[phenixbb] Clashes problem

Jianghai Zhu jzhu at cbr.med.harvard.edu
Wed Feb 13 14:40:15 PST 2008

> the answer - I don't know. Optimizing the weight you can use  
> different things, like Rfree, divinations from ideal  
> stereochemistry, LLG, or combination Rfree and divinations from  
> ideal stereochemistry, etc... Rfree seemed to me the most obvious  
> and easy, but again, I have no strong feelings or experience what is  
> better (and what "better" actually means in this context).

Based on Ian Tickle's paper http://journals.iucr.org/d/issues/2007/12/00/gx5119/gx5119.pdf 
, -LLG is slightly more stable and better than Rfree as a refinement  

> What do you mean by "less stable/reliable" ?
> The procedure that phenix.refine uses is very simple... The overall  
> target is (for xyz refinement; similar for B-factors):
> Etotal = wxc * wxc_scale * Exray + wc * Egeom
> wxc is determined as in CNS (ratio of gradient norms), wc = 1.0,  
> wxc_scale is adjustable parameter which is by default set to 0.5 or  
> so. In most of cases at "normal" resolutions the automatic weight is  
> good. If not, then you need to either play with wxc_scale manually  
> or have phenix.refine do it for you automatically by using  
> optimize_wxc. And what "optimize_wxc=true" does is just a grid  
> search: it tries different wxc_scale values and chooses the one that  
> produces the lowest Rfree. I don't see why it could be unstable or  
> not reliable. Obviously, one can use any other criterion instead of  
> Rfree.

I do have a problem with the default wxc_scale and the optimize_wxc =  
true.  But my structure is at low resolution 3.5 A.  The default  
wxc_scale really couldn't hold up the geometry and the optimize_wxc =  
true just made it worse. I have to manually set the wxc_scale = 0.1.

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