Spacegroups & FreeR columns

Two feature requests that I am working on at the moment are the inclusion of spacegroup assignment from the command line or xinfo file, and copying of an existing FreeR set from a reflection file. These are both to aid use of xia2 in an automated context.

The spacegroup assigment can be either in a USER_SPACEGROUP record within the xinfo file or with -spacegroup on the command line. This spacegroup will be used to determine the lattice for integration and the pointgroup. If these are found to be wrong an exception will be raised.

If you assign the screw axes, these need to be in order of cell axis lengths, since otherwise I don't know what order you mean. This means that you may need to assign them as P 21 2 21, say.

The FreeR flag is more straightforward - either provide FREER_FILE in the xinfo file or -freer_file on the command line - the FreeR_flag column will simply be copied out. If the new data go to a higher resolution than the existing free column I don't do anything - you should know what you are doing (I assume) if you are using this option.

Resolution limit calculation

Ok, so it looks like there will be a better way of resolution limit calculation in the next (full) release of xia2. This has taken a lot longer than I had anticipated though as the calculations are relatively complicated.

As this is such a major change, the next release will have this as a command line option to switch on (at the moment it also only works with data from Scala as well...) but it will hopefully be worth it.

An interesting side effect of this is that the processing will most likely be much faster than it currently is, since I will ditch the (perhaps unnecessary) reprocessing of the data in Mosflm prior to obtaining a robust resolution limit. Should give an approximately 30% speedup on how things currently work.

Listening to: Massive Attack

Pilatus support

Since the latest Mosflm (702) supports pilatus detectors I am adding support in xia2. This means that the next version (0.2.6.4 or 0.3.0) will be able to run "fine" with them.

As always - any problems to xia2bb or xia2.support (at) googlemail.com.

Where is 0.3.0?

So, the question is - where has the next release got to? Well, I am currently working on a "proper" way to determine the resolution limits for the data which will take account of things like Rmerge, I/sigma and so on in a hopefully holistic way. This is clearly not trivial.

If you feel that an intermediate "bugfix" release (0.2.6.4) is needed, please give me a yell!

Listening to: Amorphous Androgynous

CCP4 Study Weekend

Over the next couple of days I will be at the CCP4 study weekend in Leeds, and I have a couple of "lunchtime bytes" sessions, which due to a printing error are listed under "aix2". ;o) - Perhaps see you there

CCTBX into xia2? Result

So, the votes went 10 for, 0 against and 4 don't mind, so I will start to make use of CCTBX tools in future versions of xia2. CCTBX is free to download and pretty easy to install (binaries are available) and will also be included in CCP4 6.1 which is due sometime soon. Hopefully this won't be a problem...

http://cctbx.sourceforge.net/

Happy new year!

Ongoing developments

Right at the moment I am looking at radiation damage analysis, with the aim of being able to suggest decent subsets of the data to use to get optimal structure solution (don't worry - this won't happen for a while!)

Also looking at improving the way that the cell refinement tests in Mosflm are performed, figuring out how to make this parallel and also improving the integration of XDS into xia2 (no pun intended) to ensure that the correct indexing solution is used at all times...

Finally still chipping away at some "known bugs" for instance the old favourite, the BGSIG error.

Listening to: Tangerine Dream