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.

[email protected] (734) 764-3353 fax (734) 764-3323

http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
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