Incoming features

Following requests being worked on:

• configurable cctbx.python via env variable
• remove need for env variable XIA2_ROOT - just put directory in PATH
• user configurable background range via phil parameter / XDS processing

Plan to have these ready early next week.

Bug found in 0.3.6.1 / 2d with P1

Due to bug in Mtzdump replacement Python code this error happens:


-------------------- Integrating SWEEP1 --------------------
Processed batches 1 to 180
Weighted RMSD: 0.69 (0.17)
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => blank
"@" => abandoned
Mosaic spread: 0.680 < 0.817 < 0.990
-------------------- Preparing DEFAULT ---------------------
Status: error "'P'"

Just testing fix for this now, will be 0.3.6.2 tonight hopefully...

New CCTBX build available...

at http://cci.lbl.gov/cctbx_build/ - if you get errors in xia2 following an update (perhaps following an update to XDS) it may be worth installing this. If you have an unreleased cctbx build or a recent phenix nightly you don't need this. Thanks to Nat Echols for making a release with all the new bits xia2 needs.

xia2 0.3.6.1 released

Mainly this is a bug fix release to cope with changes in CCP4 6.3.0 latest update and the new XDS. The only other major change is that the indexing via XDS (i.e. processing with 3di or 3dii) now uses a smarter lattice determination method as previously posted. A minor change has also been that the 2d processing using Mosflm is now more reliable if your beam centre in the image headers is off...

Available in the usual place: http://xia2.sf.net

Please note you will need a recent Phenix nightly build or an unreleased cctbx build to make this work... as always any queries please contact xia2.support@gmail.com

Shameless plug

http://journals.iucr.org/d/issues/2013/07/00/ba5195/ba5195.pdf

If you were wondering about some of the things which go on under the hood of xia2, they are described in here. Worth looking at the supplementary materials, as some of the interesting stuff got pulled as the paper was too long :o(

Changes in XDS indexing...

Historically the XDS indexing used rather arbitrary criteria for the selection of the "best" solution - I was however prompted today to look at making this a little more robust, and leaning on the tools available in cctbx. Now the indexing is done in P1 as always and the P1 cell passed to iotbx.lattice_symmetry (see http://journals.iucr.org/a/issues/2004/01/00/sh5006/sh5006.pdf for more details) and only the solutions proposed from this analysis are considered from indexing.

Currently the behaviour is as before if you specify the symmetry on the command line. If however you do not it is less likely to try and process the data with too high a symmetry and generally make a mess of things. I will welcome any feedback on how effective this is.

Clearing clutter...

I have been clearing a lot of clutter from the xia2 repository over the last few days with the idea of simplifying future xia2 maintenance. Obviously I am endeavoring to not break anything however please svn update with care, if that is your usual way of getting xia2 code.