class MyModel(automodel):
    # This routine picks the residues to be refined by loop modeling
    def select_loop_atoms(self):
        return selection(self.residue_range('310:', '320:'), self.residue_range('517:', '523:'))

    def special_restraints(self, aln):
        rsr = self.restraints
        # Keep whole model but loop atoms rigid
        wholeSel = selection(self) - self.select_loop_atoms()
        r = rigid_body(wholeSel)
        rsr.rigid_bodies.append(r)

        nv = environ()
        env.io.hetatm = False
        # directories for input atom files
        env.io.atom_files_directory = ["../"]
        a = MyModel(env,
            alnfile  = ALIGNMENT,     # alignment filename
            knowns = (template1, template2), # codes of the templates
            assess_methods=(assess.DOPEHR,assess.normalized_dope), # optionally assess the models on th fly
            sequence=OUTPUT_MODEL_NAME)               # code of the target
        a.starting_model = 1           # First loop model
        a.ending_model   = 10         # Last loop model
       
        a.library_schedule = autosched.slow
        a.max_var_iterations = 300
        # Very thorough MD optimization:
        a.md_level = refine.very_slow
       
        a.make()

======================================================================

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang@bioacademy.gr

          tevang3@gmail.com

website: https://sites.google.com/site/thomasevangelidishomepage/