Monday, 25 November 2013

Incoming: parameters to control xds integration / spot profile

Adding more Phil parameters this morning to control reflecting range, beam divergence etc. however these are not for common use: only when the automatic determination of parameters has failed are these useful.

Please see XDS documentation for details:

In build 4480 & later having phil file containing

xds.integrate.delphi = 10.0
xds.integrate.reflecting_range = 0.31
xds.integrate.reflecting_range_esd = 0.045
xds.integrate.beam_divergence = 0.25
xds.integrate.beam_divergence_esd = 0.025

will allow you to control these via -phil file.phil

Thursday, 21 November 2013

Controlling XDS Refinement in Integration with Phil

By default in xia2 the REFINE= for integration refines ORIENTATION and CELL - however if you want to override this you can do so by using Phil parameters. Create a file




for example - and run with -phil whatever.phil. The former is the first pass, the second the pass when a refined orientation is used in case you want these to be different. You can select from ORIENTATION CELL BEAM DISTANCE AXIS - best to look at the XDS documentation if you want to change these.

In general you don't need to do this but some people would like the choice...

Thursday, 7 November 2013

Very big but not functional commit coming

Warning to anyone who uses xia2 from subversion - forthcoming commit will be very large as I change the indentation from 4 spaces to 2 spaces, to make the code more consistent with the cctbx way of things. I have run a bunch of tests and manually inspected at least 1000 lines of the changes to make sure that they are sensible (and they appear to be) but if you have any local modifications in your code you may / will find updating via svn causes conflicts.

Any problems please contact me at the usual address

Wednesday, 6 November 2013

xia2 broken with very latest cctbx

If you have a cctbx about 3 days old or younger you will have found errors like

Traceback (most recent call last):
  File "/Users/graeme/svn/xia2/Wrappers/XIA/", line 648, in readheader
    self._header = failover_dxtbx(self._image)
  File "/Users/graeme/svn/xia2/Wrappers/XIA/", line 471, in failover_dxtbx
    fast, slow = map(int, d.get_image_size())
AttributeError: 'Detector' object has no attribute 'get_image_size'

This relates to recent changes in cctbx; a fix for xia2 will follow later today.

Update: fix was sent to svn yesterday morning, so nightly build from last night should be fine if you hit this problem... however any problems please contact as usual.