On Mon, Apr 19, 2010 at 11:56 AM, Francis E Reyes < [email protected]> 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.) -Nat