Free set reflections

Following a question on the CCP4 BB about how many reflections to set aside for the free set (i.e. the FreeR_flag column xia2 adds to the MTZ file) it looks like the conclusion is "data processing packages should not do this" - OK, no problem. That makes the original question go away; always good...

Am keen to now remove this capability from xia2; comments to xia2.support@gmail.com please!

New ability to specify multiple directories or images via command line

As of the latest DIALS/xia2 nightly build (2015-04-24 onwards, available from http://dials.diamond.ac.uk/diamond_builds/), xia2 now supports passing multiple directories or images via the command line, e.g.:

xia2 -dials /path/to/directory1 /path/to/directory2
xia2 -dials image=/path/to/directory1/image_1_0001.cbf image=/path/to/directory2/image_2_0001.cbf

Nasty subtle bug with latest XDS

The default behaviour of XDS with REFINE= in the CORRECT step appears to have changed, which highlights a long-standing bug in xia2. The bug is that the REFINE= card was incorrectly formatted, which some of you have noticed in that the summary from the second pass of integration looks much more nasty than the first pass. This apparently was not a problem with the older version of XDS (before 1mar2015). I had initially (incorrectly) blamed the new version of XDS but Richard Gildea found the underlying bug.

A new version of xia2 will be available already with these fixes in as part of the DIALS nightly builds. The fix is however a one-liner:

In

xia2/Wrappers/XDS/XDSCorrect.py

change

'REFINE(CORRECT)=%s\n' %self._params.refine)

to 

'REFINE(CORRECT)=%s\n' %' '.join(self._params.refine))

(amazing how much effect these little changes can make!) We are in the process if instigating a more thorough testing procedure which will ensure errors like this do not occur again.

Experimental xia2/DIALS installers

We are currently testing new xia2/DIALS installers for mac/linux which provide a self-contained xia2/cctbx/DIALS installation. Instructions on downloading and installing these bundles can be found at http://dials.diamond.ac.uk/doc/installation.html. Once installed, simply sourcing the dials_env.sh script in the installation directory will make available all xia2 and DIALS commands in the current terminal. You will also need CCP4 available - but make sure to source the dials_env.sh script after the CCP4 setup script. You can also try out the new xia2 -dials option, which will use the new software DIALS to index and integrate your data, followed by scaling and merging with Aimless. As always, please send any feedback to xia2.support@gmail.com.

New wavelength_tolerance parameter

A common problem when processing multiple datasets with xia2 is when a small difference in the wavelength recorded in the image headers causes the sweeps to be grouped into more than one wavelength, when the desired outcome was for them to be processed as a single wavelength. Previously it was necessary to manually edit the .xinfo file to tell xia2 to process them as a single wavelength. Now we have added a new parameter wavelength_tolerance (default=0.0002 Å) which you can use to control whether or not different wavelengths get grouped together as a single wavelength.

Example usage:

xia2 -3dii wavelength_tolerance=0.001 /path/to/images/

xia2 CCTBX challenges? Try installing DIALS!

If you are having problems with xia2, particularly from subversion, you may find it useful to pull a DIALS build from e.g. http://dials.diamond.ac.uk/builds and install this so that xia2 picks up CCTBX from here. This will be up to date and should work, and also includes a collection of very useful tools. It will generally include support files for all of the most recent detector installations.

The DIALS project (see e.g. http://dials.diamond.ac.uk) is a collaborative project to develop a new integration package and is supported by xia2 via xia2 -dials: if you are feeling brave you can try using this for processing your data in place of e.g. XDS.

Any problems with xia2 please contact xia2.support@gmail.com. For issues with DIALS please contact dials-support@lists.sourceforge.net.

Bug found: error parsing Aimless XML file for MAD data

Found a bug in the parsing code for Aimless XML which only tries to extract the first data set (not enough testing, fail) only for MAD data sets... This will give an error something like:

Reindexing to first spacegroup setting: P 41 21 2 (h,k,l)
Status: error "('AUTOMATIC', 'DEFAULT', 'WAVE2')"

I have now fixed this in revision 4879, now testing prior to updated release... sorry for any inconvenience.