@gmx.de> wrote:
Hi,

reading about 500 models from a XYZ file with load TRAJECTORY "file" seems now to work. See output or attached picture:

FileManager.getAtomSetCollectionFromFile(d:\temp\data.xyz.gz)
FileManager opening d:\temp\data.xyz.gz
The Resolver thinks Xyz
openFile(d:\temp\data.xyz.gz): 45664 ms
reading 105861 atoms
ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false
1 models in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
502 trajectory steps read
Default Van der Waals type for model set to Babel
105861 atoms created
ModelSet: not autobonding; use  forceAutobond=true  to force automatic bond creation


But it's not possible to jump to specific frame or model using the popup menu or following scrip snippets:
frame 1.2; display (_H OR _He);
model 1.2; display (_H OR _He);
select 1.2; display (_H OR _He);

 Jmol throws always following exception:

Exception in thread "QueueThread0" java.lang.ArrayIndexOutOfBoundsException: 1
    at org.jmol.bspt.Bspf.validate(Unknown Source)
    at org.jmol.modelset.ModelCollection.initializeBspf(Unknown Source)
    at org.jmol.modelset.ModelSet.setTrajectory(Unknown Source)
    at org.jmol.modelset.ModelSet.getModelNumberIndex(Unknown Source)
    at org.jmol.viewer.Viewer.getModelNumberIndex(Unknown Source)
    at org.jmol.script.ScriptEvaluator.bitSetForModelFileNumber(Unknown Source)
    at org.jmol.script.ScriptEvaluator.atomExpression(Unknown Source)
    at org.jmol.script.ScriptEvaluator.atomExpression(Unknown Source)
    at org.jmol.script.ScriptEvaluator.select(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(Thread.java:722)


Any ideas?

Kind regards,
Andreas


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Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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