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.

Warning: Deprecating Things

Trying to clean up the interface which will in the long run help the documentation, but in the mean time will make some warnings... if you see

Warning: -spacegroup option deprecated: please use space_group='P422' instead

Warning: -resolution option deprecated: please use d_min=1.5 instead

Don't panic - this is to be expected - but you may want to change the way you run xia2 or your scripts. More of a warning for beamline / automation people! The outcome of this should however be automated generation of command-line documentation and the ability to keep "recipes" for running xia2 in tidy files....

Corner case bug spotted (thanks Luca Jovine)

If you

• use xinfo files
• use -2d
• do not set START_END

you may find you get a weird complaint about detector_class.

This is easily resolved for the moment by setting START_END to correspond to the first and last image you want to process... I need to fix this ;o) it did not used to work like this...

Thanks to Luca for pointing this out and patience in debugging...

xia2 0.3.8.0 released

Major changes:

Changes since 0.3.7.0: Added DIALS (mostly)

• Added support for DIALS software. Thanks to Richard Gildea at Diamond for most of the work.
• Create AIMLESS xml output; useful for displaying results through alternative interfaces.
• Squashed nasty bug where input spacegroup set to e.g. I222 but pointgroup derived to be P222 (think this one was reported a while back but I could not find the source at the time... sorry!)
• Squashed some other bugs which have appeared in recent history.

Changes since 0.3.6.3: Bug fixes, add CC-half, removing Scala.

• -cc_half 0.5 (say) resolution limit criterion available - suggest set -misigma 0.5 -isigma 0.5 or similar with this.
• -freer_file where free flag != FreeR_flag fixed.
• Massively trimmed all of the command line options for the pipelines and removed the use of Scala in all pipelines, replaced with Aimless (not before time!) This means that -3dr and so forth will no longer work so please use -2d, -3d, -3di etc.
• -phil command line option now deprecated: phil parameters passed on the command-line will be respected, also phil files, without this clue
• Parallelisation options: can now cleanly process sweeps from one wavelength in parallel (to aid with multi-crystal data sets) use Phil parameters multiprocessing.njob=4 multiprocessing.nproc=12 multiprocessing.mode=parallel (say) to allow processing four sweeps at a time each using 12 cores. This multi-sweep parallelisation is probably most useful in conjunction with the Phil parameter multiprocessing.type=qsub, which tells xia2 to submit jobs to a cluster, with each job using nproc cores.

Running xia2 from the GUI

A question to xia2.support last week indicated that the documentation has no information on how to run xia2 from the GUI in ccp4i. While this is rather old and cumbersome, if you are on Windows it is close to your only option.

Here is a short guide.

Obviously you need to select xia2 GUI from the main CCP4i:

This will pop up something which looks like this:

Now confusion reasonably starts: where to put in the image information? The GUI works like the xinfo files specified in the manual (http://www.ccp4.ac.uk/newsletters/newsletter48/articles/Xia2/manual.pdf) so you first actually need to define what wavelengths you have (i.e. SAD, native etc.) then associate images with these wavelengths:

What I have done here is create a new data set Demo / Native and added a Native wavelength to it, which I have given images insulin_1_001.img and onwards in /data1/gw56/demo. Hitting "run" will now process the data with xia2 / Mosflm. To use XDS select "run processing with XDS" under key parameters.

Two comments: this GUI needs to be updated, and the manual needs to include the GUI! Sorry for this omission.