[phenixbb] question on the weight for adp

Pavel Afonine pafonine at lbl.gov
Thu Sep 30 15:34:31 PDT 2010

  Hi Fengyun,

> My case is that some part of the model will be refined to large B 
> values (about 100) if the default value of wxu_scale (1.0) is used. 
> The other part of the model will have average B value of about 40, 
> which the wilson B is about 35. The corresponding 2FOFC map has very 
> poor density for the region with large B values.

"large" B-factors for atoms in poor density are expected. Also, the 
large B-factors is not always something wrong.

> If the value of wxu_scale set to be 0.1, that part with large B will 
> be refined to about 80 for B. The corresponding 2FOFC map has some 
> better (but not good enough) density for this region.
> My question is that can I keep the wxu_scale at the small value for 
> the refinement?

If it lowers B-factors, improves the R-factors and maps, then yes, keep 
whatever wxu_scale that does it. wxu_scale is just a number that 
balances target contributions arising from X-ray data and restrains and 
its absolute value doesn't have any particular meaning.


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