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.
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