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()
Hi,
how can I model a loop without changing the rest of the structure?
Best,
Matthias
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Thomas Evangelidis
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Biomedical Research Foundation, Academy of Athens
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