Monday, 14 October 2013 quick release

Enough things are broken by the new CCP4 to make a new version worthwhile:

Changes since Cope with new CCP4.
  • Mend xia2 working on Windows.
  • Cope with new version of CTRUNCATE in CCP4 6.4.0.
  • xia2ccp4i added - thanks to David Waterman.
  • Improved handling of nasty image names.
  • Mend -reversephi functionality.
  • Take spacegroup from reference reflection file correctly.
In the usual place(s)

CCP4 / Windows / xia2 fix

Missing detectors.lib from the CCP4 cctbx / dxtbx installation was the problem - easily fixed:

C:\>cd \CCP4\6.4\lib\python2.7\site-packages\dxtbx
C:\CCP4\6.4\lib\python2.7\site-packages\dxtbx>mkdir data
C:\CCP4\6.4\lib\python2.7\site-packages\dxtbx>cd data
C:\CCP4\6.4\lib\python2.7\site-packages\dxtbx\data>cp \CCP4\6.4\share\xia2\Data\detectors.lib .

This should be mended in the next update.

xia2 / Windows / CCP4 6.4

Looks like the xia2 in CCP4 6.4 is not entirely working fine on Windows - one error is my bad:

NotAvailableError: executable C:\CCP4\6.4\share\xia2\Modules\ does not exist in PATH

which I have just fixed (an update will go in a CCP4 update soon) and other errors have been found regarding the reading of image headers which CCP4 are looking into. If you find any problems do please get in touch on the usual address.

Friday, 11 October 2013

New CCP4 / ctruncate bug

Seems a three line change fixes this:

Index: Wrappers/CCP4/
--- Wrappers/CCP4/ (revision 4432)
+++ Wrappers/CCP4/ (working copy)
@@ -142,6 +142,9 @@
             if 'Acentric moments of E using Truncate method' in results:
                 moments = transpose_loggraph(
                     results['Acentric moments of E using Truncate method'])
+            elif 'Acentric moments of I' in results:
+                moments = transpose_loggraph(
+                    results['Acentric moments of I'])
             elif 'Acentric moments of E' in results:
                 moments = transpose_loggraph(
                     results['Acentric moments of E'])

Will include this in next release (and as a CCP4 update)

New CCP4

Just installed the new CCP4 - looks like the ctruncate output has changed so xia2 crashes. I will make a patch today.

Thursday, 3 October 2013

Reversephi: error(s) found

Reversephi from .xinfo file should be respected now in the committed version or the following change can be made:

[gw56@ws133 xia2.trunk]$ svn diff -r 4428 Schema/
Index: Schema/
--- Schema/       (revision 4428)
+++ Schema/       (working copy)
@@ -170,7 +170,7 @@
                                    directory = directory,
                                    image = image,
                                    beam = beam,
-                                   reversephi = False,
+                                   reversephi = reversephi,
                                    distance = distance,
                                    gain = gain,
                                    dmin = dmin,

(dumb typo which should have been flagged a long time ago)

More complex situation was found with data where the dxtbx format system reads the image headers, which involved slightly deeper changes. These are now made but N.B. that if the dxtbx header reading class correctly identifies it as reversed phi (which should be the case) then -reversephi will do exactly the opposite to what you want. 

Short answer: you should not need -reversephi or REVERSEPHI in the xinfo file: if you do please get in touch and email me an example image.

Updated xia2 release to follow, though new format classes will need to be added to your cctbx installation - instructions for this will follow.

Reversephi broken

It seems that for beamlines where the phi axis is reversed xia2 is currently broken, even when you set -reversephi on the command-line or REVERSEPHI in the sweep block in the xinfo file. Currently working on this, will release an update when this is fixed.