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  1. Jalview
  2. JAL-2781

PDB entries with unobserved residues and negative residue numbers are incorrectly mapped

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.10.2b1, 2.10.2b2, 2.10.3
    • Fix Version/s: 2.10.4
    • Component/s: Structures
    • Labels:
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      Description

      Importing and showing PDB Entries with jumps in RESNUM fields (e.g. 4im2) yields a structure where C-terminal residues do not receive a feature colour and are not labelled / or side-chains made visible when moused over in the alignment view.

      added 4im2_missing.pdb to examples/testdata to demonstrate this. Issue is only seen with SIFTS mappings enabled - plain N&W mappings work fine. Removing the HEADER line from the PDB file, triggers N&W mapping only, so issue is definitely in the SIFTS mapping routine.

      Rather than fix the SIFTS mapping routine (which works fine for Uniprot<>PDB sequence relationships), in this case the problem is that sequences extracted from coordinate files (PDB, mmCIF, whatever) shouldn't need SIFTS mappings, so that code should never execute in those cases. Recommended fix is to recognise and create 1:1 mappings (by NW or otherwise) for sequences extracted from files corresponding to PDB entries (ie those which may also yield a SIFTS file).

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              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
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                Updated:
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