On Mon, Apr 19, 2010 at 8:50 AM, Engin Özkan
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)? I would also like to point out recent work by Axel Brunger's group on
low-resolution refinement (Schröder et al, Nature, 2010 and references therein). Low-resolution refinement, while not straightforward, is becoming mainstream.
What is still needed is general-purpose minimization in torsion-angle space, which should be especially powerful for nucleic acids (since each base will be a single rigid group). This still requires more work on the minimizer to make it practical for phenix.refine.