[phenixbb] question on the weight for adp

fn1 at rice.edu fn1 at rice.edu
Thu Sep 30 15:45:34 PDT 2010

I see. Thank you very much!

Quoting Pavel Afonine <pafonine at lbl.gov>:

>  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.
> Pavel.
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