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

Nathaniel Echols nechols at lbl.gov
Mon Jan 30 07:26:57 PST 2012


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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