[phenixbb] Defining planarity for Phenix.refine

Nathaniel Echols nechols at lbl.gov
Mon Apr 19 13:56:22 PDT 2010

On Mon, Apr 19, 2010 at 11:56 AM, Francis E Reyes <
Francis.Reyes at colorado.edu> wrote:

> Now let's talk about flexibility during refinement. Without restraining the
> bases with some kind of strict geometry weight, or in the case of the OP,
> specifically restraining *coplanar* *base pairing for canonical watson
> crick pairing*, depending on the quality of the phases, I've seen
> phenix.refine and refmac pull bases that we know to be base paired in an
> A-form helix out of the 'coplanar base pair' orientation. If I were solving
> an RNA from scratch, I'd know apriori that this is a true base pair, and
> it's almost offensive that a refinement program would say otherwise. It's
> not drastic, but any RNA/DNA structural biologist will look at your
> structure and clearly see that there's something wrong with the geometry.
> While it maybe a minor nuisance to correct this manually, I can only wonder
> how it affects the refinement.

Okay; it probably isn't very difficult to add base pair restraints to
Phenix, we're just not quite sure how to make a general solution (which
would support planarity restraints in addition to H-bonds).  The main
bottlenecks right now are a) figuring out a convenient reduced
representation for base pairs, and b) identifying base pairs in a model.
 Aren't non-WC base pairs going to be very important in large RNA
structures?  Are there (free, open-source) tools that will generate a
listing of *all* base pairs found in a model, not just the canonical ones?
 (Actually, a simple and more-or-less machine-readable listing of the bonds
formed by each base pair type would be close enough.)

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