Monday, 14 February 2011

Getting and running xia2 from subversion

On a couple of occasions lately I have had folk asking about how to run with the xia2 direct from subversion. You should remember that there can always be problems with this (though I try to never commit breaking changes) however it's pretty straightforward. So, here we go:

* Check you have subversion installed!
* Make yourself a xia2-svn directory in wherever you keep your crystallographic software
svn co xia2core
svn co xia2
* Compose yourself a setup file which will (i) set up ccp4 then (ii) set up cctbx etc and if you like also set up labelit / XDS
* At the end of this file add

export XIA2CORE_ROOT=${HOME}/svn/xia2core
export XIA2_ROOT=${HOME}/svn/xia2
. ${XIA2_ROOT}/

for the bash shell or

setenv XIA2CORE_ROOT ${HOME}/xia2-svn/xia2core
setenv XIA2_ROOT ${HOME}/xia2-svn/xia2
source ${XIA2CORE_ROOT}/
source ${XIA2_ROOT}/

for (t)csh. For example. Then once you have sourced this setup file xia2 should work. If you want to update this please go to $XIA2_ROOT and run "svn update".

When reporting problems, please first run svn update in case I have fixed it. If I have not then please get in touch, mentioning that you are getting xia2 from svn.

Thursday, 3 February 2011

Big thanks to bug reporters

Hi Folks,

Just like to say thanks for all of the feedback I have been getting recently - many of the changes in the forthcoming 0.3.3 release are directly resulting from this.

Please, keep it coming!

Cheerio, Graeme

Wednesday, 2 February 2011

So what is xia2 about, then?

Thanks to Wordle, now I know...

Checking up on XDS

So the number of new-year-new-xds-why-doesn't-it-work complaints this year exceeded the energy threshold to remove the XDS version check (that, and the fact that the program has not changed how it behaves for a while now)

So, I have removed the check. I will however post when I think a new XDS build should work, and keep the checked versions up-to-date. If you like to have xia2 check for you, -check_xds_version is there for you.

However, most people don't want this it seems :o)

Contemplations on ice

So, had a request to be able to explicitly exclude ice ring regions from diffraction images in processing. In the first instance I have added a -ice command-line option which will use the following hard-coded ice ring regions, from the XDS documentation:

3.93 3.87 !ice-ring at 3.897 Angstrom
3.70 3.64 !ice-ring at 3.669 Angstrom
3.47 3.41 !ice-ring at 3.441 Angstrom
2.70 2.64 !ice-ring at 2.671 Angstrom
2.28 2.22 !ice-ring at 2.249 Angstrom

These are listed in $XIA2_ROOT/Data/ice-rings.dat, so I guess you could fiddle with them if you wanted. Perhaps a better way would be to specify explicitly regions to exclude. Comments anyone?