[phenixbb] Refining anomalous groups

Pavel Afonine pafonine at lbl.gov
Sat Jan 12 12:43:51 PST 2013

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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