I need to refine some flexible regions (mainly long loop and linker regions) of my models using some enhanced sampling engines implemented in modeller like  simulated annealing.  In this FAQ salilab.org/modeller/6v2/FAQ.html I've found the same method. Could you suggest me some example of the realization of this method in the modeller python script indicating its differences from the method proposed in the advanced tutorial (listed below).

class MyModel(automodel):
    def special_restraints(self, aln):
        rsr = self.restraints
        for ids in (('NH1:161:A', 'O1A:336:B'),
                    ('NH2:161:A', 'O1B:336:B'),
                    ('NE2:186:A', 'O2:336:B')):
            atoms = [self.atoms[i] for i in ids]
            rsr.add(forms.upper_bound(group=physical.upper_distance,
                                      feature=features.distance(*atoms),
                                      mean=3.5, stdev=0.1))

TFH,

James