Wednesday, 30 September 2009

xia2- The FreeR release

New release, pretty minor except the FreeR calculations are much improved:

Changes since

* Now able to specify number or fraction of reflections assigned to the free set, rather than the default 5 percent.
* Added trap for sdcorrection not being refined in XDS correct if multiplicity rather low. Unusual case.
* Assigning a freer_file by definition sets this as an indexing reference and also copies the spacegroup assignment. This is what you would expect!

Changes since

* User now able to assign cell constants: use with great care, as there is little in the way of nonsense trapping. This may however be used to handle cases where the solution you want is monoclinic with a pseudo-orthorhombic lattice, where the default indexing would select a different setting. This will not currently work with a Mosflm indexer. Usage is:

-cell a,b,c,alpha,beta,gamma

and the correct symmetry should also be assigned. Can also assign USER_CELL a b c alpha beta gamma in the xinfo file.

Tuesday, 15 September 2009

xia2- (quiet) release

Small change which I would like kinda tested before this becomes a mainstream feature: ability to assign unit cell constants and symmetry to use on the command-line and (untested) xinfo file.

More information at:

N.B. this is not linked as the default xia2 page, will be no xia2bb announcement.

Tuesday, 1 September 2009


Hi Folks,

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

Changes since

* 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