CCP4 6.2.0

If you try running xia2 with CCP4 6.2.0 and XDS it probably won't work, and will complain about something like "End of file".

If you get this, please get a new pointless from

http://www.ccp4.ac.uk/problems.php#6.2.0-programs

and everything should be fine.

Addendum:

My bad: this version is still buggy - better to get a version from ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre and overwrite the ccp4 one with this.

Does anyone use xia2-summary.dat?

Just found this:

[gw56@ws050 3]$ cat xia2-summary.dat
Project: AUTOMATIC
Crystal: DEFAULT
Sequence length: 0
Wavelength: WAVE1 (0.97966)
Sweep: SWEEP1
Files /data2/gw56/jcsg/12287_2L/12287_1_E1_###.img
Images: 1 to 60
Beam 105.10 101.05 => 108.95 105.04
Distance 170.00 => 169.89
Date: Sun Sep 26 14:13:49 2004
Wavelength: WAVE2 (1.00000)
Sweep: SWEEP2
Files /data2/gw56/jcsg/12287_2L/12287_1_E2_###.img
Images: 1 to 60
Beam 105.10 101.05 => 108.93 105.04
Distance 170.00 => 170.09
Date: Sun Sep 26 14:17:56 2004
For AUTOMATIC/DEFAULT/WAVE1:
High resolution limit                           1.66    7.41    1.66
Low resolution limit                            36.8    36.8    1.7
Completeness                                    97.9    96.4    85.7
Multiplicity                                    4.3     3.5     2.9
I/sigma                                         16.5    33.9    2.2
Rmerge                                          0.043   0.023   0.372
Anomalous completeness                          94.3    92.4    78.2
Anomalous multiplicity                          2.4     2.3     1.6
For AUTOMATIC/DEFAULT/WAVE2:
High resolution limit                           1.65    7.39    1.65
Low resolution limit                            36.8    36.8    1.7
Completeness                                    96.3    96.4    74.5
Multiplicity                                    4.2     3.5     2.7
I/sigma                                         17.4    35.6    2.2
Rmerge                                          0.04    0.021   0.369
Anomalous completeness                          92.1    94.2    69.9
Anomalous multiplicity                          2.3     2.3     1.5
Cell:  51.570  51.570 157.600  90.000  90.000  90.000
Spacegroup: P 41 21 2

which I remember from a long time ago - just wondering, does anyone use this? Is it worth keeping (as I clear up...)

Issues with xia2 / 3d / pointless 1.6.1

Many thanks to bug reporters. If you see:

Status: error "End of File "

at the end of a xia2 job which looks like it should have worked, and you have recently updated your pointless version, you have hit a feature resulting from a small change in pointless. Essentially when copying reflections from XDS to MTZ format there is no real orientation matrix, so pointless makes one up. It used to be [1] and was changed to [0] as it is meaningless - however reindex relies on this and therefore explodes.

Phil has fixed this in 1.6.2 (thanks Phil!) and is quite reasonably of the opinion that this is a bug in reindex...

A subsequent question to this is why I still use reindex inside xia2 now pointless does it all. "Historical reasons" would be the fair answer i.e. I haven't got around to fixing this :o)