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  1. Jalview
  2. JAL-4015

Cached PDB structure for FER1_SPIOL in the example project doesn't open in ChimeraX or PyMOL

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Critical
    • Resolution: Unresolved
    • Affects Version/s: 2.11.2.2
    • Fix Version/s: 2.11.3
    • Component/s: Structures
    • Labels:
      None
    • Environment:
    • Urgency:
      Urgent

      Description

      Steps to replicate:
      Open a release version of Jalview (e.g. 2.11.2.2) and find FER1_SPIOL in the example_2_7.jar.
      Right click on the label to choose "3D Structure Data..." and try and open the cached structure file (this is default behaviour) in ChimeraX (have structure viewer preconfigured, or PyMol).
      The structure viewer opens but does not open the structure. In ChimeraX's case no error is displayed.

      I am 99% certain that this is because the cached file (saved in /var/...) has a ".txt" extension and not (something like) ".cif" or ".pdb".

      Fetching the same structure file anew works because this gets cached with a ".cif" file extension.

      Steps to fix -- I'm not certain if the .txt filename caching happens because of the project file or newer version of Jalview caching, a mixture of both (or if newer versions of ChimeraX don't work out the content of .txt), but changing the behaviour to cache the file with a .cif or .pdb extension should fix this problem.

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            Assignee:
            jprocter Jim Procter
            Reporter:
            soares Ben Soares
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              Created:
              Updated: