Have just updated the web page to include release 0.2.6.4 - this is a bug fix for a couple of outstanding issues, namely spacegroup assignment and provision of an existing FreeR column from a file. This also fixes a number of other minor issues.
Changes since 0.2.6.3
Added possibility to give a reflection file with an existing FreeR_flag column, which will be copied to the output MTZ:
xia2 -freer_file free.mtz
or...
FREER_FILE free.mtz
in the xinfo file (in the same way as the reference reflection file - indeed, this may be the same file...)
Added command line control of the spacegroup - note well that this means that the data WILL NOT be reindexed to a standard setting.
Added support for ADSC Quantum 270.
Intelligent selection of autoindex threshold for Mosflm.
Added support for latest XDS version.
Added support for pilatus 6M mini CBF images.
Fixed problem with cell refinement giving negative mosaic spreads sometimes for 2d pipeline.
Thursday, 13 March 2008
Wednesday, 27 February 2008
Spacegroups & FreeR columns
Two feature requests that I am working on at the moment are the inclusion of spacegroup assignment from the command line or xinfo file, and copying of an existing FreeR set from a reflection file. These are both to aid use of xia2 in an automated context.
The spacegroup assigment can be either in a USER_SPACEGROUP record within the xinfo file or with -spacegroup on the command line. This spacegroup will be used to determine the lattice for integration and the pointgroup. If these are found to be wrong an exception will be raised.
If you assign the screw axes, these need to be in order of cell axis lengths, since otherwise I don't know what order you mean. This means that you may need to assign them as P 21 2 21, say.
The FreeR flag is more straightforward - either provide FREER_FILE in the xinfo file or -freer_file on the command line - the FreeR_flag column will simply be copied out. If the new data go to a higher resolution than the existing free column I don't do anything - you should know what you are doing (I assume) if you are using this option.
The spacegroup assigment can be either in a USER_SPACEGROUP record within the xinfo file or with -spacegroup on the command line. This spacegroup will be used to determine the lattice for integration and the pointgroup. If these are found to be wrong an exception will be raised.
If you assign the screw axes, these need to be in order of cell axis lengths, since otherwise I don't know what order you mean. This means that you may need to assign them as P 21 2 21, say.
The FreeR flag is more straightforward - either provide FREER_FILE in the xinfo file or -freer_file on the command line - the FreeR_flag column will simply be copied out. If the new data go to a higher resolution than the existing free column I don't do anything - you should know what you are doing (I assume) if you are using this option.
Friday, 15 February 2008
Resolution limit calculation
Ok, so it looks like there will be a better way of resolution limit calculation in the next (full) release of xia2. This has taken a lot longer than I had anticipated though as the calculations are relatively complicated.
As this is such a major change, the next release will have this as a command line option to switch on (at the moment it also only works with data from Scala as well...) but it will hopefully be worth it.
An interesting side effect of this is that the processing will most likely be much faster than it currently is, since I will ditch the (perhaps unnecessary) reprocessing of the data in Mosflm prior to obtaining a robust resolution limit. Should give an approximately 30% speedup on how things currently work.
Listening to: Massive Attack
As this is such a major change, the next release will have this as a command line option to switch on (at the moment it also only works with data from Scala as well...) but it will hopefully be worth it.
An interesting side effect of this is that the processing will most likely be much faster than it currently is, since I will ditch the (perhaps unnecessary) reprocessing of the data in Mosflm prior to obtaining a robust resolution limit. Should give an approximately 30% speedup on how things currently work.
Listening to: Massive Attack
Tuesday, 29 January 2008
Pilatus support
Since the latest Mosflm (702) supports pilatus detectors I am adding support in xia2. This means that the next version (0.2.6.4 or 0.3.0) will be able to run "fine" with them.
As always - any problems to xia2bb or xia2.support (at) googlemail.com.
As always - any problems to xia2bb or xia2.support (at) googlemail.com.
Tuesday, 15 January 2008
Where is 0.3.0?
So, the question is - where has the next release got to? Well, I am currently working on a "proper" way to determine the resolution limits for the data which will take account of things like Rmerge, I/sigma and so on in a hopefully holistic way. This is clearly not trivial.
If you feel that an intermediate "bugfix" release (0.2.6.4) is needed, please give me a yell!
Listening to: Amorphous Androgynous
If you feel that an intermediate "bugfix" release (0.2.6.4) is needed, please give me a yell!
Listening to: Amorphous Androgynous
Thursday, 3 January 2008
CCP4 Study Weekend
Over the next couple of days I will be at the CCP4 study weekend in Leeds, and I have a couple of "lunchtime bytes" sessions, which due to a printing error are listed under "aix2". ;o) - Perhaps see you there
Wednesday, 2 January 2008
CCTBX into xia2? Result
So, the votes went 10 for, 0 against and 4 don't mind, so I will start to make use of CCTBX tools in future versions of xia2. CCTBX is free to download and pretty easy to install (binaries are available) and will also be included in CCP4 6.1 which is due sometime soon. Hopefully this won't be a problem...
http://cctbx.sourceforge.net/
Happy new year!
http://cctbx.sourceforge.net/
Happy new year!
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