[phenixbb] phenix.refine questions: weights, docs, etc.

Pavel Afonine pafonine at lbl.gov
Tue May 29 08:29:28 PDT 2007


Hi,

thanks for your questions!

> 1) What's the reason for refining bss, xyz and adp in separate cycles?  CNS
> does that too while refmac (I believe) refines them simultaneously.  I
> suspect I missed something, but I thought the power of ML refinement is that
> no refinable parameters are held constant if they're not supposed to be.
> (At least, wasn't that the big deal in Sharp when it came out?)
>   

It is common practice to refine bulk solvent and scale, coordinates, 
ADPs, an other parameters separately. There are numerical issues behind 
this (see for example: Acta Cryst. (1978). A34, 791-809; /Acta Cryst./ 
(2005). D*61*, 850-855; ...). CNS does exactly the same: it refines this 
parameters separately. To my knowledge, same for REFMAC. This is not 
target specific. The power of ML refinement is that ML target 
statistically models missing scatterers in a model and and errors (/Acta 
Cryst./ (2002). A*58*, 270-282).

> 2) How does one figure the right restraint weights?  (wxc and wxc).  In
> refmac, I've always calibrated the weight with rmsd(bonds), tightening it
> until rmsd(bonds) is ~0.018 (or below for lower reso);  invariably this is
> where Rfree will decrease furthest and smoothly as well (i.e. without that
> silly rise at the end.)
>
> With phenix.refine I'm finding that I only get Rfree to drop monotonously
> when I tighten the weights (both wxc and wxu) so much that rmsd(bonds) goes
> down to ~0.002.  Would there be a different way to do this?
>   

The weights wxc for coordinates (refinement target E = wxc*Exray + 
Echem) and wxu for ADP (refinement target E = wxu*Exray + Eadp) 
refinement are determined automatically based on the gradients ratio 
(Proc. Nat. Acad. Sci. USA. 1997, 94:5018-5023.). Again, this is very 
close to what CNS does and is demonstrated to be relatively reliable. 
Since it is automatic, it may give different weights from macro-cycle to 
macro-cycle making it possible some slight oscillation in R/Rfree. You 
can also scale the weights manually by using wxc_scale and wxu_scale to 
achieve desired gap between R and Rfree and deviations from ideal values 
of bonds, angles (see phenix.refine Documentation).

> 3) There isn't currently torsional refinement, is there?  

It is under active development.

> 4) Is there good documentation for all the loads and loads of keywords?  The
> names themselves are just descriptive enough to be interesting, but
> obviously not enough to be informative if I don't just want the black box.
>   

Many of the important and popular scenarios and keywords are in 
phenix.refine Documentation. I plan to expand it before the next release.

Please let me know if you have any questions.

Pavel.


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