Hi there
I've been using JMol for about a year for visualising XYZ files and it
works great but once in a while I come across a file I can't open. They
are usually rather big (>50,000 atoms) but some are actually a lot
smaller (<5000 atoms). This is what the console says:
<console>
FileManager.openFile(C:\Program Files\JMol\sb4394.xyz)
SmarterJmolAdapter:The Resolver thinks:Xyz
openFile(C:\Program Files\JMol\sb4394.xyz) 141 ms
Exception in thread "Thread-6" java.lang.ArrayIndexOutOfBoundsException: 64
at org.jmol.viewer.Bspt$SphereIterator.hasMoreElements(Bspt.java:321)
at org.jmol.viewer.Frame.rebond(Frame.java:1100)
at org.jmol.viewer.Frame.doAutobond(Frame.java:1058)
at org.jmol.viewer.Frame.<init>(Frame.java:188)
at org.jmol.viewer.ModelManager.setClientFile(ModelManager.java:72)
at org.jmol.viewer.Viewer.openClientFile(Viewer.java:1029)
at org.jmol.viewer.Viewer.getOpenFileError1(Viewer.java:1002)
at org.jmol.viewer.Viewer.getOpenFileError(Viewer.java:987)
at org.jmol.viewer.Eval.load(Eval.java:1634)
at org.jmol.viewer.Eval.instructionDispatchLoop(Eval.java:349)
at org.jmol.viewer.Eval.run(Eval.java:289)
at java.lang.Thread.run(Unknown Source)
</console>
I tried increasing the memory heap size for the Java VM but it didn't
help. Does anyone have an idea? There is of course the possibility that
these files are corrupt but all my XYZ files are created by the same
programme and they usually work fine. Btw I'm using JMol 10.00 and Java
1.5.0_04 on Windows XP.
Here are two examples which don't work for me:
http://www2.phys.canterbury.ac.nz/~muk10/sb4394.xyz (180kB)
http://www2.phys.canterbury.ac.nz/~muk10/sb71104.xyz (3MB!)
Thanks a lot for your help!
Cheers,
Martin
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