Hi Jianghai,

the answers to both of your questions are YES:

- running phenix.refine with "wxc_scale=0" is essentially the same as performing a pure geometry regularization (no Xray contribution is accounted for). It is just less time efficient since even if you say "wxc_scale=0", phenix.refine still compute all X-ray related things like X-ray targets, R-factors, do bulk-solvent correction etc...

- yes, phenix.refine will use all your custom bond definitions regardless the value of "wxc_scale" parameter.

Pavel.


On 2/11/2008 12:43 PM, Jianghai Zhu wrote: 
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?

Thanks.

Jianghai
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