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  1. Jalview
  2. JAL-2780

PDB entries with negative residue numbers are incorrectly annotated

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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 a PDB with RESNUM fields (e.g. 4im2) containing a negative number yields a sequence where the 0'th residue's sequence features become non-positional RESNUM annotation rather than positional. Mapping to 3D coordinates is also affected - only positive numbered positions are coloured and linked to the sequence in the alignment.

      Observed with both SIFTS and Needleman and Wunsch - added examples/testdata/4IM2_nterm.pdb for unit tests

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          related with

          Bug - A problem which impairs or prevents the functions of the product. JAL-2781 PDB entries with unobserved residues and negative residue numbers are incorrectly mapped

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-2224 Structure's extracted sequence's start/end numbering misleading

          • Major - Major loss of function.
          • Open

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2007 Use PDBe numbering for sequences extracted from PDB files

          • Major - Major loss of function.
          • In Progress

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