On Friday, February 10, 2012 12:51:03 pm Jacob Keller wrote:
> Interesting to juxtapose these two responses:
>
> James Stroud:
> >How could they not be snapshots of conformations adopted in solution?
>
> David Schuller:
> > How could that possibly be the case when any structure is an average of all
> > the unit cells of the crystal over the timespan of the diffraction
> > experiment?
This pair of perspectives is the starting point for the introductory
rationale I usually present for TLSMD analysis.
The crystal structure is a snapshot, but just like a photographic snapshot
it contains blurry parts where the camera has captured a superposition
of microconformations. When you photograph an object in motion, those
microconformations correspond to a trajectory purely along time.
In a crystallographic experiment, the microconformations correspond
to samples from a trajectory in solution. Separation in time has
been transformed into separation in space (from one unit cell to
another). A TLSMD model tries to reproduce the observed blurring by
modeling it a samples from a trajectory described by TLS displacement.
The issue of averaging over the timespan of the diffraction experiment
is relevant primarily to individual atomic vibrations, not so much to
what we normally mean by "conformations" of overall protein structure.
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
