[phenixbb] question on the weight for adp
fn1 at rice.edu
fn1 at rice.edu
Thu Sep 30 15:49:00 PDT 2010
Thanks! Does this mean that I can always adjust the weights in order
to get beta map/stats? And whatever weights used will not affect the
validity of the model?
Quoting Kendall Nettles <knettles at scripps.edu>:
> 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.
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