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  1. Jalview
  2. JAL-2777

Exceptions and superposition failure when viewing PDB files with empty chain codes in Chimera

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.10.2b2
    • Fix Version/s: 2.10.3
    • Component/s: None
    • 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)

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            Assignee:
            jprocter Jim Procter
            Reporter:
            jprocter Jim Procter
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              Created:
              Updated:
              Resolved: