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?) F 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
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Jens J. Birktoft e-mail: [email protected] 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