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