Friday, 26 September 2008

xia2 released

After a fairly long delay I have put together xia2 - 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

- 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...

Monday, 15 September 2008

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.