Hi Zhiyi,

I am trying to refine a structure with two domains. The electron
> density of one domain is reasonable, but that of the other domain is
> poor. So, I am wondering whether the refinement by Phenix or Refmac
> can be done locally with two parts, the first domain is refined with
> normal restrains, the second domain is refined by rigid body and group
> B?
>

yes, you can do it in Phenix. Such functionality is exemplified for example
here:
see page 6:
http://www.phenix-online.org/presentations/latest/pavel_phenix_refine.pdf

Let me know if you have any questions.
Pavel

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