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

Jeff Headd jjheadd at lbl.gov
Tue Sep 6 11:27:24 PDT 2011


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: 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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