>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!).
Why, Cl- of course! Call it “Echols’ chloride.” (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. Because those blobs are most likely waters, it being 55 M or so! But admittedly, unless their being actually waters is used to assert something, I don’t think it matters that much. Most likely they are waters though. 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> ]. JPK
