Jmol users:
We need a suitable color for carbohydrate that meshes well with other
STRUCTURE colors such as these:
http://www.umass.edu/molvis/drums/codes.html
Thanks,
Bob
On Sun, Sep 5, 2010 at 1:48 PM, Eric Martz <ema...@microbio.umass.edu>wrote:
> 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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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
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