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

Nathaniel Echols nechols at lbl.gov
Thu Sep 1 08:24:52 PDT 2011

On Thu, Sep 1, 2011 at 8:07 AM, jens j birktoft <jens.knold at gmail.com> wrote:
> 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.


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