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    *
                *   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!

Wednesday 19 January 2011

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 I think that this is superceded by the LogFiles/bioxhit.xml and the optional -ispyb_xml_out which I know are used.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

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/xia2.py", line 45, in 
    from xia2setup import write_xinfo
  File "/home/gw56/svn/xia2/Applications/xia2setup.py", line 35, in 
    from Handlers.CommandLine import CommandLine
  File "/home/gw56/svn/xia2/Handlers/CommandLine.py", line 1513, in 
    CommandLine.setup()
  File "/home/gw56/svn/xia2/Handlers/CommandLine.py", 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

Anti-alias

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/XDS.py 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

Reminder!

http://xia2.blogspot.com/2010/05/summary-of-command-line-options.html

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!