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I realised that the command-line argument documentation is (woefully) out of date.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