On 04/05/2010 06:50 PM, Robert Hanson wrote:
> Thanks, Peter. Yes, that's a killer. Definitely not ready to read 16,000,000
> atoms! But I have added a new option that lets you load some smaller number
> of biomolecule transformations. Looks like we'll have to let Rolf open that
> one for us.... ;)
>
Using Jmol 12.0.RC4_dev rev 12773 I opened the full 1m4x biological unit
file with all atoms successfully. It took about 520 minutes CPU time and
21 GB of memory. (Until the memory was filled the CPU usage raised up to
2400%, then it stayed at 100% for several hours.)
(When I tried this before the same amount of memory was used but Jmol
somehow got stuck and I never got anything rendered.)
You can't really work interactively (unless you have a CPU that is at
least 600 times faster than a 1.6 GHz Itanium processor) because it
takes about one minute for a command to work on all atoms.
But at least you can work with script commands.
When I tried to export an image with "write png" I got the following
error message:
JPG64
java.lang.ArrayIndexOutOfBoundsException: -1
at org.jmol.g3d.Hermite3D.renderHermiteRibbon(Unknown Source)
at org.jmol.g3d.Graphics3D.drawHermite(Unknown Source)
at org.jmol.shapebio.BioShapeRenderer.renderHermiteRibbon(Unknown
Source)
at org.jmol.shapebio.CartoonRenderer.render1(Unknown Source)
at org.jmol.shapebio.CartoonRenderer.renderBioShape(Unknown Source)
at org.jmol.shapebio.BioShapeRenderer.render(Unknown Source)
at org.jmol.shape.ShapeRenderer.render(Unknown Source)
at org.jmol.viewer.RepaintManager.render1(Unknown Source)
at org.jmol.viewer.RepaintManager.render(Unknown Source)
at org.jmol.viewer.Viewer.render(Unknown Source)
at org.jmol.viewer.Viewer.getImage(Unknown Source)
at org.jmol.viewer.Viewer.getScreenImage(Unknown Source)
at org.jmol.viewer.Viewer.renderScreenImage(Unknown Source)
at org.jmol.viewer.Viewer.renderScreenImage(Unknown Source)
at org.openscience.jmol.app.jmolpanel.DisplayPanel.paint(Unknown Source)
at javax.swing.JComponent.paintToOffscreen(JComponent.java:5124)
at
javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:278)
at javax.swing.RepaintManager.paint(RepaintManager.java:1224)
at javax.swing.JComponent._paintImmediately(JComponent.java:5072)
at javax.swing.JComponent.paintImmediately(JComponent.java:4882)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:785)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:713)
at
javax.swing.RepaintManager.seqPaintDirtyRegions(RepaintManager.java:693)
at
javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueUtilities.java:125)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:597)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
rendering error?
Regards,
Rolf
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