Re: [phenixbb] question on the weight for adp

Hi Kendall, 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? Fengyun Quoting Kendall Nettles :

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. Kendall

On Sep 30, 2010, at 6:36 PM, "Pavel Afonine" wrote:

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Hi Fengyun,

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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.

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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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