[phenixbb] refinement for non-standard DNA base

Nigel Moriarty nwmoriarty at lbl.gov
Thu Sep 11 09:22:35 PDT 2014


It's likely you need to change the "group" in the restraints CIF to RNA.
The atom names should also be the standard names on the backbone. I'm happy
to ensure that it works if you send me the files.



NB. Any files sent to me will be held in strictest confidence.

On Thu, Sep 11, 2014 at 9:02 AM, John Cheong <john123cheong at gmail.com>

> Hi,
> I have 5-fluoro-Uracil in my DNA:protein complex.
> I modeled 5-F-dU into the map, ran eLBOW for geometry file and did
> refinement.
> After the refinement, 5-F-dU is not connected to the neighboring
> nucleotides and the phosphate oxygens are rotated to wrong positions.
> Can anyone teach me how to refine with non-standard DNA base ?
> Any help or advice would be appreciated.
> John
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
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
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