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  1. Jalview
  2. JAL-2157

Cannot import PDB 4uj3

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    Details

    • Type: Bug
    • Status: Resolved
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: 2.10.0
    • Fix Version/s: None
    • Component/s: Structures
    • Labels:

      Description


      Regression on PDB import functionality - originally noticed when trying to view PDB structures for ENSEMBL locus view.

      1. Import 4uj3 via PDB fetcher
      --> successful in 2.9.0b2 - fails in 2.9.1 develop
      2. View [cached] structure for all chains
      --> 2.9.0b2
       . cached view results in chains mapped as extracted from file. Unmapped regions are insertions (presumably)

      3. I tried saving a project from 2.9.0b2 and importing it to 2.9.1 develop (attached).
      --> Project imported in to 2.9.1 fine
      4. Repeat step 2: view cached structure
      --> 2.9.1 develop - fails to get chain mapping correct

      Console output:
      Could not get source DB Ref
      Could not get source DB Ref
      Getting mapping for: 4UJ3|A : seq- PDB|4uj3|4UJ3|A
      Getting mapping for: 4UJ3|B : seq- PDB|4uj3|4UJ3|B
      Getting mapping for: 4UJ3|C : seq- PDB|4uj3|4UJ3|C
      Could not get source DB Ref
      Could not get source DB Ref
      Could not get source DB Ref
      Could not get source DB Ref
      Could not get source DB Ref
      Getting mapping for: 4UJ3|D : seq- PDB|4uj3|4UJ3|D
      Getting mapping for: 4UJ3|E : seq- PDB|4uj3|4UJ3|E
      Getting mapping for: 4UJ3|F : seq- PDB|4uj3|4UJ3|F
      Getting mapping for: 4UJ3|G : seq- PDB|4uj3|4UJ3|G
      Could not get source DB Ref
      Could not get source DB Ref
      Could not get source DB Ref
      Could not get source DB Ref
      Could not get source DB Ref
      Getting mapping for: 4UJ3|H : seq- PDB|4uj3|4UJ3|H
      Getting mapping for: 4UJ3|I : seq- PDB|4uj3|4UJ3|I
      Getting mapping for: 4UJ3|J : seq- PDB|4uj3|4UJ3|J
      Getting mapping for: 4UJ3|K : seq- PDB|4uj3|4UJ3|K
      Getting mapping for: 4UJ3|L : seq- PDB|4uj3|4UJ3|L
      Could not get source DB Ref
      Could not get source DB Ref
      Could not get source DB Ref
      Could not get source DB Ref
      Could not get source DB Ref
      Getting mapping for: 4UJ3|M : seq- PDB|4uj3|4UJ3|M
      Getting mapping for: 4UJ3|N : seq- PDB|4uj3|4UJ3|N
      Getting mapping for: 4UJ3|O : seq- PDB|4uj3|4UJ3|O
      Getting mapping for: 4UJ3|P : seq- PDB|4uj3|4UJ3|P
      Getting mapping for: 4UJ3|Q : seq- PDB|4uj3|4UJ3|Q
      Could not get source DB Ref
      Could not get source DB Ref
      Could not get source DB Ref
      Could not get source DB Ref
      Could not get source DB Ref
      Could not get source DB Ref
      Getting mapping for: 4UJ3|R : seq- PDB|4uj3|4UJ3|R
      Getting mapping for: 4UJ3|S : seq- PDB|4uj3|4UJ3|S
      Getting mapping for: 4UJ3|T : seq- PDB|4uj3|4UJ3|T
      Getting mapping for: 4UJ3|U : seq- PDB|4uj3|4UJ3|U
      Getting mapping for: 4UJ3|V : seq- PDB|4uj3|4UJ3|V
      Getting mapping for: 4UJ3|W : seq- PDB|4uj3|4UJ3|W
      Getting mapping for: 4UJ3|X : seq- PDB|4uj3|4UJ3|X
      network: Connecting socket://127.0.0.1:61367 with proxy=DIRECT
      Could not get source DB Ref

      View mapping shows chain/chain mapping has been corrupted:

      Sequence ⟷ Structure mapping details
      Method: inferred with Needleman & Wunsch alignment
      PDB Sequence is :
      Sequence = RDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTIKAQIWDTAGLERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIYRIVSQK
      No of residues = 176

      Score = 8790
      Length of alignment = 175
      Sequence PDB|4uj3|4UJ3|D : 5 - 179 (Sequence length = 175)
      Sequence 4UJ3|A : 4 - 179 (Sequence length = 176)

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated: