[phenixbb] R-factor difference between phenix and sftools

Nathaniel Echols nechols at lbl.gov
Mon Oct 13 11:54:03 PDT 2014

On Sun, Oct 12, 2014 at 11:25 AM, Simon Jenni <jenni at crystal.harvard.edu>

> However, when I calculate the R-factors with sftools, I get a discrepancy
> between the phenix and sftools results:
>    sftools << eof
>    read com_001_f_model.mtz
>    Y
>    select col R_FREE_FLAGS > 0
>    correl col FOBS FMODEL
>    select invert
>    correl col FOBS FMODEL
>    quit
>    Y
>    eof
>    R-work: 33.6
>    R-free: 38.1
> Does anyone perhaps know what causes this difference?

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.  Try using F-obs-filtered, which will be
on the same scale.

(This doesn't explain however why phenix.cc_star nonetheless produces the
expected output.  Can you please send me the logfile?)

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20141013/fe0e9999/attachment.htm>

More information about the phenixbb mailing list