[phenixbb] Defining planarity for Phenix.refine

Nathaniel Echols nechols at lbl.gov
Mon Apr 19 10:50:44 PDT 2010

On Mon, Apr 19, 2010 at 8:50 AM, Engin Özkan <eozkan at stanford.edu> wrote:

> 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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100419/692a1daf/attachment-0002.htm>

More information about the phenixbb mailing list