Tuesday, 20 January 2009

Hey! Why do I have one extra batch?

Just had an interesting user query which caused some confusion but relates to a perfectly reasonable cause - a data set with N frames in it had N+1 batches in the Scala log file using the XDS/XSCALE processing. Cause is very simple - reflections which are measured on the last image but have a centroid on the "next" image which was not measured could get assigned to batch N+1 by pointless, during the reconstruction of the orientation matrix.

So, if you see this it is not really something wrong, just an artefact. As far as I can tell this made no difference to the quality of the data set.

Friday, 16 January 2009

xia2 updates / ccp4 6.1+

So an important question came in yesterday - if I want to update xia2 and I have ccp4 6.1 installed, what do I do? There is a version of xia2 in ccp4 6.1. As it happens you can just delete the xiaroot directory and proceed as usual, or you can drop the new xia2 in place and just fix the setup.sh scripts.

XIA2_CCP4_61=1 is set in there, which should be maintained to tell xia2 about the updated Scala version. In the future this will be fixed to be determined dynamically.

Wednesday, 14 January 2009

xia2 web page

Hi Folks,

I have also updated the web page to make the downloads more obvious and updated the documentation on how to run xia2 - if you have any comments on this please get in touch or leave a comment on the blog...



xia2 release

Hi Folks,

New release of xia2 is now available, with the following changes:

Changes since

- Fixed to work correctly with XDS and Rigaku Saturn/RAXIS detectors.
- Better determination of resolution limits.
- Correct merging of data from XSCALE (needs to invert the I=F*F scale factor...)
- Fixed output of scalepack unmerged output using 3d pipeline.
- Use fewer frames for background calculation with 3dii pipeline - speeds things up a fair amount.
- Write chef output files with correct SD correction parameters.
- Print SD correction factors for scala runs - if these are bigger than about 2 there is something properly wrong. Also print the same from XDS CORRECT step.

Release available from the usual place: http://www.ccp4.ac.uk/xia

Thursday, 8 January 2009

xia2: updates

A couple of updates and notes. Firstly the patch release which includes unscaling of XDS data (i.e. converting back to photon counts from F^2 ~ I scaling) has been delayed by the CCP4 release and the holidays - I need to finish testing and release! Sorry! If you are using xia2 -3d with -parallel and xds_par bombs out, it may be that the stack size is not big enough (I have just found this) so it could be worth making it larger.

Release soon, I promise!