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
