Dear Ian and contributors to this interesting thread,
(please, scroll down a little bit)
Am 15.09.10 23:34, schrieb Ian Tickle:
> I should just like to point out that the main source of the
> disagreement here seems to be that people have very different ideas
> about what a 'model' is or should be. Strictly a model is a purely
> mathematical construct, in this case it consists of the appropriate
> equation for the calculated structure factor and the best-fit values
> of the various parameters (scattering factors, atomic positions,
> occupancies, B factors, TLS parameters etc.) that appear in it. A
> mathematical model is inevitably going to be an imperfect
> representation of reality, but hopefully it's the best one we can come
> up with, in the sense of best explaining the data without significant
> overfitting.
>
> The problem arises because many users of the PDB, and I suspect many
> contributors to this BB, particularly non-crystallographers, don't see
> it like that, because they view a PDB file as a physical model, i.e.
> not as the best fit to the data (assuming that the
> non-crystallographers even know what the data are!), but the closest
> representation of reality. The difference between the N-H bond
> lengths that Ed referred to illustrates the distinction between the
> mathematical and the physical model. The mathematical model requires
> that the bond length is 0.86 Ang because that value gives the best fit
> of the assumed spherical scattering factor of H to the deformation
> density of the X-H covalent bond. The physical model requires that it
> be 1.00 Ang because that is the internuclear distance found by
> spectroscopic methods& predicted by QM calculations. The same goes
> for B factors and TLS: to a large extent they are a mathematical
> construct whose purpose is to provide an optimal fit to the data. The
> connection of Bs& TLS with reality is tenuous at best, nevertheless
> people obviously would like to have a physical interpretation such as
> rigid-body correlated motion. The fact that Bragg scattering provides
> no information about correlated motion (you need to measure the
> diffuse scattering for that) doesn't seem to deter them!
>
> I have no doubt in my mind that it is the mathematical model that
> should be published, because hopefully it's the best available
> interpretation of the data. Whether that involves publishing the
> riding H atoms explicitly, or alternatively the formulae and
> parameters that were used to calculate their positions I don't mind,
> as long as I can faithfully reproduce the Fcalcs to check the validity
> of the model. Then users of the PDB are free to *interpret* the
> mathematical models as physical models in a appropriate manner (e.g.
> by adjusting the bond lengths to H), and crystallographers have the
> untainted mathematical models needed to reproduce the Fcalcs.
so, wouldn't be the deposition of the final model's Fcalc, Phic (and
their weights) along with the final coordinates be the best solution?
The final Fcalc are our best model and can be used to reproduce the
final statistics (which would remove the sfcheck annoyance) and to
reproduce the final electron density maps, and the coordinates can be
used for what ever purpose they are needed, irrespective of adding
riding hydrogens or not.
Best regards,
Dirk.
--
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Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
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D-81377 Munich
Germany
Phone: +49-89-2180-76845
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