Windows...

Does anyone use xia2 / DIALS on MS Windows? Would you want to? Was pointed out to me that the changes referred to in the previous post would not work gracefully on MS Windows due to the c:\ type file paths... this should probably be fixed anyhow. Shout if you have an opinion.

New logs in the LogFiles directory; more image= options

If you look in LogFiles and you use xia2 -dials you will find some new stuff in there:

Graemes-MacBook-Pro-2:image_range graeme$ ls LogFiles/

AUTOMATIC_DEFAULT_NATIVE_truncate.log AUTOMATIC_DEFAULT_pointless.log

AUTOMATIC_DEFAULT_aimless.log SWEEP1_INDEX.log

AUTOMATIC_DEFAULT_aimless_xml.xml SWEEP1_LATTICE.log

This now includes the indexing log file and the lattice determination one; these can be useful to see how xia2 made it's decisions.

Also, if you want to combine some data from several sweeps, but only use limited image ranges, you can with:

xia2 unify_setting=true -atom Ti -small_molecule -dials image=/Users/graeme/data/i04-KTP/1/KTP_1_0001.cbf:1:100 image=/Users/graeme/data/i04-KTP/2/KTP_2_0001.cbf:1:100

so this will use the first 100 images of two sweeps and will make this xinfo file:

BEGIN PROJECT AUTOMATIC

BEGIN CRYSTAL DEFAULT

BEGIN HA_INFO

ATOM ti

!NUMBER_PER_MONOMER N

!NUMBER_TOTAL M

END HA_INFO

BEGIN WAVELENGTH SAD

WAVELENGTH 0.729320

END WAVELENGTH SAD

BEGIN SWEEP SWEEP1

WAVELENGTH SAD

DIRECTORY /Users/graeme/data/i04-KTP/1

IMAGE KTP_1_0001.cbf

START_END 1 100

END SWEEP SWEEP1

BEGIN SWEEP SWEEP2

WAVELENGTH SAD

DIRECTORY /Users/graeme/data/i04-KTP/2

IMAGE KTP_2_0001.cbf

START_END 1 100

END SWEEP SWEEP2

END CRYSTAL DEFAULT

END PROJECT AUTOMATIC

Word of warning though that this will currently (as of noon today) only cope with one subset per sweep; should be easy enough to add multiple image ranges for this though need to think what syntax to use... as always feedback welcome to xia2.support@gmail.com; to get this you will need to pull a new DIALS nightly build later today or tomorrow.

More output: how much is too much?

Request of additional output from xia2 e.g. in the indexing table:

------------------- Autoindexing SWEEP1 --------------------

All possible indexing solutions:

oP   6.39  10.59  12.80  90.00  90.00  90.00

mP   6.39  12.80  10.59  90.00  89.99  90.00

aP   6.39  10.59  12.80  90.00  90.00  89.99

Indexing solution:

oP   6.39  10.59  12.80  90.00  90.00  90.00

adding the R.M.S.D., metric penalty etc. from for example dials.index.  This will however make for more "junk" in the output and will also depend on the package being run underneath. Also requested was number of spots indexed vs. total number of spots. This will make for more information in the output which could make it cluttered and will also have the potential to "break" other software which uses this.

Thoughts anyone?

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.