[phenixbb] R-factor difference between phenix and sftools

Nathaniel Echols nechols at lbl.gov
Mon Oct 13 14:02:38 PDT 2014

On Mon, Oct 13, 2014 at 11:54 AM, Nathaniel Echols <nechols at lbl.gov> wrote:

> In the default phenix.refine output MTZ, the "F-obs" column will not be
> scaled to F-model.  My guess is that your input data have already been
> placed on an absolute scale based on the Wilson statistics, so the results
> are reasonably close, but when I tried using the same commands on an XFEL
> dataset I got an R-factor of 192.

Okay, this statement is at least partially incorrect - your data are
clearly on the correct scale in the phenix.refine output file, but the data
in the file I used are not.  (I'm going to blame this on the weirdness of
certain XFEL data.)

However, I did eventually figure out the problem: SFTOOLS is using a
different formula for the R-factor.  If you give it the command "correl
help", it will include this:

  RFACT      Rfactor in percent
             ( 200*Sum|col1-col2|/sum(col1+col2) )

Which disagrees with our source code, and the Rupp textbook, and Kay's
wiki, and Wikipedia, all of which use sum(col1) as the denominator
(assuming col1 == F-obs, but in our code it's written more generally).  In
other words: the R-factors from SFTOOLS cannot be meaningfully compared to
the R-factors from refinement.

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