[phenixbb] structure factors for PDB deposition

Pavel Afonine pafonine at lbl.gov
Tue Jan 22 10:03:49 PST 2013

Hi Wolfram,

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

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).


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.
> (+) 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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> phenixbb at phenix-online.org
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