Hi Frank, I agree with what Tim has just posted. Personally I would not think occupancy=0, since this would mean the atom is not where you placed it (i.e. nowhere near). This could be useful if all your ligand has the same partial occupancy or, if you have multiple poses, the sum of occupancies of the single atoms equals that of the whole ligand. None of the above seems to fit your case.
Another possibility is to define the whole ligand and letting the B-factors for those atoms go very high, but this provides an information on "coordinates" which some would just take for granted... if that structure ends up in the PDB, the less experienced readers would be tempted to say that x,y,z are the coordinates of that atom, which we would know from the B factors they are not. Since a PDB file contains a model (i.e. our understanding and interpretation of the electron density maps), omitting those atoms seems to me the more correct way. Having said so, I agree some important information is missing, but this can be explained in the paper supporting the entry. If the structure is only for internal use, then people dealing with it should be warned and the insanely-high B-factors option might be preferable. Hope this helps, Ciao Marco 2014-06-13 10:45 GMT+01:00 Frank von Delft <frank.vonde...@sgc.ox.ac.uk>: > Hi all - talking about ligands, a quick question on that old conundrum, > of what to do about invisible atoms -- build them with occ=0, or omit > them? > > For bits of protein, I know all the arguments; personally I prefer > omitting atoms because: > > - for amino acid sidechains, their presence is implied in the residue > name. > - for whole residues, their presence is implied in the sequence > numbering > > However: what about ligands? Nowhere else in the PDB file is their > presence implied - or have I missed something? > > (Certainly disorder in a ligand is important information that needs to be > captured!) > > Cheers > phx >
