Parallel mosflm & rotation axis

If you have a rotation axis which is not perpendicular to the beam (or very close to such) you may have noticed that the parallel integration sometimes falls over: this is because the postrefinement radius of convergence is ~ 1 degree, but the orientation may differ by more than this.

Next version I'll add support for the mosflm AUTOMATCH keyword which helps here, but only for mosflm version 7.0.5 as it was broken beforehand.

xia2 in CCP4 6.1.2

Just a quick heads-up. It's likely that the xia2 included in CCP4 6.1.2 will not work out-of-the-box with XDS, as it's a little long in the tooth. I would therefore advise if you are going to use 6.1.2 to drop the latest xia2 over the top of the one found in $CCP4/share/XIAROOT (or just delete that one) so as to avoid any conflicts / weirdness.

CCP4 6.1.x dependency

In order to simplify the distribution of xia2 - and remove all of the binaries - I'm aiming to move to using CCP4 6.1 *only*. Since it's been around for a while and is available for all of the platforms supported by xia2, this should not be a big problem...

Shout if it is!

xia2 moving to sourceforge

Since I am moving towards using CCTBX for much of the underlying functionality, xia2 will get smaller. This will in turn mean that it can be kept on a public repository, so I am moving it to sourceforge.net to keep it "next door".

As a test, moved the core to

svn co https://xia2core.svn.sourceforge.net/svnroot/xia2core/trunk xia2core

and this appears to work correctly.

-3d / -3dii + RAXIS bug

Thanks to a bug report a corner case has been identified, between the use of the 3d or 3dii pipeline and RAXIS (general Rigaku?) detectors. in XDSIndexer and XDSIndexerII I compute the low resolution limit from the spot list. For Rigaku detectors however distance is defined to be negative, which causes problems. Adding this small fix:

        if distance < 0.0:
            distance *= -1

After

        distance = values[14]

Will however fix the problem (I think!)

Buried in coding

Hi Folks,

The release of the first CCTBX-powered version of xia2 is kind-of on hold right now, first because I want to pick Ralf's brains about bundling CCTBX with xia2 when he is over here, and also because I'm trying to do some real catch-up on the coding of new features / enhancements / bug fixes which have been waiting forever to actually go in. Right now I have added the optimization of corrections to apply to the data in scaling, and now I'm working on the inclusion of chef for the analysis of radiation damage. Then a lot of testing / debugging and documentation will follow, hopefully resulting in the release of the new version.

For the first time I will lean towards a "test release" mentality, where new features need to explicitly switched on through a command-line flag. This is to make sure that the results are sensible (indeed, better) before making them the default...

So, watch this space...

Pseudocentring trap #2

Ok, now trapped for all of the pipelines - woo! This has involved substantial amount of pretty low-level work, so I'd be delighted to hear if anyone finds this useful! Thanks also to Ralf Grosse-Kunstleve and Nick Sauter - without CCTBX and their help this test would never have been implemented.

Now to try the first bundling of a cctbx powered xia2!