[phenixbb] [MSpam] Re: Clashes problem
PAfonine at lbl.gov
Mon Feb 11 13:00:28 PST 2008
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.
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?
> phenixbb mailing list
> phenixbb at phenix-online.org
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