Normally, geometries supplied in PDB format are automatically recognized. However, if there are two or more PDB geometries in the one run, then only the first PDB geometry will be recognized, by default. If PDB is present, then the format of the associated geometry is defined as being PDB. PDB is only necessary when more than one PDB geometry is present, although no harm will result from having PDB present for the first PDB geometry.
To select parts of a PDB file, see CHAINS, ALT_A, ALT_R (obsolete)