[phenixbb] Restraints for keeping base-pairs co-planar in RNA/DNA

Francis E Reyes Francis.Reyes at Colorado.EDU
Tue Sep 6 11:11:46 PDT 2011

Use secondary structure restraints (verify that PROBE detects all of the base pairs or manually build them and supply to phenix.refine) and reference structure restraints (build a dummy helix that matches your sequence). 

Question for phenix developers.. what's the relationship between secondary structure restraints and reference structure restraints? Does using a reference structure include any additional restraints generated by secondary structure restraints? (as applied to nucleic acid base pairing?)

On Sep 1, 2011, at 9:07 AM, jens j birktoft wrote:

> Hi everybody:
> What would be proper approach to generate restraints that will keep base pairs coplanar (or nearly coplanar) in RNA/DNA helical structures?  Hydrogen bonds by themselves are not sufficient, at least not for low resolution refinement, <4Å
> Jens 
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Jens J. Birktoft
> e-mail: jens.knold at gmail.com
> slow-mail: Dept. Chemistry, NYU, 350 CPW , Suite 9F, New York, NY 10025
> Phone: 212-749-5057
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Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

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