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Mark, On Tue, 2010-09-14 at 13:34 -0400, Dr. Mark Mayer wrote: > Where does the crystallographic community stand > on deposition of coordinates with riding > hydrogens? Surely community is divided on this. There could be arguments made both ways. Personally, I think that riding hydrogens can be calculated if necessary using the same algorithms/parameters employed upon refinement. It is true that different programs may use different parameter sets and reproducing exactly the same set of riding hydrogens may be difficult without exact knowledge of which version was used and ability to unearth that old version of the software. This may preclude one from getting exactly the same riding hydrogen positions (how large that difference would be I honestly don't know). But really, who cares? What is the benefit of knowing exactly where this or that riding hydrogen was? Maybe there is some benefit of such comparison in method development, but I would think its rather limited. I wholeheartedly agree with Ethan (even though that is not strictly what he said :) that some minor benefit here is completely negated by the danger of perception that somehow models tell us where hydrogens are. It is bad enough that, in my estimate, roughly 10% of atomic coordinates in the PDB are unwarranted as they come from disordered residues with exact spatial positions unsupported by electron density. Let's not add more things that PDB users may over-interpret. Cheers, Ed.