[phenixbb] structure factors for PDB deposition

Richard Gildea rjgildea at lbl.gov
Tue Jan 22 11:07:30 PST 2013

On 22 January 2013 10:03, Pavel Afonine <pafonine at lbl.gov> wrote:

> 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.
>> (+) 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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Hi Wolfram,

You can use the option write_reflection_cif_file=True in phenix.refine to
output an mmCIF reflection file that contains the same data as in the MTZ
file as described by Pavel. I recently fixed a bug regarding output of
anomalous arrays to the mmCIF file, so it would probably be best to try
with the latest nightly build  The use of mmCIF for PDB deposition is an
area we are actively working on right now, so we expect things to improve
in this area in the near future.




Richard Gildea

Software Developer
Physical Biosciences Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd
Mail Stop 64R0121
CA 94720-8118
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