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/XDS.py to add

'May 10, 2010'

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

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 http://www.nature.com/emboj/journal/v29/n2/abs/emboj2009352a.html.

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.

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I realised that the command-line argument documentation is (woefully) out of date.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...