Hi,
I just tried to upgrade our Jmol installation to 12.0.18 (binary download),
but I noticed the following problem (e.g. PDB ID 3CDZ )
Exception in thread "QueueThread1" java.lang.ClassCastException:
java.lang.String cannot be cast to java.util.BitSet
at org.jmol.modelset.AtomCollection.getAtomBits(Unknown Source)
at org.jmol.modelset.BondCollection.getAtomBits(Unknown Source)
at org.jmol.modelset.ModelCollection.getAtomBits(Unknown Source)
at org.jmol.modelset.ModelSet.getAtomBits(Unknown Source)
at org.jmol.viewer.Viewer.getAtomBits(Unknown Source)
at org.jmol.script.ScriptEvaluator.getAtomBits(Unknown Source)
at org.jmol.script.ScriptEvaluator.atomExpression(Unknown Source)
at org.jmol.script.ScriptEvaluator.lookupValue(Unknown Source)
at org.jmol.script.ScriptEvaluator.lookupIdentifierValue(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:637)
when executing the script:
load 'http://www.rcsb.org/pdb/files/3CDZ.pdb.gz';set measurementUnits
ANGSTROMS; select all; spacefill off; wireframe off; backbone off; cartoon
on; color cartoon structure; color structure; select ligand;wireframe
0.16;spacefill 0.5; color cpk ; select all; set antialiasDisplay true;
Can you take a look?
Thanks,
Andreas
--
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------
------------------------------------------------------------------------------
Download new Adobe(R) Flash(R) Builder(TM) 4
The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly
Flex(R) Builder(TM)) enable the development of rich applications that run
across multiple browsers and platforms. Download your free trials today!
http://p.sf.net/sfu/adobe-dev2dev
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
