Dear Bob,
The following 2 commands crash Jmol 12.0.11:
load 1dlh.pdb.gz
color structure
The crash occurs with 1dlh.pdb.gz or 1dlh.pdb (as received from the PDB)
but NOT with e.g. 1d66.pdb, 1pgb.pdb.gz, 2vaa.pdb.gz.
So it seems to be related to something specific in 1dlh.pdb.
Here's a clue: the following 3 commands do NOT crash Jmol:
load 1dlh.pdb
select (:a,:b) and protein
color structure
but the following 3 commands DO CRASH jmol:
load 1dlh.pdb
select :a,:b
color structure
also
load 1dlh.pdb
select not protein
color structure
The report in the java console:
Exception in thread "QueueThread0" java.lang.ArrayIndexOutOfBoundsException: 7
at org.jmol.viewer.ColorManager.getColixAtomPalette(Unknown Source)
at org.jmol.viewer.Viewer.getColixAtomPalette(Unknown Source)
at org.jmol.shape.Shape.setColix(Unknown Source)
at org.jmol.shape.Balls.setProperty(Unknown Source)
at org.jmol.shape.Shape.setShapeProperty(Unknown Source)
at org.jmol.viewer.ShapeManager.setShapeProperty(Unknown Source)
at org.jmol.script.ScriptEvaluator.setShapeProperty(Unknown Source)
at org.jmol.script.ScriptEvaluator.colorShape(Unknown Source)
at org.jmol.script.ScriptEvaluator.color(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:613)
Thanks, -Eric
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