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[ccp4bb]: summary: reduce size of Rfree set

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Dear all,

The question was:
> I refined a structure against data to 2.3 A, where the Rfree set
> included 2600 reflections (5 % of data). I now have data to a much
> higher resolution, and putting 5 % of data in the Rfree means  11000
> reflections, which is quite a lot. I would like to use a smaller
> fraction for the Rfree set (say 1 %). For this, I need only to keep 1
> every 5 reflections of the "low resolution" free set.
> Any hints on how I can do this ?

Eleanor Dodson, Randy Read and Tassos Perrakis suggested to get a new
Rfree set with the desired size, and to remove bias with annealing or
throuh model coordinates randomisation (pdbset).

Anyway, Randy also suggested a way to reduce Rfree set size, using
> However, if you do want to keep 1 in 5 of your old test data, you can do
> it fairly easily in sftools.  I'll assume the working data have a 1 in
> column RFREE and the test data have a 0.  I'll also assume you have a
> column called F_Old which contains the original amplitudes.  Then do the
> following in sftools:
> read my.mtz
> select col rfree = 0          ! only old test data
> calc col rfree = rfree(0.2)   ! keeps 1 in 5 of old test data
> select all
> select col F_old absent       ! only new data
> calc col rfree = rfree(0.01)  ! flag 1% of new data
> select all
> write my_new.mtz

Tassos and Eleanor also suggested to use arp_warp, either to remove bias
in the new Rfree set, or to build the structure from scratch.

thanks for everybody's help



Laurent Maveyraud               
Groupe de Cristallographie Biologique  -  IPBS-CNRS

205, route de Narbonne       	 Tel (+33) 05 61 17 54 35
31077 TOULOUSE CEDEX        	 Fax (+33) 05 61 17 54 48
France                       	 mailto:laurent.maveyraud@ipbs.fr