Uploaded image for project: 'Jalview'
  1. Jalview
  2. JAL-2691

Not all chains are mapped when multimeric assemblies are imported via CIF file

    XMLWordPrintable

    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.10.2
    • Fix Version/s: 2.10.2b1
    • Component/s: Structures
    • Labels:
      None

      Description

      Multimeric assemblies (e.g. https://www.ebi.ac.uk/pdbe/entry/pdb/2pjy/analysis#assembly_1 ) contain multiple copies of the same chains found in the asymmetric unit. Importing an assembly as mmCIF results in all these chains being shown as sequences, but when the structure is displayed (in Jmol), all the copies of a chain are only mapped to one of the 3D coordinate sets.

      This shouldn't happen, because the 'PDBEntry' instance created on each sequence should specify the chain's chain code as well as the mmCIF file that the chain came from.

        Attachments

          Issue Links

          duplicates

          Bug - A problem which impairs or prevents the functions of the product. JAL-2225 structure viewer doesn't get mappings for all chains when viewing 'cached' structures

          • Major - Major loss of function.
          • Closed
          related with

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2694 detect and map duplicate chains for biological assemblies

          • Major - Major loss of function.
          • Open

          Bug - A problem which impairs or prevents the functions of the product. JAL-3355 Not all structure chain mappings restored from Jalview project

          • Critical - Crashes, loss of data, severe memory leak.
          • In Progress

          Bug - A problem which impairs or prevents the functions of the product. JAL-3489 Not all chains mapped for multimeric structure loaded from file

          • Major - Major loss of function.
          • Ready for testing

            Activity

              People

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

                Dates

                Created:
                Updated:
                Resolved: