Models containing 100,000 or more atoms, or residues numbered 10,000 or higher, cannot be represented in traditional PDB format (as the atom serial number is a fixed 5 digits, and the residue number 4 digits). If this variable is set True, the default, MODELLER will work around this problem by reading a slightly-modified PDB format, hybrid-36, which allows for up to 87,440,031 atoms and residue numbers up to 2,436,111. (See also IOData.two_char_chain for similar handling of chain IDs longer than a single character.) This can be set False to strictly conform to the traditional PDB format.
Note that MODELLER will always use hybrid-36 to write out PDB files, as hybrid-36 is the same as traditional PDB for small numbers of atoms and residues. (Thus, to maximize compatibility, avoid large atom or residue numbers if possible.)
Use of the mmCIF format is encouraged when working with large systems.