[phenixbb] question about refinement in a SAD data set

Pascal EGEA pascal at msg.ucsf.edu
Sun Mar 30 15:39:32 PDT 2008

Dear All,
I am trying to refine a seleno met structures at 2.2 Ang resolution
I used Auto_Sol and Auto_Build and it worked great since it found the  
4 semets with occupancies of about 0.85 to 0.95. and most of the  
model was built. Phenix generated  an exptl_fp_phases.mtz with the  
Rfree flag. so far so good. I have a couple of questions because I am  
not quite to understand what phenix.refine is doing at this stage?
1- If I refine  using the experimental phases mtz file generated by  
the auto_sol run, the occupancies for the seleniums change quite a  
bit and they drop to 0.75-0.80 and that does not sound right to me?  
What am I doing wrong? should I fix occupancies for the seleniums to  
the values evaluated at the end of the auto_build run (Rfree=27/  
2- This experimental phases mtz file contains FP and the HL  
coefficients for the phases but there are no more anomalous  
differences.   If I try to refine f' and f" using it,  Phenix tells  
me that there is no anomalous information contained in this file. So  
how do you refine f' and f"? and what is the practical reason for  
this AutoSol generated mtz file to not contain the anomalous  
differences that were used to locate the seleniums.

Thanks in advance for the explanation

Pascal F. Egea, PhD
Post Doctoral Researcher
University of California San Francisco
Department of Biophysics and Biochemistry
Robert Stroud Laboratory
pascal at msg.ucsf.edu

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