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  1. Jalview
  2. JAL-1622

T-Coffee alignment score example doesn't superpose in chimera

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Critical
    • Resolution: Fixed
    • Affects Version/s: 2.8.2, 2.8.2b1
    • Fix Version/s: 2.9
    • Component/s: Structures
    • Labels:
      None

      Description

      The t-coffee example file (http://source.jalview.org/gitweb/?p=jalview.git;a=blob_plain;f=test/jalview/io/tcoffee.fasta_aln;hb=4cf475567facc11b4be0f6e0849c73cbfc98508d) doesn't seem to be superposed when Chimera is chosen as a structure viewer. Possibly related to the multiple models problem (JAL-1533).

      To reproduce:
      1. import the tcoffee.fasta_aln example file.
      2. Fetch DB References->PDB to retrieve structures (this is slow - see JAL-1621)
      3. try to do 'View all 8 structures' with Chimera selected as viewer.

      In Jalview 2.8.1b1, the superpose succeeds. In 2.8.2 - with Jmol selected as a viewer, it also succeeds.

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          related with

          Bug - A problem which impairs or prevents the functions of the product. JAL-1851 PDB sequence mapping wrong for 1PHT if 'Trim retrieved sequences' is selected

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-1757 Jmol alignment incorrect if PDB file has alternate CA positions

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Closed

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated:
                Resolved: