Thursday, 24 July 2008

xia2 released

xia2 has been released, and can be found in the usual place. The following changes have been made:

Changes since

Now supports CCP4 6.1 (forthcoming release) though you may need to add XIA2_CCP4_61=1 to your environment. This release should include xia2.
Added -resolution keyword, also support for this on a per-wavelength basis in the xinfo file.
Added support for reverse-phi data collection - either add reversephi to the xinfo file or -reversephi to the command line.

The last of these has been tested on only one data set from the Australian Synchrotron, so please shout if you get any problems. If you are a Labelit user, you may need to update to get this functionality. Also fixed the "KeyError aP" bug, which was due to an ancient version of iotbx.lattice_symmetry being picked up.

As always, if you have any problems please drop me a line...

Tuesday, 22 July 2008

Reverse Phi

Another feature in the next release ( will be to support data reduction from reverse-phi beamlines. This will need either "-reversephi" on the command line or REVERSEPHI within the sweep block in the .xinfo file...

Monday, 21 July 2008

CCP4 6.1

Next release of xia2 will include support for CCP4 6.1, since it is going to be included in there. Only thing you need to do is to export XIA2_CCP4_61=1 to tell it...

User defined resolution limits

So, this is something people have been asking for a while now and I have been resisting - well I have finally given in! In the next release of xia2 there will be support for an overall resolution range set from the command line or per wavelength / sweep resolution limits from the .xinfo file. This allows you to get complete control over what the system is doing and also gets around the currently a little bit broken resolution limit setting.

You don't need to do this though - it works as before otherwise.

You may find it is a bit faster (or much faster!) with this switched on though, since xia2 doesn't end up fussing around for the right resolution limit.

Friday, 11 July 2008

-freer_file but column not FreeR_flag

Had a bug report that adding the FREER_FILE option to a .xinfo file or -freer_flag to the command line caused a very nasty error if the file in question did not have a column named FreeR_flag. This is ok, except that the default in Phenix is now different. To fix this please download:

and run

tar xvfz patch-3156.tar.gz -C $XIA2_ROOT

this will update the wrapper for CAD and add a new module called FindFreeFlag. This runs MTZDUMP and looks at the column names to guess which is right. You free column should be called (something)free(something) and be of type I...

Tuesday, 1 July 2008

XIA2 release

Hello, World,

Have just updated the xia2 web page with the latest version of xia2 - - which includes:

- Now handles complex image names with e.g. + in them correctly.

- New option for processing -3dii added - this will run the 3D pipeline (XDS, XSCALE) using all images for spot picking and autoindexing - useful for properly tricky cases.

- Now correctly propogate the profile information to Mosflm when not using Mosflm for autoindexing - this is done by running a "fake" autoindexing task.

- Use the raster information for the cell refinement test, and changed the selection of images for this.

- Added support for the output of BioXHIT XML in the LogFiles directory - for project tracking.

- Now copy the XDS log files ("LP" files) into the LogFiles directory - as always these are the most up-to-date versions from

- Added support for latest release of XDS (June 2, 2008.)

As always, please get in touch if you have any problems...