if I only display meshribbon and hbonds
load pdb file
cpk off
wireframe off
meshribbon
connect auto hbond
hbonds 50
spin
while rotation the mesh changes color (bug or feature?)
the property
ribbonedge on
which restores the original Jmol cartoon style had had only a short stay
during past Jmol versions, was this intended?
if bonds are added to a partial wireframe representation, they are
created invisible
load pdb file
cpk off
wireframe off
select [PRO]
wireframe 70
# not 50
select protein and *.O
connect modify double (*.C and within(group, selected))
neither the visible bonds alter their style nor the invisible bonds get
visible. I think that every newly created/modified bond should be
visible as it gets created.
...
* exposure of 'bondcount' as an atom property:
select bondcount=2
how are double bounds counted? At the moment this a connected atoms
count (rename to boundedcount ?) and only selects *.OG and *.SG (which
is correct, if not >C=O)
select bondcount=3 and carbon
connect modify aromatic
the graph is a bit stochastic. I would prefer if either inner and outer
bonds regularly change in showing hbond style bond or only the inner
bonds are hbond style.
rotating such a graph often results in
Exception in thread "AWT-EventQueue-0"
java.lang.ArrayIndexOutOfBoundsException: 188856
at org.jmol.g3d.Graphics3D.plotPixelsClipped(Graphics3D.java:1260)
at
org.jmol.g3d.Circle3D.plot8FilledCircleCenteredClipped(Circle3D.java:133)
at
org.jmol.g3d.Circle3D.plotFilledCircleCenteredClipped(Circle3D.java:163)
at
org.jmol.g3d.Graphics3D.fillScreenedCircleCentered(Graphics3D.java:365)
at org.jmol.viewer.BallsRenderer.render(BallsRenderer.java:83)
at org.jmol.viewer.BallsRenderer.render(BallsRenderer.java:58)
at org.jmol.viewer.ShapeRenderer.render(ShapeRenderer.java:60)
at org.jmol.viewer.FrameRenderer.render(FrameRenderer.java:55)
at org.jmol.viewer.RepaintManager.render(RepaintManager.java:216)
at org.jmol.viewer.Viewer.render1(Viewer.java:1482)
at org.jmol.viewer.Viewer.renderScreenImage(Viewer.java:1434)
at org.openscience.jmol.app.DisplayPanel.paint(DisplayPanel.java:100)
at javax.swing.JComponent.paintWithOffscreenBuffer(Unknown Source)
at javax.swing.JComponent.paintDoubleBuffered(Unknown Source)
at javax.swing.JComponent._paintImmediately(Unknown Source)
at javax.swing.JComponent.paintImmediately(Unknown Source)
at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
at
javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(Unknown
Source)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
Regards, Jan
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