[phenixbb] Geometry Restraints - Anisotropic truncation

Leonid Sazanov sazanov at mrc-mbu.cam.ac.uk
Tue May 1 07:38:51 PDT 2012

> 1) maps calculated using all (unmodified) data by phenix.refine, 
> phenix.maps and similar tools are better than maps calculated using 
> anisotropy truncated data. So, yes, for the purpose of map calculation 
> there is no need to do anything: Phenix map calculation tools deal 
> with anisotropy very well.

That is not our experience in cases of really severe anisotropy.

> 2) phenix.refine refinement may fail if one uses original anisotropic 
> data set. This is probably because the ML target does not use 
> experimental sigmas (and anisotropy correction by UCLA server is 
> nothing but Miller index dependent removing the data by sigma 
> criterion - yeah, that old well criticized practice of throwing away 
> the data that you worked hard to measure!). May be using sigmas in ML 
> calculation could solve the problem but that has to be proved.

UCLA server removes all the data beyond set ellipsoid, it does not deal 
with individual reflections by sigma.
Also one can set its own resolution limits on UCLA server, depending on 
personally preferred criteria.
As for throwing away data, what is the difference here from "throwing 
away data" when we cut the resolution isotropically (one high res limit) 
using whatever criterion (I/sigma, R, correlation) one prefers?


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