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  1. Jalview
  2. JAL-1836

Error processing PDB 4q4h

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Critical
    • Resolution: Fixed
    • Affects Version/s: 2.8.2, 2.8.2b1, 2.9
    • Fix Version/s: 2.10.0
    • Component/s: None
    • Labels:

      Description

      While testing JAL-1829, I discovered that the StructureSelectionManager class throws an ArrayIndexOutOfBoundsException while attempting to load some PDB structures concurrently, this happens on both JMol and Chimera

      To reproduce:
      - fetch the following sequences from PDB: 3nh6; 4rvc; 4q4h.
      - select all of the sequence and attempt to view all structures for them together.

      Stack trace for JMol:
      Squashed Jmol callback handler error:
      java.lang.ArrayIndexOutOfBoundsException: -2
      at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:521)
      at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:323)
      at jalview.ext.jmol.JalviewJmolBinding.notifyFileLoaded(JalviewJmolBinding.java:1185)
      at jalview.ext.jmol.JalviewJmolBinding.notifyCallback(JalviewJmolBinding.java:995)
      at org.jmol.viewer.StatusManager.setFileLoadStatus(Unknown Source)
      at org.jmol.viewer.Viewer.setFileLoadStatus(Unknown Source)
      at org.jmol.viewer.Viewer.createModelSetAndReturnError(Unknown Source)
      at org.jmol.viewer.Viewer.loadModelFromFile(Unknown Source)
      at org.jmol.script.ScriptEval.cmdLoad(Unknown Source)
      at org.jmol.script.ScriptEval.processCommand(Unknown Source)
      at org.jmol.script.ScriptEval.commandLoop(Unknown Source)
      at org.jmol.script.ScriptEval.dispatchCommands(Unknown Source)
      at org.jmol.script.ScriptEval.executeCommands(Unknown Source)
      at org.jmol.script.ScriptEval.evaluateCompiledScript(Unknown Source)
      at org.jmol.script.ScriptManager.evalStringWaitStatusQueued(Unknown Source)
      at org.jmol.viewer.Viewer.evalStringWaitStatusQueued(Unknown Source)
      at org.jmol.script.ScriptQueueThread.runNextScript(Unknown Source)
      at org.jmol.script.ScriptQueueThread.run1(Unknown Source)
      at org.jmol.thread.JmolThread.run(Unknown Source)


      Stack trace for Chimera:
      ERROR: jalview.bin.Jalview - Couldn't open /var/folders/yk/7sbd4m7x5gbf5_lx4kz8rd99t8z5dm/T/jalview2451205814476899932.xml in Chimera viewer!
      java.lang.ArrayIndexOutOfBoundsException: -2
      at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:521)
      at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:323)
      at jalview.gui.ChimeraViewFrame.run(ChimeraViewFrame.java:861)
      at java.lang.Thread.run(Thread.java:745)
      ERROR - Couldn't open /var/folders/yk/7sbd4m7x5gbf5_lx4kz8rd99t8z5dm/T/jalview2451205814476899932.xml in Chimera viewer!
      java.lang.ArrayIndexOutOfBoundsException: -2
      at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:521)
      at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:323)
      at jalview.gui.ChimeraViewFrame.run(ChimeraViewFrame.java:861)
      at java.lang.Thread.run(Thread.java:745)

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              tcnofoegbu Tochukwu Charles N Ofoegbu
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                Dates

                Created:
                Updated:
                Resolved: