[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>
wrote:
> 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?)
-Nat
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