Sunday, 23 May 2010

Latest XDS

Just found out that there is a new version of XDS out there - it appears to work fine with xia2, but you will need to do the usual edits of ${XIA2_ROOT}/Wrappers/XDS/ to add

'May 10, 2010'

to the list of supported versions. Next version of xia2 will include this.

Wednesday, 19 May 2010

Multi-crystal progress

So - hooda thunkit - it turns out that this is hard. Nevertheless it's going somewhere though there's a hint of the whac-a-mole debugging going on here. At the moment it's working towards handling the trying-to-assemble-a-dataset-from-dozens-of-crystals turf - so assuming a (small) handful of degrees of data from each - along the lines of

Most interesting part of this is that all of the program steps need to be hardened against what would usually be fatal errors - negative scales and the like - and just plough on regardless. An interesting paradigm.

Wednesday, 5 May 2010

Summary of command line options

I realised that the command-line argument documentation is (woefully) out of date. Until I think of a better way to handle the command line (perhaps using Phil from CCTBX) this will be hard to correct. However, here are the current list of "useful" options:

  • -debug
  • -interactive (for selecting images for autoindexing with Mosflm, Labelit)
  • -2d (old mosflm / scala)
  • -2dr (new mosflm / scala - recommended)
  • -3d (old XDS / XSCALE)
  • -3dr (new XDS / XSCALE) 
  • -3dii / 3diir (as -3d/3dr, using all frames for autoindex)
  • -indexer -integrater -scaler - manually specify the integrater, indexer, scaler to use
  • -image /process/this/sweep
  • -beam x,y (Mosflm reference frame)
  • -atom Se (say) - switch on separation of anomalous pairs
  • -project foo
  • -crystal bar
  • -xinfo project.xinfo
  • -parallel N (set to 1 to swtich off parallel processing)
  • -xparallel N (use multiple machines for XDS - requires working forkintegrate scripts)
  • -spacegroup P212121
  • -resolution 2.8
  • -freer_file free.mtz
  • -reference_reflection_file reference.mtz (to get standard indexing, will copy spacegroup, free column)
That's all for the moment - most of these I never use so I had to consult the code...