Dear Modellers,

I am tring to set up my script to build a multimeric model with loop refinement. The script looks like:

log.verbose()

class dope_loopmodel(dope_loopmodel):
    def special_patches(self, aln):
        # Rename both chains and renumber the residues in each
        self.rename_segments(segment_ids=['A', 'B'],
                             renumber_residues=[1, 1])
env = environ()
env.io.hetatm = True
a = dope_loopmodel(env, alnfile='TvLDH-1bdm.ali',
              knowns='1bdm', sequence='TvLDH',
              assess_methods=(assess.DOPE, assess.GA341))
a.starting_model = 1
a.ending_model = 2

# Very thorough VTFM optimization:
a.library_schedule = autosched.slow
a.max_var_iterations = 300

# Thorough MD optimization:
a.md_level = refine.very_slow

# Repeat the whole cycle 2 times and do not stop unless obj.func. > 1E6
a.repeat_optimization = 2
a.max_molpdf = 1e6


a.loop.starting_model = 1           # First loop model
a.loop.ending_model   = 1           # Last loop model
a.loop.md_level       = refine.fast # Loop model refinement level

a.make()

automodel.final_malign3d = True

It seems that the script works but I would like to check if all optimization steps have been done. How could I check it? Please, if you note errors in the script, give me suggestions

Moreover, I built a model with an HETATM residue. If I want to treat it as flexible residue: how could I do that?

Thank you in advance.

Bests

Simone