On Wed, Jan 21, 2015 at 12:24 PM, Keller, Jacob <kell...@janelia.hhmi.org> wrote:
> I think this will probably never happen, but maybe there could be a > confidence value associated with each atom in structures a posteriori, > although it might be difficult to find the right automatable criteria for > this value. The element would be assigned by being the most likely one, and > confidence assigned thereafter. Too much of a pain to implement, probably, > and maybe not worth the trouble. Perhaps, though, Nat’s program could be > used to do this. [ doi:10.1107/S1399004714001308 > <http://dx.doi.org/10.1107/S1399004714001308> ]. > Unfortunately that implementation isn't really "quantitative" in the sense you describe - not for lack of interest on our part, but rather because coming up with a unified score based on many disparate and arguably incomplete criteria is quite difficult. The initial goal was to go after the "low-hanging fruit" of ions that are relatively obvious and/or whose identity is well-known, which would otherwise need to be placed manually. But as we tried to make clear in the paper, this isn't a substitute for common sense and prior knowledge. (By the way, for what it's worth, I think both Na and Cl are simultaneously over- and under-represented in the PDB - there are many spurious atoms, but at least as many that were overlooked and labeled as water. From the perspective of a methods developer, however, the false positives are much more of a pain to deal with in an automated workflow.) -Nat
