[phenixbb] Refinement use of Friedel pairs

[Pavel Afonine]

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
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>
> 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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