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  1. Jalview
  2. JAL-4577

structures with no biopolymer chains generate (non-fatal) exceptions when mapping them to a sequence

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: 2.11.5.0, 2.11.4.2
    • Fix Version/s: None
    • Component/s: Structures
    • Labels:
      None

      Description

      Import a structure onto a sequence which has no biopolymer - such as the attached ligysis 'prepared' ligand interaction file: 'https://www.compbio.dundee.ac.uk/ligysis/files/2g87_A_trans.cif?prot_id=P02699&seg_id=1'

      Jalview generates exceptions like:
      ERROR - Falling back on Needleman & Wunsch alignment
      Exception in thread "Thread-26" java.lang.IndexOutOfBoundsException: fromIndex < 0: -1
      at java.base/java.util.BitSet.checkRange(BitSet.java:363)
      at java.base/java.util.BitSet.set(BitSet.java:482)
      at jalview.structure.AtomSpecModel.addRange(AtomSpecModel.java:80)
      at jalview.structures.models.AAStructureBindingModel.addAtomSpecRange(AAStructureBindingModel.java:1509)
      at jalview.structures.models.AAStructureBindingModel.buildColoursMap(AAStructureBindingModel.java:1438)
      at jalview.structures.models.AAStructureBindingModel.colourBySequence(AAStructureBindingModel.java:1194)
      at jalview.structures.models.AAStructureBindingModel.updateColours(AAStructureBindingModel.java:1322)
      at jalview.gui.AppJmol.showFilesInViewer(AppJmol.java:384)
      at jalview.gui.AppJmol.run(AppJmol.java:281)
      at java.base/java.lang.Thread.run(Thread.java:829)

      generated by command: java -jar build/libs/jalview-all-TEST-j11.jar --open ~/Documents/Jalview/Javier/LIGYSIS-June-25/P02699_1_rf.sto --seqid=OPSD_BOVIN --structure ./2g87_A_trans.cif --allstructures ./2g87_A_trans.cif --allstructuresviewerid=jmol --nosuperpose

      (build is JAL-4354 - import multiple strucures from URL)

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            Assignee:
            jprocter James Procter
            Reporter:
            jprocter James Procter
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              Dates

              Created:
              Updated: