3. October, 2006
Bob,
I have been experiencing Jmol hanging up and becoming unresponsive
when the size of the problem I ask it to perform becomes large. Two
examples:
1. When looking at the relatively small protein, flavodoxin (1flv), I
am able to use the "isosurface" command to draw a solvent surface
around the flavinmononucleotide ligand (31 atoms), ["isosurface select
(ligand] ignore(not ligand) solvent"], but when I attempt to use the
same command on the protein portion of the molecule (1326 atoms)
["isosurface select(protein] ignore(not protein) solvent"], Jmol
becomes unresponsive and no surface is generated.
2. When looking at the structure for the 50S subunit of the 70S
ribosome (2j01), which was reported in this week's issue of Science,
I am able to load the structure into Jmol (89408 atoms), but when I
attempt to render the structure with the "cartoon on" command, Jmol
hangs up and becomes unresponsive; no cartoons are generated. I am
not having this problem with version 10.3.1. The Jmol Java console
window gives the following message:
Exception in thread "AWT-EventQueue-0"
java.lang.ArrayIndexOutOfBoundsException: 119
at org.jmol.viewer.CartoonRenderer.getScreens(CartoonRenderer.java:170)
at org.jmol.viewer.CartoonRenderer.initializeChain
(CartoonRenderer.java:129)
at org.jmol.viewer.CartoonRenderer.renderMpspolymer
(CartoonRenderer.java:105)
at org.jmol.viewer.MpsRenderer.render(MpsRenderer.java:43)
at org.jmol.viewer.ShapeRenderer.render(ShapeRenderer.java:60)
at org.jmol.viewer.FrameRenderer.render(FrameRenderer.java:62)
at org.jmol.viewer.RepaintManager.render(RepaintManager.java:155)
at org.jmol.viewer.Viewer.getImage(Viewer.java:2029)
at org.jmol.viewer.Viewer.renderScreenImage(Viewer.java:2013)
at org.openscience.jmol.app.DisplayPanel.paint(DisplayPanel.java:105)
at javax.swing.JComponent._paintImmediately(JComponent.java:4881)
at javax.swing.JComponent.paintImmediately(JComponent.java:4667)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:
477)
at javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run
(SystemEventQueueUtilities.java:114)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:461)
at java.awt.EventDispatchThread.pumpOneEventForHierarchy
(EventDispatchThread.java:269)
at java.awt.EventDispatchThread.pumpEventsForHierarchy
(EventDispatchThread.java:190)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:
184)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:
176)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
Any ideas?
Warren
!~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Warren Gallagher
Chemistry Department
Phillips 437
University of Wisconsin-Eau Claire
Eau Claire, WI 54702
TEL: (715) 836-5388
FAX: (715) 836-4979
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