Hi Francis,
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?)
Secondary structure restraints and reference model restraints act independently. The secondary structure restraints are added to the target function as distance restraints (H-bonds or pseudo H-bonds), while the reference model restraints are added as torsion-based restraints. We are working on ways of combining the two intuitions, but in theory they should complement each other in a well-built model. Jeff
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
+++++++++++++++++++++++++++++++++++++++++++++++++++++++
Jens J. Birktoft e-mail: [email protected] slow-mail: Dept. Chemistry, NYU, 350 CPW , Suite 9F, New York, NY 10025 Phone: 212-749-5057
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
--------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb