Wednesday, 27 February 2008

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.

Friday, 15 February 2008

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