[phenixbb] Refinement use of Friedel pairs
Pavel Afonine
PAfonine at lbl.gov
Wed Jul 11 10:31:18 PDT 2007
Hi Mark,
this is controlled by main.force_anomalous_flag_to_be_equal_to parameter
which is set to None by default.
Here are the possible scenarios:
1) main.force_anomalous_flag_to_be_equal_to=None (default option):
phenix.refine will use all Fobs: Fobs(+) and Fobs(-) as independent
reflections.
2) main.force_anomalous_flag_to_be_equal_to=True:
phenix.refine will generate missing Bijvoet mates.
3) main.force_anomalous_flag_to_be_equal_to=False:
phenix.refine will merge Fobs(+) and Fobs(-), that is instead of two
separate Fobs(+) and Fobs(-) it will use F_mean = (Fobs(+) + Fobs(-))/2
The default is probably the best option
(main.force_anomalous_flag_to_be_equal_to=None).
Look "*group_anomalous refinement*" paragraph in phenix.refine
Documentation to see how to use and refine f' and f''.
Pavel.
Mark A Saper wrote:
> I am refining a structure containing SeMet with data collected at peak
> wavelength. Provided I give the f' and f'', will phenix.refine
> calculate F+ and F- structure factors and use the provided FOBS+ and
> FOBS- ? CNS does this. Refmac only uses f' and I get >6 sigma Fo-Fc
> peaks on the Se.
>
> Thanks for your help.
>
> _________________________________
>
> *Mark A. Saper, Ph.D.*
>
> Associate Professor of Biological Chemistry
>
> Biophysics Research Division, University of Michigan
>
> 930 N University Ave
>
> Ann Arbor MI 48109-1055 U.S.A.
>
>
> saper at umich.edu <mailto:saper at umich.edu> (734) 764-3353
> fax (734) 764-3323
>
> http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
>
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