Trying to hold a range of atoms rigid during optimization. I get an error message. Can anyone spot what I’m doing wrong here?
Code: class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms
rsr.add(secondary_structure.alpha(self.residue_range('138:A','149:A'))) rsr.add(secondary_structure.alpha(self.residue_range('523:B','530:B'))) r1 = rigid_body(self.residue_range('152:A','384:A')) rsr.rigid_bodies.append(rigid_body(r1))
a = MyModel(env, alnfile='KdpD_full_align.ali', knowns=('KdpD_GAF_bent_dimerA','KdpD_GAF_bent_dimerB','4CTI_mod_HAMP-delA','4CTI_mod_HAMP-delB'), sequence='KdpD_GDK_homodimer', assess_methods=(assess.DOPE, # #soap_protein_od.Scorer(), assess.GA341)) a.starting_model = 1 a.ending_model = 5
a.make() ———— Result:
Traceback (most recent call last): File "model-single-restraint.py", line 28, in <module> a.make() File "/Library/modeller-9.19/modlib/modeller/automodel/automodel.py", line 112, in make self.homcsr(exit_stage) File "/Library/modeller-9.19/modlib/modeller/automodel/automodel.py", line 561, in homcsr self.mkhomcsr(selection(self), aln) File "/Library/modeller-9.19/modlib/modeller/automodel/automodel.py", line 649, in mkhomcsr self.special_restraints(aln) File "model-single-restraint.py", line 15, in special_restraints rsr.rigid_bodies.append(rigid_body(r1)) File "/Library/modeller-9.19/modlib/modeller/util/modlist.py", line 77, in append self[dim] = obj File "/Library/modeller-9.19/modlib/modeller/util/modlist.py", line 38, in __setitem__ self._setfunc(ret, val) File "/Library/modeller-9.19/modlib/modeller/rigid_body_list.py", line 24, in _setfunc _modeller.mod_rigid_body_set(mdl.modpt, indx, obj._get_base_atoms(mdl), File "/Library/modeller-9.19/modlib/modeller/rigid_body.py", line 18, in _get_base_atoms return mdl.get_list_atom_indices(self._atoms, None) File "/Library/modeller-9.19/modlib/modeller/coordinates.py", line 298, in get_list_atom_indices (objinds, mdl) = obj.get_atom_indices() AttributeError: 'rigid_body' object has no attribute 'get_atom_indices'