Thursday, 28 January 2010

Weirdness managed

So it seems that this should have been a problem for a lot longer. Thanks to Ralf GWK and Phil Evans for a chat about this which clarified things. Now will pass environment through to the underlying programs correctly (is the intention) though this turned out to be a moderately low level change. Have made this now, and will test, next planned release which should be available sometime soon will contain this fix...

Wednesday, 27 January 2010

Pointless (latest) and Phenix (latest) slight weirdness

It appears that the combination of the latest (6.1.3) CCP4 and the latest (1.6) Phenix will cause problems for pointless. This will exhibit itself in xia2 as:

 Status: error "no element found: line 27, column 0"

as a result of pointless having an error like:

/scratch/xtal/ccp4/ccp4-6.1.3/bin/pointless: symbol lookup error: /scratch/xtal/ccp4/ccp4-6.1.3/bin/pointless: undefined symbol: _ZNK5cctbx5sgtbx16space_group_type13lookup_symbolEv

I found installing a CCTBX from made the problem "go away", but I have no idea why. Investigating!

Tuesday, 26 January 2010

Resolution limits ignored? Fix!

Hi Folks,

Got an error report from Chip Lesburg, that the -i_over_sigma_limit was ignored. This was perfectly accurate, and it turns out that yes, it was ignored. Fix is to change the calls to determine_scaled_resolution in Modules/ and Modules/ to replace 2.0 and 3.0 respectively to Flags.get_i_over_sigma_limit(). Will be fixed in next version.

Yes, these Python modules are nasty code, refactoring them is a separate problem!


Tuesday, 19 January 2010

Resolution limit things

So, I got a complaint from someone who works with membrane proteins, who complained (accurately) that xia2 falls over at the resolution limit calculation step. This was because it assumes a Wilson plot, but this is only meaningful for better than about 4A.

xia2 should now cope - if the data are not there for a Wilson plot calculation it will fail over to a simple hunt for where I/sigma is about 1. Gets it out of a corner here anyway...

Monday, 4 January 2010

Happy new XDS

Happy new year folks. As is traditional this time of year, XDS changes. Fortunately the new one works (or appears to) just fine with xia2, so all that is necessary is to change the date string in $XIA2_ROOT/Wrappers/XDS/ Next update will of course include this change...