[phenixbb] question on the weight for adp

Kendall Nettles knettles at scripps.edu
Thu Sep 30 15:47:12 PDT 2010

Hi Fengyun, 
I would add to Pavel's comment that the answer is empirical, and I would first try the optimize weights option, or if you really want to have one set weight for all cycles then set up half a dozen jobs in parallel and see which gives best maps/stats. I would bet the optimize weights on each cycle would likely perform best, though.

On Sep 30, 2010, at 6:36 PM, "Pavel Afonine" <pafonine at lbl.gov> wrote:

>  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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