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  1. Jalview
  2. JAL-2213

"view 3d structure" maps spurious structures to sequences

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    Details

    • Type: Task
    • Status: Closed
    • Priority: Blocker
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.10.0
    • Component/s: Structures
    • Labels:

      Description

      Something seems to have broken with the structure chooser dialog.

      1. import example feredoxin alignment (uniref50.fa)
      2. select all sequences
      3. right click and select 'view 3d structure...'
      4. 4 structures should be highlighted. Hit view to view them.

      The chooser will say that dbrefs are being retrieved for 4 sequences. After this, a 'Sequence names updated' window appears. Contents are:
      Your sequences have been verified against known sequence databases. Some of the ids have been
       altered, most likely the start/end residue will have been updated.
       Save your alignment to maintain the updated id.

      Q93XJ9_SOLTU SEQUENCE NOT %100 MATCH
      FER1_SPIOL SEQUENCE NOT %100 MATCH
      FER2_ARATH SEQUENCE NOT %100 MATCH
      FER1_MAIZE SEQUENCE NOT %100 MATCH
      Q93XJ9_SOLTU SEQUENCE NOT %100 MATCH
      FER1_MAIZE SEQUENCE NOT %100 MATCH
      FER1_SPIOL SEQUENCE NOT %100 MATCH
      FER2_ARATH SEQUENCE NOT %100 MATCH
      FER1_MAIZE HAS 52 PREFIXED RESIDUES COMPARED TO PDB
      FER1_MAIZE HAS 0 PREFIXED RESIDUES COMPARED TO PDB
      FER1_MAIZE SEQUENCE NOT %100 MATCH
      FER1_MAIZE SEQUENCE NOT %100 MATCH
      FER1_MAIZE SEQUENCE NOT %100 MATCH
      FER1_MAIZE SEQUENCE NOT %100 MATCH
      FER1_MAIZE SEQUENCE NOT %100 MATCH
      FER1_MAIZE SEQUENCE NOT %100 MATCH
      FER1_MAIZE SEQUENCE NOT %100 MATCH
      FER1_MAIZE SEQUENCE NOT %100 MATCH
      FER1_MAIZE SEQUENCE NOT %100 MATCH
      FER1_MAIZE SEQUENCE NOT %100 MATCH
      FER1_MAIZE SEQUENCE NOT %100 MATCH
      FER1_MAIZE SEQUENCE NOT %100 MATCH
      FER1_SPIOL SEQUENCE NOT %100 MATCH

      Eventually structure view appears, but superposition does not reliably occur.

      Looking at the RESNUM features, FER1_MAIZE seems to have mappings to additional structures, even though they are not actually viewed.

      If 'Fetch db refs->Standard DBs' is performed before step 2, then no 'Sequence names updated' window is shown, and no spurious PDB mappings appear on the alignment.
       

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              jprocter Jim Procter
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                Created:
                Updated:
                Resolved: