Uploaded image for project: 'Jalview'
  1. Jalview
  2. JAL-2161

create representative sequence groups for identical chains in PDB files

    XMLWordPrintable

    Details

    • Type: New Feature
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: Structures
    • Labels:
      None

      Description

      Currently, Jalview treats each chain found in a PDB file as an independent sequence with a shared PDB ID. This is fine for distinct molecules, but doesn't make much sense for chains which have identical sequences, particularly if they are obligate oligomers.

      For PDB structures containing multiple identical chains, Jalview should show just the representative chains, in the same way that one Uniprot sequence corresponds to N-chains in a PDB structure (according to SIFTS mappings).

      It should also be possible to expand/collapse the chain representatives to show individual chains. This is because in many cases, although multiple copies of a biopolymer are present, they may not all have the same conformations or structural environments.

        Attachments

          Issue Links

            Activity

              People

              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
              Votes:
              0 Vote for this issue
              Watchers:
              1 Start watching this issue

                Dates

                Created:
                Updated: