This is the index used internally to identify the residue; residues are numbered sequentially starting from 1.
# This demonstrates relating PDB residue numbers with residue indices. from modeller import * log.verbose() env = Environ() env.io.atom_files_directory = ['../atom_files'] mdl = Model(env, file='2abx') print("Mapping from residue indices to PDB residue and chain names:") for r in mdl.residues: print("%6d %3s:%s %s" % (r.index, r.num, r.chain.name, r.pdb_name))