[phenixbb] r-work and r-free for specific resolution range(s)

Nathaniel Echols nechols at lbl.gov
Wed Aug 4 10:37:45 PDT 2010

On Wed, Aug 4, 2010 at 10:22 AM, Kay Diederichs <
kay.diederichs at uni-konstanz.de> wrote:

> is there a way to get the R-factor statistics from phenix.refine, for a
> specific resolution range, e.g. 2.5-2.6A ? The reason I ask is that I would
> like to specify the same resolution range as the data reduction program
> does.

phenix.refine will print R-factors by resolution shell, but the number of
shells it decides to use varies with the number of reflections - for a
really small structure (e.g. amyloid peptide) you will have only one
resolution shell (the argument being that R-free statistics aren't reliable
if you have very few reflections in the test set).  You can set an upper
limit on this (refinement.main.max_number_of_resolution_bins), but it won't
give you ten shells if phenix.refine wants to use, say, five.  There may be
another way to get this information that I'm not aware of, but I've always
done it directly in Python.

I've been working on a project that potentially requires changing
phenix.model_vs_data to report these statistics; my plan was to use the last
of ten shells, since both HKL2000 and SCALA report everything that way
(don't know about XDS since I haven't used it).  Is this sensible, or does
it need to be more flexible and accept explicit resolution ranges?  (I'm not
actually sure whether this is possible right now, but 10 shells is easy.)

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