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

Hi, 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. Christian Am Montag 30 Januar 2012 16:26:57 schrieb Nathaniel Echols:

On Mon, Jan 30, 2012 at 3:43 AM, Simon Kolstoe 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb