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  1. Jalview
  2. JAL-2158

Extra residue sporadically appended to PDB Sequences parsed with JmolParser

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Trivial
    • Resolution: Unresolved
    • Affects Version/s: 2.10.0
    • Fix Version/s: None
    • Component/s: None
    • Labels:

      Description

      Extra residues from HETATM records are sporadically appended to PDB sequences imported via JmolParser. This occurs because the fix for JAL-2148 was computational and based on the assumption that HETATMs with resNum gap > 2 usually occurs after the 'TER' statement.

      However, on very rare occasions an exception to aforementioned assumption is encountered, resulting to extra residue(s) being appended to the end of the sequence. The 'TER' positions for the first and intermediate chains can be accurately determined, so this usually happens ONLY for the last chain of such PDB entries.

      Apart from the annoyance of having an extra unwanted residue appended to a sequence, there is no apparent side effect of this bug on the overall functionality of the system. The PDB entry 3GCH provides a good illustration for this bug.

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              Assignee:
              jprocter James Procter
              Reporter:
              tcnofoegbu Tochukwu Charles N Ofoegbu
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                Created:
                Updated: