On Mon, Apr 19, 2010 at 8:50 AM, Engin Özkan <span dir="ltr"><<a href="mailto:eozkan@stanford.edu">eozkan@stanford.edu</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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.</blockquote><div><br>
</div><div>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)?</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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.<br>
</blockquote><div><br></div><div>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.</div>
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