On Sun, Oct 12, 2014 at 11:25 AM, Simon Jenni <jenni@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