Hi Pavel, thanks a lot for your fast response! Here some clarification: - somehow, the adjustments of the B weights were not taken into account at all. Ie. a "diff" on the pdb-files from jobs run with wxu_scale=0.5 and wxu_scale=2.0 shows that they are identical. While the log file acknowledges the "Command line parameter definitions" for wxu_scale=1 and wxc_scale=2, during the refinement section it states that wxc_scale = 1.0 and wxu_scale= 2.16. - yes, I included a TLS refinement. Are TLS refinement ans wxu_scale mutually exclusive? How would one proceed in this situation? Cheers Jan On 9/18/07, Pavel Afonine wrote:

Hi Jan,

...

in the final stages of refining a structure, I would like to optimize the restraint weights for geometry and B factors.

Good idea! Although phenix.refine computes "optimal" weight automatically, the values vary from structure to structure.

...

It seems to work fine for geometry by defining "refinement.target_weights.wxc_scale=1.0".

Yes, I would try an array of values 0.25, 0.5, 1.0, 1.5, 2.0, 2.5.

...

However, when the respective definition for B-factors does not seem to have an impact at all.

This is very weird. We exercise this in out tests regularly, so it changing wxu_scale should have an impact. It may be that values range for you structure is somehow different... Can you try the extreme values: very big (wxu_scale=10) and very small (wxu_scale=0.1) and see if this makes a difference? Are you using TLS (if yes, then this behavior is explainable)?

...

The main reason why I try to fiddle around with the B-weights is that coot gives me a whole bunch of red bars in the Temperature factor variance analysis...

The variability of ADP depends on many factors: resolution, model used for global motion (TLS), how internal degrees of freedom modeled ... I do not know if Coot analysis takes this all into account. Otherwise I would use the "red bars" analysis with some care.

Pavel.

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

I will chime in. Is it possible for phenix.refine to get the TLS parameters from a previous run? then we can change wxu_scale value during an individual_adp refinement in the presence of fixed TLS parameters. Jianghai On Tue, 2007-09-18 at 09:45 -0700, Pavel Afonine wrote:

Yes, I'm copying the response for exactly the same question that I wrote a week ago or so...

Part 1:

Playing with wxu_scale is how you change the strength of ADP restraints in all cases except when you do combined "TLS+individual ADP" refinement. In order to make the TLS refinement very robust and efficient we re-refined ~350 TLS containing structures from PDB performing the grid search for wxu_scale parameter and we found some "optimal" values for wxu_scale as a function of resolution. We use these values in automatic adjustment that you are mentioning. So currently there is no way you can turn off this adjustment; however I realize that users may want to play with wxu_scale themselves and skip the adjustments so I will provide this option in future.

Part 2:

As a possible solution to keep going now you can try this two-step refinement: step 1: Refine your model with default strategy (strategy=individual_sites+individual_adp) making sure that the ADP restraints are tight enough (play with wxu_scale) to produce the B-factors distribution that you like. step 2: Refine the best model out of "step 1" with the strategy=individual_sites+group_adp+tls. This will preserve the distribution of B-factors in the model from "step 1" and will add TLS model on top of it.

Please let me know if you have any questions/problems! Pavel.

Jan Abendroth wrote:

...

Hi Pavel, thanks a lot for your fast response! Here some clarification: - somehow, the adjustments of the B weights were not taken into account at all. Ie. a "diff" on the pdb-files from jobs run with wxu_scale=0.5 and wxu_scale=2.0 shows that they are identical. While the log file acknowledges the "Command line parameter definitions" for wxu_scale=1 and wxc_scale=2, during the refinement section it states that wxc_scale = 1.0 and wxu_scale=2.16. - yes, I included a TLS refinement. Are TLS refinement ans wxu_scale mutually exclusive? How would one proceed in this situation?

Cheers Jan

On 9/18/07, *Pavel Afonine* mailto:[email protected]> wrote:

Hi Jan,

> in the final stages of refining a structure, I would like to optimize > the restraint weights for geometry and B factors.

Good idea! Although phenix.refine computes "optimal" weight automatically, the values vary from structure to structure.

> It seems to work fine for geometry by defining > "refinement.target_weights.wxc_scale=1.0 ".

Yes, I would try an array of values 0.25, 0.5, 1.0, 1.5, 2.0, 2.5.

> However, when the respective definition for B-factors does not seem to > have an impact at all.

This is very weird. We exercise this in out tests regularly, so it changing wxu_scale should have an impact. It may be that values range for you structure is somehow different... Can you try the extreme values: very big (wxu_scale=10) and very small (wxu_scale=0.1) and see if this makes a difference? Are you using TLS (if yes, then this behavior is explainable)?

> The main reason why I try to fiddle around with the B-weights is that > coot gives me a whole bunch of red bars in the Temperature factor > variance analysis...

The variability of ADP depends on many factors: resolution, model used for global motion (TLS), how internal degrees of freedom modeled ... I do not know if Coot analysis takes this all into account. Otherwise I would use the "red bars" analysis with some care.

Pavel.

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

------------------------------------------------------------------------

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb