Hi Wolfram,

each phenix.refine run creates a MTZ file that contains four sections of data:

1) original data as supplied at input;
2) data actually used in refinement (which may miss a few outliers, truncated by resolution and/or sigma if requested by the user, Fobs obtained from Iobs using French&Wilson method, etc);
3) Fmodel: total model structure factors including all scales, etc. They can be used to reproduce reported R-factors exactly;
4) Map coefficients: 2mFo-DFmodel (with and without filling missing Fobs), mFobs-DFmodel and anomalous difference map (f input data is anomalous: that is contains Fobs(+) and Fobs(-)).

R-free flags are part of 1) and 2) above.

That's the file that is supposed to go to PDB one way or another (as MTZ or CIF).

Pavel

On 1/22/13 9:28 AM, wtempel wrote:

Hello all,
based on ${prefix}_001_f_model.mtz from phenix.refine, I would like to
prepare a cif file with structure factors.
FOBS, SIGFOBS, R_FREE_FLAGS, FMODEL, PHIFMODEL, FOM are available in
(+) and (-) versions, presumably representing Bijvoet pairs.
My questions are:
1) are FMODEL, PHIFMODEL the most appropriate columns for calculated
amplitudes and phases for the purpose of PDB deposition?
2) I understand that the PDB sf_tool does not accommodate separate
(+)/(-) columns for some of the items. A job for
phenix.reciprocal_space_arrays and a reflection file without anomalous
differences?
Alternatively, I imagine that phenix has a tailored procedure just for
the preparation of PDB deposition, but I may not have used the correct
web search terms to find the instructions.
Thank you in anticipation,
Wolfram Tempel
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