Two sets of identifiers. mmCIF names chains and residues twice: author names (auth_*, what papers and
viewers show) and the PDB's own names (label_*, one label chain per molecule, residues numbered along the
sequence). Tools use author names by default; pass --label to use label_* instead, or set
MMCIFTOOLS_SCHEME=label for every tool. Edits change one scheme only. Residue and atom names are the same in
both, so mmcif_rplresname and mmcif_uniqname change both name columns.
Related tables stay in step. Removing atoms also removes their rows in _atom_site_anisotrop and
_struct_conn; renaming chains or renumbering residues updates the same two tables. Other categories that
mention chains or residues (_struct_conf, _pdbx_poly_seq_scheme, ...) are left as they were.
Entities. Every molecule belongs to an entity: polymer, non-polymer, branched (glycans) or water.
mmcif_selentity / mmcif_delentity select by entity, which keeps modified residues (HETATM records inside a
chain, such as MSE or the modified nucleotides of a tRNA) with their chain; mmcif_delhetatm removes them.
No fixed columns. Chain identifiers can be longer than one character, and there are no limits on atom or
residue numbers. mmcif_topdb refuses structures that do not fit the PDB format.