Tuesday 1 September 2009

xia2 0.3.0.3

Hi Folks,

A release update, 0.3.0.3 which includes a number of changes and very important bug fixes. Here are the main changes:

Changes since 0.3.0.0

* Now automatically determine the number of available processor cores.
* Implemented check for centring of crystallographic basis from autoindexing.
* Started to use CCTBX - this will be bundled with the release from now on...
* Now runs "smart scaling" i.e. will customise the scaling model used to the data. This can seriously improve the xia2 run time in cases where some of the default scaling models do not converge.
* Now also includes running of CHEF for radiation damage, which will slice and dice your data into dose groups, then run a correctly time sequenced radiation damage analysis. N.B. for data measured in "dose mode" the doses will be scaled to < 1,000,000 to ensure that the output is tidy.
* Corner case of running XDS pipelines from data from a Rigaku setup. The low resolution was previously calculated to be 0.0! D'oh!
* Added access to reference reflection file functionality to the command line - -reference_reflection_file foo.mtz.
* Fixed the use of the -image command-line option. Now works.
* Removed all of the binaries from the distribution, so now you need to be using CCP4 6.1.0 or later!
* Will correctly handle reindexing with the 3d pipeline (XDS/XSCALE) with trigonal spacegroups and multiple sweeps. Many thanks to Wolfgang Kabsch for a lot of help with this.


As things stand I don't include CCTBX - so you will need to have this installed, information at http://cci.lbl.gov.

3 comments:

Graeme Winter said...

Annoyingly I forgot to test for windows in the Mosflm startup: Need to change:

diff -r1.284 -r1.285
301,303c301,308
< if not os.path.exists(os.path.join(
< os.environ['CCP4'], 'bin', 'ipmosflm')):
< raise RuntimeError, 'CCP4 mosflm binary missing'
---
> if os.name == 'nt':
> if not os.path.exists(os.path.join(
> os.environ['CCP4'], 'bin', 'ipmosflm.exe')):
> raise RuntimeError, 'CCP4 mosflm binary missing'
> else:
> if not os.path.exists(os.path.join(
> os.environ['CCP4'], 'bin', 'ipmosflm')):
> raise RuntimeError, 'CCP4 mosflm binary missing'

or - just remove this section of code :o)

Graeme Winter said...

Oh crikey. Same for pointless, no doubt also for other programs :o(

Graeme Winter said...

Have now patched the release...