On Wed, Jan 21, 2015 at 10:17 AM, Keller, Jacob <[email protected]> wrote:
> I see your point about not knowing that it’s a chloride, but I think you > would agree that it is certainly more likely a chloride than map-noise, and > perhaps more likely than water as well. Would you agree that chloride is > the best guess, at least? > No, I think "I don't know" is the most honest and scientifically robust answer. For those who insist on annotating every density blob, UNX atoms are the PDB's officially supported method for doing so (unless this has changed recently), or UNK/UNL for unknown amino acids and ligands. These are not without their own problems but they at least make both the presence of an atom and the uncertainty about its identity explicit. Since the PDB is certainly tainted by structures modeled in accordance with > the “most likely” outlook, one now has to be cautious about all structures. > This is true, but "everyone else is just as sloppy" is a poor excuse for further polluting the database. -Nat
