[phenixbb] Refining f'/f"?

Leigh Allen c.leigh.allen at gmail.com
Thu May 7 11:53:31 PDT 2009


I'm new to the world of x-ray crystallography.  I just solved my first SAD
structure and I'm on to the refinement stage.  The difference map generated
by phenix.refine has really big positive peaks all around my MET residues.
If I switch the atoms to MSE, then I get large negative peaks.  Firstly, I'm
not sure if I'm supposed to represent these residues as MET or MSE because
it's a "native," high resolution (1.85) dataset, but it the protein had MSE
residues.  When scaling this data, I did not keep F(+) and F(-) separate.
The protein's phases were generated using SAD data to 2.7A, which using
SHARP led to a remarkably interpretable map that allowed me to build in the
protein by hand. My second question is, how should I handle the issue with
large + MET/large - MSE peaks?  Do I need to rescale my data to treat it as
anomalous data or is there something I can do within Phenix to fix my
problem.  I tried the phenix.refine GUI and set it up to refine f' and f",
but it appears that nothing really changed.


Leigh Allen

Ph.D Candidate
McCafferty Lab
Department of Chemistry
Duke University
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