[phenixbb] DNA pucker

Nigel Moriarty nwmoriarty at lbl.gov
Mon Apr 30 09:35:08 PDT 2018


Fred

If you change the input geometry to be C3'-endo, phenix.refine will
maintain the geometry by applying the appropriate restraints. I can see how
specifying the desired pucker would be nice. If you send me the files, I
will work on it.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Fri, Apr 27, 2018 at 1:54 PM, Dyda <dyda at ulti.niddk.nih.gov> wrote:

>
> Hi,
>
> Is it possible and if so how to change the pucker restraint
> for a particular DNA nucleotide from C2'-endo to C3'-endo
> in phenix.refine? I have a problem with a terminal nucleotide
> that is in an active site and the current C2'-endo doesn't
> seem consistent with the 2Fo-Fc map.
>
> Thanks for your help.
>
>  [32m********************************************************
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