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. -- ******************************************************* Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax: +49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW: www.genzentrum.lmu.de *******************************************************
