On Monday, 06 March, 2017 19:54:23 Keller, Jacob wrote:
> Dear Crystallographers (and cryo-EM practitioners,)
>
> I do not understand why there is a discrepancy between what crystallographers
> use to models disordered regions (b-factors/occupancies) and what the cryo-EM
> world uses ("local resolution.")
In both the EM and the X_ray world "uncertainty" is a property of the model,
while "resolution" is a property of the data.
For a crystal structure the resolution is known as soon as you collect the data;
you don't even need to solve the structure. It is a single number, or if you
want to get fancy an anisotropic tensor. In neither case is it a model for
disorder.
As I understand it (I am definitely out of my comfort zone here) EM does not
have easily determined uniform resolution. Instead you estimate the resolution
by looking at the image-to-image correlation after superposition, where the
correlation is computed only over some local region. You can have a core
region where images superimpose well and thus have high correlation (good
resolution), and at the same time have distal regions where there is
image-to-image
variation yielding imperfect superposition, lower correlation, and poor
resolution. That local resolution can still be calculated in advance of
fitting a molecular model. When you do fit a molecular model you may
deal with uncertainty by including B factors (well, ADPs) and occupancies
just as you would for a crystal structure.
Ethan
> I am tempted to say that "local resolution" is a misnomer, since I have been
> trained to think of resolution as a simple optical or physical characteristic
> of the experiment, and things that are blurry can in fact be "resolved" while
> disordered-one might think of the blurred wings of an insect in a
> long-exposure photograph, in which the resolution is of course ample to see
> the wings-but is there a good reason why the two different terms/concepts are
> used in the different fields? Could crystallographers learn from or
> appropriate the concept of local resolution to good benefit, or perhaps vice
> versa? Anyway, if there is a good reason for the discrepancy, fine, but
> otherwise, having these different measures prevents straightforward
> comparisons which would otherwise be helpful.
>
> All the best,
>
> Jacob Keller
>
>
>
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
