Thursday, 27 January 2011

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    *
                *                 *
                *                                         *

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


Wednesday, 19 January 2011


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:


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 I think that this is superceded by the LogFiles/bioxhit.xml and the optional -ispyb_xml_out which I know are used.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.

Checking command-line arguments...

A problem people have been reporting for a while is that xia2 does not fail loudly when you tell it nonsense. Well, I have now added something which does:

gw56@ws050 nonsense]$ xia2 -3d -nonsense /data/gw56/dl/Cowan/Insulin/insulin/
Traceback (most recent call last):
  File "/home/gw56/svn/xia2/Applications/", line 45, in 
    from xia2setup import write_xinfo
  File "/home/gw56/svn/xia2/Applications/", line 35, in 
    from Handlers.CommandLine import CommandLine
  File "/home/gw56/svn/xia2/Handlers/", line 1513, in 
  File "/home/gw56/svn/xia2/Handlers/", line 349, in setup
    raise RuntimeError, nonsense
RuntimeError: Unknown command-line options: -nonsense

however this will only spot nonsense beginning with '-' as the directory stuff is handled elsewhere. Will be included in next release. Note to self: should really move this to a proper option parser.

Friday, 14 January 2011


So - sometimes people use an alias in their shell to point at programs rather thank tinkering with their path. I have to warn you that xia2 is not smart enough to "get" this - so for instance aliasing xds rather than putting it in your path will stop xia2 -3d from working.

If someone would like to look into fixing this, please feel free to get in touch. Until then, you have been warned ;o)

Wednesday, 12 January 2011

New year, new XDS

Following Kay's email, the new XDS appears to work fine with xia2. As usual, a little editing will be needed in $XIA2_ROOT/Wrappers/XDS/ around line 78  -

    supported_versions = ['December 28, 2009',
                          'February 3, 2010',
                          'May 10, 2010',
                          'December 6, 2010']

As always, this will be fixed in the next released build.

Friday, 7 January 2011


Using -resolution ...

Quick note - not sure that the interaction of -resolution with -3d is working quite correctly, so please run with -3dold if you want to specify the resolution!