[phenixbb] R-factor difference between phenix and sftools

Pavel Afonine pafonine at lbl.gov
Mon Oct 13 14:16:23 PDT 2014

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.


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 
> <mailto: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
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