The question of unique atom numbers is not just a PDB question, but a serious mmCIF and DDL question. At present _atom_site.id is the key for the atom_site category and "must uniquely identify a record in the ATOM_SITE list" Certainly you may define a new and different key instead, but you would be making a major change in mmCIF in so doing. You don't re-use an atom number when you have alternate pisitions for an atom. It would seem similar in concept not to re-use them for multiple models. -- H. J. Bernstein