| 3. October, 2006 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. 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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