[phenixbb] Picking Rfree in thin resolution shells using command line

Christian Roth christian.roth at bbz.uni-leipzig.de
Tue Jan 31 04:06:06 PST 2012


I worked with crystals with 40 fold NCS and did a refinement with random picks 
and in thin shells. The difference in the R-values from the respective runs 
were comparable. and the dletaR was around 4.5 to 6% in both cases. So if 
there is a bias due to NCS it is equally strong in both cases. 
I found a paper from Fabiola et.al Acta CrystD (2006) D62 227-238 about the 
effects of NCS. For me it was quite complicated to follow all the mathematical 
things, but they mentioned, if I understood and rememberit correctly, that 
they excluded up to 60 % of the data from the refinement to remove the model 
bias. The data/parameter ratio will become a real problem I guess.


Am Montag 30 Januar 2012 16:26:57 schrieb Nathaniel Echols:
> On Mon, Jan 30, 2012 at 3:43 AM, Simon Kolstoe <s.kolstoe at ucl.ac.uk> wrote:
> > I see from a quick google that it is possible to pick my Rfree's using
> > thin resolution shells (coz I've got 20 fold NCS), however as I am
> > someone who tries to avoid the GUI where at all possible,
> Why?  Some things are simply easier to do in the GUI, or at least more
> obvious - otherwise we wouldn't bother writing one.
> > could someone let me know what the command line way of doing this is?
> In phenix.refine, you probably want something like this (some
> parameters optional, but the defaults are probably not what most
> people expect):
> xray_data.r_free_flags.generate=True
> xray_data.r_free_flags.fraction=0.05
> xray_data.r_free_flags.max_free=None
> xray_data.r_free_flags.use_dataman_shells=True
> xray_data.r_free_flags.n_shells=20
> Randy and Paul claim that this doesn't help very much with the NCS
> issue, however.
> -Nat
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