This method is called automatically by AutoModel after the default restraints are generated. By default, it does nothing. However, you can redefine it to add additional user-defined restraints to those calculated by AutoModel. Symmetry restraints, excluded atom pairs, and rigid body definitions can also be set up in this routine. The routine is passed aln, which is the alignment between the templates and the target sequence. See section 2.2.11 for an example.