[phenixbb] [MSpam] Re: Clashes problem

Jianghai Zhu jzhu at cbr.med.harvard.edu
Mon Feb 11 12:43:45 PST 2008

> 2) Minimise the geometry of the protonated model from 1) withOUT X- 
> ray term with:
> 	phenix.geometry_minimization --max-iterations=N input_h.pdb

I have a question about geometry_minimization.  I think wxc_scale = 0  
is the same as phenix.geometry_minimization.  But I have some external  
bond definitions defined in the eff file.  So if I use wxc_scale = 0  
and phenix.refine, will those external bonds be imposed on the model  
as the default geometries?



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