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  1. Jalview
  2. JAL-2007

Use PDBe numbering for sequences extracted from PDB files

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      Description

      PDBResNum coordinate system is a String based numbering system which could literally hold any kind of value i.e. negative resNums, insertion codes, 'None', etc. While the PDBResNum fields (in combination with insertion codes) are guaranteed to be distinct, they should only be used for annotation purposes and not for positional mapping.

      The PDBe coordinate system (a.k.a. MSD numbering) refers to each distinct residue by its order (here distinct means a different resNum field, or a different insertion code).

      Currently Jalview creates sequences from an imported PDB file which have a 'Start' property derived from an integer value extracted from the ResNum field of the first residue in each chain. This causes problems in the UI and for some positional calculations when the extracted start coordinate is 0 or less.

      Recommendation: By default, Jalview should number sequences according to the PDBe numbering, which is a change in behaviour from previous versions. The ResNum and InsCode fields will still be visible via the PDBRESNUM features added to the sequence.

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              Assignee:
              jprocter Jim Procter
              Reporter:
              tcnofoegbu Tochukwu Charles N Ofoegbu
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