[phenixbb] Defining planarity for Phenix.refine
Francis E Reyes
Francis.Reyes at Colorado.EDU
Mon Apr 19 11:56:01 PDT 2010
On Apr 19, 2010, at 11:50 AM, Nathaniel Echols wrote:
> On Mon, Apr 19, 2010 at 8:50 AM, Engin Özkan <eozkan at stanford.edu>
> I should say that I have never worked with DNA in crystal
> structures, and due to its structure, it might be better suited to
> parameterization that allows accurate rigid bodies. I just don't know.
> I'm not a nucleic acid crystallographer either, but aren't the
> helices (especially A-form) significantly more flexible than, say, a
> protein alpha-helix (or entire globular domain)?
Let's be clear on what is meant by 'flexible'. In solution, A-form
RNA helicies are generally not flexible. They're fairly rigid in
solution and that can be observed by many of inline probing experiments.
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.
Francis Reyes M.Sc.
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
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