From: Robert H. <ha...@st...> - 2010-09-06 02:11:22
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http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol_12.zip On Sun, Sep 5, 2010 at 1:48 PM, Eric Martz <em...@mi...>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 > > > > ------------------------------------------------------------------------------ > This SF.net Dev2Dev email is sponsored by: > > Show off your parallel programming skills. > Enter the Intel(R) Threading Challenge 2010. > http://p.sf.net/sfu/intel-thread-sfd > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- 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 |