[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?
Thanks.
Jianghai
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