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.

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.

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...

Thanks,

Graeme

xia2 release 0.2.7.2

Hi Folks,

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

Changes since 0.2.7.0

- 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

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!

xia2 0.2.7.0 released

After a fairly long delay I have put together xia2 0.2.7.0 - this has had a pretty significant amount of testing so should be more solid than previous versions - this is a worthwhile update. Anyhow, here are the changes:

Changes since 0.2.6.6

- All command line options now echoed to the standard output if -debug selected.
- Command line options now copied to .xinfo file when operating in automatic mode.
- XDS: low resolution limit determined from spot list from IDXREF.
- Now include explicit python version check in xia2 main program.
- High resolution limits for integration now assessed from Wilson plot rather than integration program log output.
- If no images are given, a more helpful error message is produced than before, viz:

------------------------------------------
| No images assigned for crystal DEFAULT |
------------------------------------------

- If images are not readable (i.e. a permissions problem) then warnings will be sent to the debug channel (switch on -debug = for more information.)
- If in automatic mode an image is given in place of a directory, xia2 will now complain in a more helpful way.
- Resolution limits will now be based on analysis of the reflection files rather than the program output, since this will generally give a more helpful answer...
- Now correctly set the reindex matrix for running correct with multiple sweeps of data for non primitive matrix (subtle bug, thanks to Kay Diederichs for helping to fix this one.)
- If images are missing from a sweep, xia2 will now tell you this before starting processing rather than giving a strange error - if the images are unreadable you will also be told.

The biggest fix is the sorting out of resolution limits - you should no longer find xia2 wondering off and then falling over, with ever decreasing resolution limits, in -3d mode. All available from the usual place...

Unhelpful error messages

So, this is an old bug which I still need to fix, but since I have had a user report (again) that it is a problem, I thought a description of what the problem is would be helpful.

If you see:

"no Integrater implementations assigned for scaling"

This means you have not given xia2 any data for processing. The classic case is that you run xia2 in completely automatic mode and include the image name, viz:

xia2 -3d /data/graeme/s15a/xtal8/xtal8_1_001.img

Since the last argument should be a directory xia2 gets confused. This is simple to fix, I know, and will be for the next release.

Another perhaps more interesting cause of this is when the images are not readable - either they belong to someone else or someone has messed with the permissions. Again I need to check this, but it is harder...

So there you go, if you see this message check that you are giving a directory and that the images are readable.