[phenixbb] Modeling Disordered Domains

Nathaniel Echols nechols at lbl.gov
Mon Apr 4 11:48:21 PDT 2011

On Mon, Apr 4, 2011 at 11:11 AM, Damian Ekiert <dcekiert at scripps.edu> wrote:
> On a final note, regarding those pesky missing side chains: any thoughts on
> trying to employ a "Ringer"-like approach to model some of these (Fraser, et
> al., Nature 2009, 462(7273):669-673)?  Is this practical (maybe this would
> add to many additional parameters)?

This is potentially useful for finding and building alternate
conformers (something that most programs don't do - the only one I'm
aware of is qFit: http://smb.slac.stanford.edu/qFitServer/qFit.jsp).
But Ringer still relies on having some interpretable (albeit weak)
density for the sidechains, and was designed to look at static rather
than dynamic disorder.  (A somewhat artificial distinction, but
appropriate enough when talking about refinement.)  It is also limited
to relatively high resolution, usually better than 2.0A, not because
of data-to-parameter ratio, but because the maps at lower resolutions
just don't have enough detail to detect alternate conformations with
any degree of confidence.

Regarding missing or patchy domains, Pavel recently added a feature
that should at least improve the phases and refinement behavior, but
I'll let him describe it since I don't really understand what it does.
 I do not know of cases where people have found a reasonable way to
model these explicitly, other than placing a rigid domain and letting
the B-factors go crazy.


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