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I realised that the command-line argument documentation is (woefully) out of date.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

xia2 0.3.1.6 released

Much delayed release, now seems to be working well. Also includes support for recent XDS &c.

Sorry for the delay, thankyou for your patience.

Changes since 0.3.1.0

• Fixed bug where the resolution limit was not reset in an indexer solution elimination.
• Added support for XDS from Dec 09.
• Fixed some of the issues found in the resolution limit determination when processing low resolution data.
• Fixed use of I/sigma limit assignment.
• Added command-line control of individual indexer, integrater, scaler.
• Repaired regular expression for image matching, to cope with images where there is e.g. 3.5 in the template. This was previously misinterpreted as an image name of the form setup.NNNN.
• Implemented new resolution limit pipelines, based on new merging code to give more robust control: -2dr and -3dr (recommended.) Fine control over the choices can be made using the -isigma, -misigma, -completeness and -rmerge command line options.
• Added interactive indexing mechanism, where user can assign images to use for autoindexing, e.g.:

  Existing images for indexing: 1, 90, 180
  >1, 60, 120, 180
  New images for indexing: 1, 60, 120, 180
   

  Assign -interactive on the command line (Mosflm and Labelit indexers)

Multi crystal data analysis... started!

Ok, so have finally made a start on the multi-crystal analysis (the resolution limits stuff will be released soon, after some more testing) and crikey it's gonna be fun. Should get the ol' grey cells working though.

Initial plans are to build this through the xinfo hierarchy - deifining multiple crystals within the same project - but if you have a better idea for the interface please shout!

xia2 for small molecule data

Have wondered about extending xia2 to work with data from small molecule crystals - a few of the assumptions would need to change, not least in the indexing, scaling and description of the geometry. However, should be doable.

Interested? If so please drop me a line.

Resolution limit overhaul...

Not before time, have finally overhauled the resolution limit calculations. At the moment they rely on a separate piece of code to merge the reflections after scaling, and some curve fitting to decide some limits. The defaults are:

- I/sigma > 1
- Mn(I/sigma) > 2
- completeness anything
- Rmerge anything

And are accessed through the command line as -isigma -misigma -completeness [0,1] -rmerge. This will form the kernel of the next release 0.3.1.5. N.B. to access the new resolution limit code, use pipelines -2dr -3dr in place of -2d -3d. Worth it.

Also includes: changes to workflow for these pipelines, use of Scala sd correction automation stuff, -interactive mode for autoindexing with Mosflm / Labelit to allow guidance of image selection.

xia2 moves to sourceforge.net

Now seems to be working right, and also appears to have managed to include the history. Access from the command-line via:

svn co https://xia2core.svn.sourceforge.net/svnroot/xia2core/trunk/xia2core xia2core
svn co https://xia2.svn.sourceforge.net/svnroot/xia2/trunk/xia2 xia2

which will give you access to the current state of the trunk - no guarantees! Can also download a tarball of the trunk in a similar way. I will now be using this as the primary repository - only reason to move may be if sourceforge.net proves unreliable - unlikely.

If you'd like to have write access, to contribute to the development, please shout!