[phenixbb] some general refine questions

Pavel Afonine pafonine at lbl.gov
Wed Jul 4 22:26:25 PDT 2007

Hi Bill and all interested in this,

> Why is the weight multiplied by 0.5 by default?  Since changing that  
> to 1.0 slightly increases freeR, I assume it is the default for some  
> reason.

the total target for refinement of coordinates in phenix.refine is 
defined as:
Etotal = wc_scale * wxc * Exray + wc * Egeom

Similar for refinement of isotropic or anisotropic ADP.

- Exray is least-squares (LS), maximum-likelihood (ML) or any other kind 
of x-ray target;
- Egeom is geometry restrains target (Ebonds + Eangles + Eplanarities + 
Enonboned +...);
- wc = 1.0 and used to exclude geometry restraints by setting wc = 0.0;
- wxc ~ ratio of gradient's norms for geometry and x-ray targets as 
defined in (Adams et al, 1997, PNAS, Vol. 94, p. 5018);
- wc_scale is 'ad hoc' scale found empirically to be ok for most of the 
cases at medium resolution. It should be optimized at higher and lower 
resolutions. The default values are most likely NOT optimal at 
resolutions higher then 1.5A. Currently we are working on making it 
resolution dependent rather than one single value for all resolutions.

It is advised to play with wc_scale manually if:
- Rfree or Rfree - Rwork look not realistic;
- geometry deviations look not good (too tight or too loose at given 
However, once again, the default values for most of cases at "normal" 
resolution are OK.

In future we are planning to work out more robust and sophisticated 
methodology for automatic weights determination.


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