# [phenixbb] R-factor difference between phenix and sftools

Simon Jenni jenni at crystal.harvard.edu
Mon Oct 13 14:27:31 PDT 2014

```Thanks to all, and especially Nat for finding out the cause (different
formula for R-factor calculation in sftools and phenix)!
All the best, Simon

On Mon, Oct 13, 2014 at 5:16 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

>  Interesting.. I use this formula to calculate R-factor between two data
> sets when I cannot choose which one to call "Fobs" and which one to call
> "Fcalc". But clearly, this is not exact what we call R-factor.
>
> Pavel
>
> On 10/13/14 2:02 PM, Nathaniel Echols wrote:
>
> 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.
>
>  -Nat
>
>
> _______________________________________________
> phenixbb mailing listphenixbb at phenix-online.orghttp://phenix-online.org/mailman/listinfo/phenixbb
>
>
>
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