xia2 0.3.1.0 release: this is a big one

Hi Folks,

A new xia2 release for you, this time with added radiation damage analysis and html report generation. Release notes below, download available from the usual place. This isa substantial update over the last release and includes the changes reported below.

Cheers,

Graeme

Changes since 0.3.0.6

• Added -xparallel command line option to allow use of forkinitegrate on a cluster with the 3d pipeline.
• Allow for xia2html (work by Peter Briggs) and (beta) ISPyB output (latter more useful for synchrotron sources, former handy if you want a report.
• Smart scaling mode switched on by default.
• Chef now run by default, for radiation damage analysis, e.g.
  

  Group 1: 2-wedge data collection
  Group 2: Single wedge
  Significant radiation damage detected:
  Rd analysis (12287/LREM): 15.17
  Rd analysis (12287/INFL): 7.89
  Rd analysis (12287/PEAK): 12.82
  Conclusion: cut off after DOSE ~ 608.8
   

  
  
• Blank images now handled more gracefully.
• Overloaded and blank images now correctly reported in the summary output, along with abandoned images for the processing with Mosflm. Also postrefinement results.
• Substantially cleaned up the program output.

Finally, a paper

http://journals.iucr.org/j/issues/2010/01/00/issconts.html

Couldn't have planned it

Whoda thunkit? Seems that xia can mean "summer" in chinese (according to Natalie Zhao of CCP4) and so the logo could look like this!

Clustery parallelism goodness

So, I had a request the other day to look at how xia2 could work on a cluster. Back in the day this was a consideration, but it kind of dropped by the wayside what with multi-cpu machines becoming the norm and anyway with Mosflm and Scala, the bottleneck simply moves to scaling. Well, I am reminded that XDS works nice with clusters, so I have added a "secret command line option" which will tell XDS to integrate in parallel across N jobs, using (by default) all of the CPU's in each. -xparallel.

For those cases where you simply have a lot of images, it can be really nice to use XDS like this. Just running a slightly bonkers example just now (1440 degrees, reasonably big unit cell, 1.75A) and it goes from 2h 39m 43s on one eight core machine to 19m 41s over 16.

There's plenty of time to be trimmed from this yet, too - watching top while this happened was just painful! This will be available in the forthcoming 0.3.1.0 release. Just keep in mind you need to configure your forkintegrate scripts to run with your cluster environment - feel free to get in touch for pointers with this.

www.xia2.org now live

"Proper" project web pages now live at:

http://www.xia2.org/

Broken xia2 cure-all

A couple of questions came in recently for which the answer appeared to be:

- remove $CCP4/share/XIAROOT (which is obsolete)
- source cctbx setup after CCP4 as the latter pollutes the environment

This will probably fix the problem, particularly if it complains about iotbx :o)

Better output as HTML

Work has started on the HTMLification of the xia2 output with some success already:

http://www.ccp4.ac.uk/xia/xia2html/

Any comments? Please send to the usual places! Feedback is what drives development.