Wednesday, 13 May 2009

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!

Monday, 11 May 2009

Pseudocentring trap #1

So one example which has been a thorn in my side has been 2PBL, JCSG sample number 45453 - this is really primitive, but indexes as centred because it nearly is (i.e. the lattice points are systematically weak rather than absent as they would be if it were centred) - now nailed this one for -3dii, where I have a lot of information about the diffraction pattern.

Now for -3d.

Then -2d, which will involve me adding my own spot search. Statistics much stronger using the whole data set though! Oh, and since neither Mosflm nor Labelit can index this case correctly, some hacking of orientation matrices.

End of all this though, it'll be another data set defeated by automation. Always good.

CCTBX simpler now

Following a very sensible suggestion from Ben Eisenbraun, I will aim to provide versions of xia2 with CCTBX bundled in there - this will make installation more straightforward, though will also include a "lite" version which will work as the current one does, and will assume that the cctbx.python in the path is right.

Of course, it'll also complain if it is not ;o)

Friday, 8 May 2009

CCTBX complexities

CCTBX-using applications are best launched using cctbx.python rather than a standard system python - however, you may have named it something different, right? So what I will do is at the same time change the way that the launcher scripts work - if you have defined the environment variable XIA2_PYTHON this will be used for the execution, else cctbx.python will be - this means that if you have carefully installed one for xia2 to use, you can tell the program by e.g. exporting XIA2_PYTHON=/usr/xtal/cctbx/cctbx_build/bin/cctbx.python, which will then be executed even if it does not occur in the path.

Probably will make for a simpler life.

Just have to figure out how to test for an environment variable being set on Windows :o(