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On Wednesday 10 January 2007 22:37, Eric Bennett wrote: > Ethan Merritt wrote: > > >The best results (R, Rfree, geometry) are obtained by explicit inclusion > >of hydrogens via the riding-hydrogen model. This is also a basis for the > >Molprobity validation tools. > > But you still don't include them explicitly in the final model, which > is what this discussion is really about. To the contrary, they *are* included explicitly in the final model. Their inclusion is documented in the header record I quoted before, the one that states the model includes riding hydrogen atoms. In a similar (and similarly problematic) manner, other header records tell you that - an anisotropic B correction was or was not applied - that certain sets of atoms were modeled using TLS - that one of several bulk solvent models is in effect - etc, etc All of these *are* part of the final model. Without this information, a 3rd party could not replicate the results. At the same time, many programs and many non-crystallographers fail to take account of these aspects of the model. Yes, it is a problem. But the answer to the problem is to improve the programs and to educate the end-consumers of our work. I think it would be absurd to suggest that we should pass up the methods to create and refine better models, just because the details of the methodology will not be well understood by people from outside the field. > Has anyone done a large-scale study of whether modeling all > geometrically reasonable common rotamers improves R, Rfree, and > geometry for various possible definitions of a "disordered side > chain"? It sounds from Kevin's comments like no large study has been > done. But in the end, that is probably the only way to conclusively > resolve this question: by looking at whether making educated guesses > for disordered side chains (you'd have to carefully define > "disordered") improves the model's agreement with the experimental > data. All of our theoretical arguments in this thread wouldn't mean > that much in the face of some conclusive evidence one way or the > other. I am not aware of any such study. But it sounds like a perfectly reasonable thing to investigate.
