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 https://xia2core.svn.sourceforge.net/svnroot/xia2core/trunk/xia2core xia2core
svn co https://xia2.svn.sourceforge.net/svnroot/xia2/trunk/xia2 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
. ${XIA2CORE_ROOT}/setup.sh
. ${XIA2_ROOT}/setup.sh

for the bash shell or

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

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.

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

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?

Deprecating old versions of Scala

The Scala in CCP4 6.0.2 still appears to be "supported" in xia2 however the version is 5 years old now and has to have special code! I am therefore removing support for this, so you will need to be using CCP4 6.1 or later (which I am 99% sure you need anyway)

If you see this:

                *******************************************
                *    SCALA - continuous scaling program   *
                *                                         *
                *    Version: 3.2.25                      *
                *    Date   : 21/9/2006                   *
                *                                         *
                *   Phil Evans, MRC LMB, Cambridge, UK    *
                *   pre@mrc-lmb.cam.ac.uk                 *
                *                                         *
                *******************************************

when you type "scala" xia2 will probably stop working after a forthcomin update. Need to reduce the effects of code bloat.

Sorry!

Decrufting!

Prior to setting about doing some "real" development work with xia2 which is well past due, I am clearing out some of the cruft of things which really are no longer needed. One thing I identified was:

-ehtpx_xml_out

which produces an XML file fill of not-a-lot. I think that this is superceded by the LogFiles/bioxhit.xml and the optional -ispyb_xml_out which I know are used. I will remove this as I am 99% sure it's redundant - this post is so that anyone googling can find out where it went.