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  1. Jalview
  2. JAL-1824

problems with multiple chain pdbs

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Blocker
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.9
    • Component/s: Structures
    • Labels:
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      Description

      Odd things happen when you retrieve two multichain PDB structures and start to work with them in the same alignment.

      Step 1. Retrieve retrieve 1rgx and 3hmj
      (or any two proteins with more than two chains each)
      I had all the annotation options ticked and saw as expected several chains for both structures with annotation.

      Step 2. select all chains and use the '3d structure ...' dialog to open a jmol view with the 'Best quality' selection.
      - this step sort of works fine - though it would be useful to have the option of not attempting to superimpose chains, since that isn't always what one wants to do.

      Step 3. leave that view open and select ‘3d structure..’ for all selected sequences again but this time, go to ‘cached files’
      * You'll see that a second PDBEntry has been added to all the chains for each file indicating a mapping to the last chain in the file.
      * hitting the view button will now raise an exception:

      Exception in thread "AWT-EventQueue-0" java.lang.IndexOutOfBoundsException: Invalid index
      at javax.swing.DefaultRowSorter.convertRowIndexToModel(DefaultRowSorter.java:514)
      at javax.swing.JTable.convertRowIndexToModel(JTable.java:2642)
      at javax.swing.JTable.getValueAt(JTable.java:2717)
      at jalview.gui.StructureChooser.ok_ActionPerformed(StructureChooser.java:724)
      at jalview.jbgui.GStructureChooser$2.actionPerformed(GStructureChooser.java:206)
      at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
      at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2346)
      at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
      at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
      at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
      at java.awt.Component.processMouseEvent(Component.java:6525)
      at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
      at java.awt.Component.processEvent(Component.java:6290)
      at java.awt.Container.processEvent(Container.java:2234)
      at java.awt.Component.dispatchEventImpl(Component.java:4881)
      at java.awt.Container.dispatchEventImpl(Container.java:2292)
      at java.awt.Component.dispatchEvent(Component.java:4703)

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              Assignee:
              tcnofoegbu Tochukwu Charles N Ofoegbu
              Reporter:
              jprocter Jim Procter
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                Created:
                Updated:
                Resolved: