John

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.

Cheers

Nigel

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

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

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
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