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  1. Jalview
  2. JAL-1333

Support UCSF Chimera as a linked Structure Viewer

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    • Epic Name:
      UCSF Chimera

      Description

      UCSF Chimera has a scripting interface that would allow Jalview to interact with it in the same way that Cytoscape allows users to view structures linked with residue interaction networks.

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          jprocter Jim Procter added a comment -
          currently available as a prototype in the 'nextrel' build (Release_2_8_2_Branch)

          Enable chimera as the structure viewer by adding the line

          STRUCTURE_DISPLAY=CHIMERA

          to your ~/.jalview_properties before launching Jalview.

          You'll also need to install chimera, and make sure Jalview can find it. Search paths are hardwired here:
          http://source.jalview.org/gitweb/?p=jalview.git;a=blob;f=src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java;hb=5776f8fbf1b6c23caec6cd23d76902d228119332#l865

          Ideally, this routine would also search a set of user configured chimera paths (e.g. from jalview.bin.Cache.getDefault("CHIMERA_PATHS"))


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          jprocter Jim Procter added a comment - currently available as a prototype in the 'nextrel' build (Release_2_8_2_Branch) Enable chimera as the structure viewer by adding the line STRUCTURE_DISPLAY=CHIMERA to your ~/.jalview_properties before launching Jalview. You'll also need to install chimera, and make sure Jalview can find it. Search paths are hardwired here: http://source.jalview.org/gitweb/?p=jalview.git;a=blob;f=src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java;hb=5776f8fbf1b6c23caec6cd23d76902d228119332#l865 Ideally, this routine would also search a set of user configured chimera paths (e.g. from jalview.bin.Cache.getDefault("CHIMERA_PATHS"))

            People

            • Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              jprocter Jim Procter
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              • Created:
                Updated: