[phenixbb] Clashes problem

Pavel Afonine PAfonine at lbl.gov
Wed Feb 13 14:44:49 PST 2008

> 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 
> indicator. 

What does "stable" mean?

> 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.

This is because optimize_wxc minimizes your Rfree and it does not look 
at the geometry (this is said in the Manual): it chooses whatever weight 
that gives you the lowest Rfree. I agree that using combined "Rfree + 
geometry" could be a better thing to do (especially at lower 
resolutions). I'll put it in my list of things to try and implement if 


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