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<p>Dear Modellers,</p>
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<p>I am tring to set up my script to build a multimeric model with loop refinement. The script looks like:</p>
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<p>log.verbose()<br /><br />class dope_loopmodel(dope_loopmodel):<br /> def special_patches(self, aln):<br /> # Rename both chains and renumber the residues in each<br /> self.rename_segments(segment_ids=['A', 'B'],<br /> renumber_residues=[1, 1])<br />env = environ()<br />env.io.hetatm = True<br />a = dope_loopmodel(env, alnfile='TvLDH-1bdm.ali',<br /> knowns='1bdm', sequence='TvLDH',<br /> assess_methods=(assess.DOPE, assess.GA341))<br />a.starting_model = 1<br />a.ending_model = 2<br /><br /># Very thorough VTFM optimization:<br />a.library_schedule = autosched.slow<br />a.max_var_iterations = 300<br /><br /># Thorough MD optimization:<br />a.md_level = refine.very_slow<br /><br /># Repeat the whole cycle 2 times and do not stop unless obj.func. > 1E6<br />a.repeat_optimization = 2<br />a.max_molpdf = 1e6<br /><br /><br />a.loop.starting_model = 1 # First loop model<br />a.loop.ending_model = 1 # Last loop model<br />a.loop.md_level = refine.fast # Loop model refinement level<br /><br />a.make()<br /><br />automodel.final_malign3d = True</p>
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<p>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</p>
<p>Moreover, I built a model with an HETATM residue. If I want to treat it as flexible residue: how could I do that?</p>
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<p>Thank you in advance.</p>
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<p>Bests</p>
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<p>Simone</p>
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