[phenixbb] Refining anomalous groups
mbfrolow at post.tau.ac.il
Sat Jan 12 10:32:20 PST 2013
Is the use of I+ I- with apparently larger impact on the final
structure is not a sufficient justification? In structures with good diffraction data and sufficient resolution we frequently see S atoms
on the anomalous difference map.
On Jan 12, 2013, at 20:13 , Pavel Afonine <pafonine at lbl.gov> wrote:
>> There's probably no reason why it needs to be this hidden - it seems very safe so far, but until we've had more chances to test it we prefer to minimize the number of features that can potentially break.
> My understanding is that this option will select all atoms that are heavier than some defined value, and then it will refine f' and f'' for them. This may mean that you will be refining f' and f'' for atoms that were not anomalously scattering; that is you will be refining parameters that do not need to be refined. While this may be harmless (though someone needs to prove it) I believe it is suboptimal: 1) runtime wise, and 2) unnecessary refined parameters may mop up other model errors. Analogy could be: refining occupancy of fully occupied atoms.
>>> Will be the event of refinement of anomalous dispersion parameters f' and f"
>>> recorded in PDB file?
>> I am not sure whether phenix.refine includes anything in the headers -
> It does output it like this:
> REMARK 3 ANOMALOUS SCATTERER GROUPS DETAILS.
> REMARK 3 NUMBER OF ANOMALOUS SCATTERER GROUPS : 2
> REMARK 3 ANOMALOUS SCATTERER GROUP : 1
> REMARK 3 SELECTION: name BR
> REMARK 3 fp : -0.8792
> REMARK 3 fdp : 5.8029
> REMARK 3 ANOMALOUS SCATTERER GROUP : 2
> REMARK 3 SELECTION: name CO
> REMARK 3 fp : 0.0000
> REMARK 3 fdp : 0.0000
> but does not read.
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Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor
e-mail: mbfrolow at post.tau.ac.il
Cellular: 0547 459 608
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