[phenixbb] Refining anomalous groups
mbfrolow at post.tau.ac.il
Sat Jan 12 14:37:22 PST 2013
I understand all that :-\
However in may hands manual selection of anomalous scatterers for the refinement never worked. Well
"never" is too strong. Couple of times I have tried I did not succeed. As you say, generally we can survive
without this refinement, and with the first resistance I have abandoned the task. Usually I do not abandon
task. I may hunt them (tasks and structures) for years and then I make my kill. I just wanted to try "bullet-proof" automatic anomalous
refinement and then to dig in outputs to understand what I did wrong. Most probably atom selection syntax in Phenix which, due to existence of GUI I
never spent enough time to study.
My best, will be happy if you will comment :-)
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
On Jan 12, 2013, at 22:43 , Pavel Afonine <pafonine at lbl.gov> wrote:
> Hi Felix,
>> Is the use of I+ I- with apparently larger impact on the final
>> structure is not a sufficient justification?
> yes, this is true. Did any one doubt it? If you know which atoms are anomalous scatterers and you have I+ and I- then it is a valid idea to refine their f' and f''. However, automatically making decision to refine f' and f'' just based on atom heaviness and presence of I+ and I- seems questionable to me. May be it's just fine but so far I haven't see logic and convincing arguments for doing this.
>> In structures with good diffraction data and sufficient resolution we frequently see S atoms
>> on the anomalous difference map.
> Sure. This is good knowledge sufficient to make decision to refine their f' and f''. Decisions about choice of refinement strategy and model parametrization have to be supported by the experimental data and model quality. In this case you know that your sulfurs are anomalous scatterers and you use this knowledge to decide refining their f' and f''.
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