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