Details
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Type: Bug
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Status: Closed
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Priority: Major
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Resolution: Fixed
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Affects Version/s: 2.10.2b2
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Fix Version/s: 2.10.3
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Component/s: None
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Labels:None
Description
PDB files produced by modelling tools often lack PDB chain codes (like the one attached). Importing these to view in Chimera yields the following exception:
Time for creating model: 68 ms
Exception in thread "Thread-132" java.lang.NullPointerException
at java.util.Collections.sort(Collections.java:175)
at jalview.ext.rbvi.chimera.AtomSpecModel.getAtomSpec(AtomSpecModel.java:130)
at jalview.ext.rbvi.chimera.ChimeraCommands.buildColourCommands(ChimeraCommands.java:121)
at jalview.ext.rbvi.chimera.ChimeraCommands.getColourBySequenceCommand(ChimeraCommands.java:75)
at jalview.ext.rbvi.chimera.JalviewChimeraBinding.getColourBySequenceCommands(JalviewChimeraBinding.java:701)
at jalview.structures.models.AAStructureBindingModel.colourBySequence(AAStructureBindingModel.java:814)
at jalview.gui.JalviewChimeraBindingModel.updateColours(JalviewChimeraBindingModel.java:90)
at jalview.gui.ChimeraViewFrame.run(ChimeraViewFrame.java:638)
at java.lang.Thread.run(Thread.java:745)
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at java.util.Collections.sort(Collections.java:175)
at jalview.ext.rbvi.chimera.AtomSpecModel.getAtomSpec(AtomSpecModel.java:130)
at jalview.ext.rbvi.chimera.ChimeraCommands.buildColourCommands(ChimeraCommands.java:121)
at jalview.ext.rbvi.chimera.ChimeraCommands.getColourBySequenceCommand(ChimeraCommands.java:75)
at jalview.ext.rbvi.chimera.JalviewChimeraBinding.getColourBySequenceCommands(JalviewChimeraBinding.java:701)
at jalview.structures.models.AAStructureBindingModel.colourBySequence(AAStructureBindingModel.java:814)
at jalview.gui.StructureViewerBase.seqColour_actionPerformed(StructureViewerBase.java:906)
at jalview.gui.StructureViewerBase.updateTitleAndMenus(StructureViewerBase.java:1024)
at jalview.gui.JalviewChimeraBindingModel$1.run(JalviewChimeraBindingModel.java:73)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Time for creating model: 68 ms
Exception in thread "Thread-132" java.lang.NullPointerException
at java.util.Collections.sort(Collections.java:175)
at jalview.ext.rbvi.chimera.AtomSpecModel.getAtomSpec(AtomSpecModel.java:130)
at jalview.ext.rbvi.chimera.ChimeraCommands.buildColourCommands(ChimeraCommands.java:121)
at jalview.ext.rbvi.chimera.ChimeraCommands.getColourBySequenceCommand(ChimeraCommands.java:75)
at jalview.ext.rbvi.chimera.JalviewChimeraBinding.getColourBySequenceCommands(JalviewChimeraBinding.java:701)
at jalview.structures.models.AAStructureBindingModel.colourBySequence(AAStructureBindingModel.java:814)
at jalview.gui.JalviewChimeraBindingModel.updateColours(JalviewChimeraBindingModel.java:90)
at jalview.gui.ChimeraViewFrame.run(ChimeraViewFrame.java:638)
at java.lang.Thread.run(Thread.java:745)
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at java.util.Collections.sort(Collections.java:175)
at jalview.ext.rbvi.chimera.AtomSpecModel.getAtomSpec(AtomSpecModel.java:130)
at jalview.ext.rbvi.chimera.ChimeraCommands.buildColourCommands(ChimeraCommands.java:121)
at jalview.ext.rbvi.chimera.ChimeraCommands.getColourBySequenceCommand(ChimeraCommands.java:75)
at jalview.ext.rbvi.chimera.JalviewChimeraBinding.getColourBySequenceCommands(JalviewChimeraBinding.java:701)
at jalview.structures.models.AAStructureBindingModel.colourBySequence(AAStructureBindingModel.java:814)
at jalview.gui.StructureViewerBase.seqColour_actionPerformed(StructureViewerBase.java:906)
at jalview.gui.StructureViewerBase.updateTitleAndMenus(StructureViewerBase.java:1024)
at jalview.gui.JalviewChimeraBindingModel$1.run(JalviewChimeraBindingModel.java:73)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)