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Dear Mischa Machius,
Mischa Machius wrote:
> ...
That aside, what is the purpose of rmsd's?
I think one can indeed agree that the structure of an object does not
change with the resolution one looks at it. From that, one can conclude,
that one should use the same target values for bond lengths, etc., for
all resolutions. This assumes that geometric descriptors, like rmsd's,
tell us about the physical plausibility of a given model. They are
independent of diffraction data and are thus a valid concept even in the
limit of zero reflections. They are used to make sure that we have a
plausible model despite the lousy quality of our diffraction data. We
use other tests (such as R factors, map correlation, and so on) to tell
us how well the model corresponds to the data, but that's a different
issue. Thus, it is the well-founded expectations about the physical
reality that should trump the experimental data in all resolution
ranges. Note that this does not preclude the discovery of new features,
because we have ways of detecting where the model doesn't fit the data.
Here, I agree: the model should make sense both physically and
chemically and explain the observed data to a good degree.
...
However, one can also use rmsd's to guide the refinement process itself.
For example, at low resolution, we can't distinguish between bond
lengths of 1.4 or 1.6Å. Should we therefore not allow the bond lengths
to vary much more than at high resolution? Target rmsd's should
therefore be higher at low resolution than at high resolution, not the
other way around. They should go parallel with the coordinate error. The
argument is that using constraints (i.e. low rmsd's) at low resolution
gives the impression of a precision that is way too high compared to the
information content of the data. This assumes using rmsd's as error
models, which we have to match to experimental errors.
> ...
Here, I disagree: as you stated above, the model should make physically
and chemically sense. If you allow a larger deviation from expected
chemistry only because the lower resolution of the observed data doesn't
allow for a more precise model, you will violate that physical/chemical
reasoning. The underlying problem is, as Gerard has pointed out, that
there is no good single model that would explain low resolution data. In
principle, one should describe these data with multiple models, but this
is prohibitive given the low amount of data. I also think that the best
that one can currently do with low resolution data is to use a single
model tightly restrained to expected chemistry together with TLS to
describe at least partially the model's rigid body flexibility.
Best regards,
Dirk.
--
****************************************
Dirk Kostrewa
Paul Scherrer Institut
Biomolecular Research, OFLC/110
CH-5232 Villigen PSI, Switzerland
Phone: +41-56-310-4722
Fax: +41-56-310-5288
E-mail: [EMAIL PROTECTED]
http://sb.web.psi.ch
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