[phenixbb] 0 for wxc_scale and wxu_scale?

Pavel Afonine pafonine at lbl.gov
Wed Nov 26 08:29:08 PST 2008

Hi Michaela,

which version of PHENIX you are using? Please make sure you are using 
the latest version.
> I am refining a structure with a resolution of 2.1 Angstroem using Phenix.
> The spacegroup is P 31 2 1 (No. 152) with a twin fraction of 0.37 and twin 
> law -h,-k,l.
> In the refinement procedure the NCS (4 chains) constraints are on, using 
> individual sites, ADP and occupancy refinement.

Just a suggestion to quickly try out... What happens if you turn off the 
NCS restraints and do some refinement without using NCS (with and/or 
without optimizing the weights)? I know it depends on many factors, but 
I've seen a good number of cases at around 2A resolution where the 
refinement was better if NCS is not used.

> In the last refinement step, I use the option to optimize the values for 
> wxu_scale and wxc_scale. These values are optimizes to 0 for wxc_scale and 
> close to 0 for wxu_scale (0.2)

It's all relative, the absolute values don't tell you much. If the R-, 
R-free and Rfree-R are better after wxc_scale and/or wxu_scale 
optimization and the geometry makes sense, then you got better model.

> Interestingly I obtain better R values (0.1948/0.2184), than without the 
> optimization by using the default values (0.1391/0.2438 Rwork/Rfree).

Clearly, (0.1948/0.2184) is much better than (0.1391/0.2438). Some 10% 
gap between R and Rfree at 2.1A resolution is bad.

> How is it possible that wxu_scale and wxc_scale can be optimized to 0 by 
> having better statistics?
> The total refinement target is defined as
> Etotal= wxc_scale x wxc x Exray + wc x Egeom
> As I understand it, the crystallographic refinement target (Exray) would now 
> not be considered in the refinement procedure.
> Would this refinement procedure be valid?

It doesn't happen in all macro-cycles and this is important.
You can also try to play with the weights manually by trying different 
values for wxc_scale and wxu_scale.

> And how is wxc (output of target weights: x-ray data) defined?

See phenix.refine documentation page:
section "8. Target weights calculation". With some variations, the 
implementation is very close to what's described there.

Please let us know if you have any other questions or problems!


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