Restraints for keeping base-pairs co-planar in RNA/DNA
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 *
On Thu, Sep 1, 2011 at 8:07 AM, jens j birktoft
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
The only way to do this right now is to define custom planarity restraints, like this: refinement.geometry_restraints.edits { planarity { action= *add delete change atom_selection= (chain A and resseq 1 and (name X or name Y or name Z or ...)) or (chain B and resseq 10 and (name X or ....)) sigma= 0.1 } } Increasing sigma will make it looser, but I'm not sure what the scale is. It will probably need to be relatively high to allow for propeller twist (or other deformations - I've long since forgotten what these are); the individual base planarity restraints will continue to keep those very flat and rigid. We've discussed adding this restraint internally, but we haven't decided the best way to implement it - I suppose we could at least streamline the definition of custom planes. However, we are short on good test cases, so if anyone has an example of a *small* structure that needs the additional restraints, please contact me off-list. -Nat
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
+++++++++++++++++++++++++++++++++++++++++++++++++++++++
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
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
participants (4)
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Francis E Reyes -
Jeff Headd -
jens j birktoft -
Nathaniel Echols