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:

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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Technically, it will affect validity of the model. Let's say you adjust weights so that geometry is weighted down to essentially zero - you are very likely to get invalid model (unless it's ultrahigh res and you don't need restraints anyway). On the opposite, if you use restraints that are extremely tight, you will tilt the balance towards idealized model which will be not the best you can get from the data. The question of correct weights is a tricky one, but the good ole approach of minimizing Rfree (or maximizing log-likelihood) while keeping the rmsd_bonds within 0.02ish will not lead you astray. On Thu, 2010-09-30 at 17:49 -0500, [email protected] wrote:

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:

...

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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