Friday, 24 October 2014

Corner case bug spotted (thanks Luca Jovine)

If you

  • use xinfo files
  • use -2d
  • do not set START_END
you may find you get a weird complaint about detector_class.

This is easily resolved for the moment by setting START_END to correspond to the first and last image you want to process... I need to fix this ;o) it did not used to work like this...

Thanks to Luca for pointing this out and patience in debugging...

Monday, 20 October 2014

xia2 released

Major changes:

Changes since Added DIALS (mostly)
  • Added support for DIALS software. Thanks to Richard Gildea at Diamond for most of the work.
  • Create AIMLESS xml output; useful for displaying results through alternative interfaces.
  • Squashed nasty bug where input spacegroup set to e.g. I222 but pointgroup derived to be P222 (think this one was reported a while back but I could not find the source at the time... sorry!)
  • Squashed some other bugs which have appeared in recent history.
Changes since Bug fixes, add CC-half, removing Scala.
  • -cc_half 0.5 (say) resolution limit criterion available - suggest set -misigma 0.5 -isigma 0.5 or similar with this.
  • -freer_file where free flag != FreeR_flag fixed.
  • Massively trimmed all of the command line options for the pipelines and removed the use of Scala in all pipelines, replaced with Aimless (not before time!) This means that -3dr and so forth will no longer work so please use -2d, -3d, -3di etc.
  • -phil command line option now deprecated: phil parameters passed on the command-line will be respected, also phil files, without this clue
  • Parallelisation options: can now cleanly process sweeps from one wavelength in parallel (to aid with multi-crystal data sets) use Phil parameters multiprocessing.njob=4 multiprocessing.nproc=12 multiprocessing.mode=parallel (say) to allow processing four sweeps at a time each using 12 cores. This multi-sweep parallelisation is probably most useful in conjunction with the Phil parameter multiprocessing.type=qsub, which tells xia2 to submit jobs to a cluster, with each job using nproc cores.