Tuesday, 15 March 2011

Much belated xia2 release

In the usual place, changes since
  • Support for new XDS build.
  • Small bug fix / improvement in XDS indexer implementation.
  • Capability to ptovide refined experimental geometry via XDS GXPARM.XDS - useful for polycrystal data reduction.
  • Now check what you tell the program, viz:
    gw56@ws050 nonsense]$ xia2 -3d -nonsense /data/gw56/dl/Cowan/Insulin/insulin/
    Traceback (most recent call last):
      File "/home/gw56/svn/xia2/Applications/xia2.py", line 45, in 
        from xia2setup import write_xinfo
      File "/home/gw56/svn/xia2/Applications/xia2setup.py", line 35, in 
        from Handlers.CommandLine import CommandLine
      File "/home/gw56/svn/xia2/Handlers/CommandLine.py", line 1513, in 
      File "/home/gw56/svn/xia2/Handlers/CommandLine.py", line 349, in setup
        raise RuntimeError, nonsense
    RuntimeError: Unknown command-line options: -nonsense
    and complain if you type in something xia2 does not understand.
  • Removed a lot of cruft from the xia2 code base in preparation for some more substantial refactoring.
  • Found bug which meant that the labelit beam centre computed in the setup phase was not used - mostly this is not important, unless you are using -3dii.
  • Added -ice command-line argument, which will exclude measurements from regions which are typically where ice rings land. Will need to add more subtle mechanism which will allow specific regions to be excluded.
  • Specifying resolution with 3d(r) pipeline now works correctly.
  • Removed XDS version check by default, which was annoying every new year. If you would like to check that the XDS version is explicitly supported, add -check_xds_version to the command-line.
  • Added table of scala runs to sweep name in the debug output, helpful for reviewing in polycrystal data reduction cases.
  • Mosaic spread used from Mosflm is now average of all images, not the first or last image.
  • Fixed header reading for new Pilatus instruments at DLS and elsewhere.
  • Added capacity to pass in known globally postrefined experimental setup via -xparm GXPARM.XDS, only useful with XDS processing pipelines.
  • Removed use of ccp4 printpeaks tool, which crashes on new pilatus images, replace with Mosflm for the moment. Move to replacement with labelit code at later stage planned.

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