Date: Wed, 4 Aug 2010 10:37:45 -0700 From: Nathaniel Echols To: PHENIX user mailing list Subject: Re: [phenixbb] r-work and r-free for specific resolution range(s) Message-ID: Content-Type: text/plain; charset="iso-8859-1"

On Wed, Aug 4, 2010 at 10:22 AM, Kay Diederichs< [email protected]> 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.)

-Nat

Hi Nat, in fact this is a small protein, and phenix.refine only outputs a single resolution shell. phenix.model_vs_data currently does not give R-factors; it would be worthwhile to enhance this, and to have it accept shell limits. XDS has 9 shells whose limits are calculated internally, and one overall. For XSCALE, one can specify up to 20 RESOLUTION_SHELLS . In the meantime, I resort to sftools <