Monday, 3 December 2012

Checking out xia2

Hi Folks,

Some have tried to use the subversion version of xia2 and found the commands don't work as they need a password - this is correct! Here are the correct commands:

svn checkout xia2core
svn checkout xia2

Best wishes all,


Update: kudos to JPT for sending correction to above commands.

Wednesday, 14 November 2012

xia2 release

Can be found in the usual place - updates:

Changes since
  • -hdr_in mode - pass in text file containing image header. Can also generate this file with xia2 with -hdr_out example.hdr
  • -xparm_ub mode for XDS processing only, provide a UB matrix (XDS XPARM file) to match the orientation to: primarily useful if you record data from several regions on a sample, and the sample has close-to symmetry (i.e. you almost certainly don't need this)
  • Removed usage of BINSORT_SCR as this is being deprecated by CCP4.
  • Allow Phil overrides on selection of autoindexing solutions, where indexing can give large variations in unit cell constants (e.g. low resolution virus data)
  • Properly set the resolution in CAD copying free R flags.
  • Allow access to profile grid size through the Phil interface: xds.parameter.profile_grid_size = 13, 13
  • Implement TRUSTED_REGION through Phil as suggested by Luca Jovine
  • Updates to process simulated data from SIM_MX
  • More measures of anomalous signal in output.
  • Corrected citations in output
  • Replaced TRUNCATE with CTRUNCATE
Download has also slimmed down a little, as a lot of cruft has been removed. As always, please shout to if you have any trouble.

Friday, 26 October 2012

xia2 svn "upgrade" on

If anyone uses xia2 from subversion, this is important. Following an upgrade of xia2 on the svn checkout instructions have changed - I received this:

Your cloned repository code in project xia2core is now ready for use.

Old repository url:

New repository checkout command: svn checkout --username=graeme_winter svn+ssh:// xia2core-code

You and any other developers should do a fresh checkout using the new repository location.

Once I have done this process for myself I will post some new xia2 / svn instructions.

Tuesday, 20 March 2012

Nasty bug spotted: resolution in sweep block, -3d

It seems some of the refactoring I did recently left a bug lying around if you put a resolution in a sweep block e.g.



DIRECTORY /Users/graeme/data/12847
IMAGE 12847_4_001.img
EPOCH 1106329906
BEAM 109.02 105.01

DIRECTORY /Users/graeme/data/12847
IMAGE 12847_5_001.img
EPOCH 1106332719
BEAM 109.04 105.01


This has now bee squashed and will be mended in Symptom is endless scaling loop talking about Resolution 1.0.

Wednesday, 7 March 2012

Manual in development

Busy writing a manual - if you think you would like to help debug it, please drop me a line. If you're really keen you can check it out of the xia2 subversion, it's in there.

Monday, 27 February 2012

xia2 0.3.4 release

xia2 is now available from the usual places, changes below. I would now suggest people get Aimless (and a new Pointless) from Phil Evans:

and run -2da / -3da / -3daii

As always, any problems please drop an email to


Changes since
 - Use Phil to override XDS parameters.
 - Mended issue on OS X Lion with default -parallel (was coming out at 1)
 - Use Pointless in place of Reindex; Aimless in place of Scala; no limit to number of batches which can be processed.

Changes since

 - Fixed bug in polarization correction vector for Pilatus data.
 - Fixed bug relating to assigning spacegroup on command-line.
 - Begun work on supporting Pilatus 300K for small molecule crystallography. Have now successfully processed data from Diamond Light Source beamline I19 EH2. N.B. Only works -3dii!

Friday, 24 February 2012

Just cooking up for a release - 0.3.4

Which should be a useful one... however appears to have disappeared for a moment so it'll have to wait. Hopefully today!

Where possible remove limitations

So, have been using Aimless for a little while now, which does not need recompiling for lots of batches. Using this with Reindex replaced with Pointless means you can now process data sets with many many images. By way of a test case: 70 180 degree sweeps @ 1 degree / frame from a small molecule crystal processed fine. This is most likely to be useful with Pilatus data. Would suggest -3da (and a local install of recent Pointless / Aimless versions) to do this kind of thing. Will be released shortly unless you want to get it from svn.

Wednesday, 22 February 2012

OS X Lion (ii)

OK, now the machine is working and crikey it works very well. First time I have had a laptop which is quicker at parallel processing than my 8-core Xeon workstation. Nice.

Unfortunately spotted some bugs in the xia2 implementation on there. Seems that they have changed the output on the program I used to guess the number of cpu's so they were not all being used. Now they will be.

Tuesday, 21 February 2012

Making OS X Lion work

Luckily just got my hands on a new and funky macbook pro with OS X Lion to help with user support. Here's how to turn it from a pretty paperweight into a computer (i.e. install compilers)

(1) install your updates to latest OS X
(2) get apple ID for app store
(3) install XCode from app store
(4) register as apple developer
(5) XCode -> preferences -> download (add command-line tools) -> install

Tuesday, 24 January 2012


One of the most common (and it has to be said, most reasonable) complaints I have heard about xia2 is the absence of the manual. I am now working on this, to be included in the next release of the program.

The first version will no doubt be rather rough, so I will welcome any feedback on it when it becomes available.

Thursday, 19 January 2012

Testing in preparation for release

Finally gearing up for a release, got to run some extensive testing first.

Tuesday, 17 January 2012

Mosflm / Pilatus

The beta for mosflm 7.0.8 appears to work much better with Pilatus data than the released 7.0.7 version - if you're using data from a 2M or 6M, I would strongly recommend the upgrade.