[phenixbb] Discrepancy between R-factors from phenix.refine vs phenix Generate "Table 1"

Nathaniel Echols nechols at lbl.gov
Wed May 29 16:16:50 PDT 2013

On Wed, May 29, 2013 at 4:13 PM, Sam Stampfer <Samuel.Stampfer at tufts.edu> wrote:
> I am preparing my structure for deposition and ran it through the Generate
> "Table 1" function in phenix. The inputs I gave it were my .mtz structure
> factors file, the final pdb coordinate file, and the log file from hkl2000.
> I did not provide unmerged data.
> My pdb file (which had been refined using phenix.refine) had values of
> r_work=0.2342 r_free=0.2603
> However, phenix.model_vs_data (from Generate "Table 1") gave me
> r_work=0.2940 r_free=0.3150

This is definitely not the intended behavior.  Could you please send
me the inputs off-list?


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