Normally, coordinates are read automatically from Sequence.atom_file when needed (or when Structure.reread() is called). This function instead reads coordinates explicitly in PDB format from file, which is either a filename or a readable file handle (see modfile.File()), ignoring atom_file. This is useful if you want to load an alternative conformation, or you want to read the structure from a file handle rather than a named file. (The sequence of the PDB must still match that in the alignment, of course.)
Note that Structure.reread(), and certain structural alignment functions (alignment.salign() and alignment.malign3d()) will overwrite this conformation with that named in Sequence.atom_file.