>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. > > Okay, so why don’t we recommend that this chloride be modeled as UNX? > What’s the problem? > If you do that then what chemical type you are going to put into that rightmost column of ATOM record of PDB file? Note, that must be a valid chemical element symbol so that you can use such PDB file to calculate R-factors, maps and whatnot (Obviously, "X" would not work!).
> (And why not make every water into UNX for good measure as well?) > Why not indeed, except that I would not call it water but "Dummy Atom" with an element type of your choice. Pavel
