Hello. I want to define restraints while modeling with ligand and I want to define different restraints. I use the following script --------------------------------------------------------------------------------------------- ... class mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints for ids in (('OD1:282:B', 'CA:765:B'), ('OD2:282:B', 'CA:765:B'), ('OD1:285:B','CA:765:B'), ('OD2:460:B', 'CA:765:B'), ('OE2:152:A', 'CA:765:B')): atoms = [self.atoms[i] for i in ids] rsr.add(forms.upper_bound(group=physical.upper_distance, feature=features.distance(*atoms), mean=2.5, stdev=0.1))
def special_restraints(self, aln): rsr2 = self.restraints for ids1 in (('OE2:152:A', 'CA:765:B')): atoms = [self.atoms[j] for j in ids1] rsr2.add(forms.upper_bound(group=physical.upper_distance, feature=features.distance(*atoms), mean=2.3, stdev=0.1))
env = environ() env.io.hetatm = True env.io.water = True ...
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Then I get this error
-------------------------------------------------------------------------------------------- Traceback (most recent call last): File "model-ca.py", line 32, in ? a.make() File "C:\Program Files\Modeller9v1\modlib\modeller\automodel\automodel.py", line 108, in make self.homcsr(exit_stage) File "C:\Program Files\Modeller9v1\modlib\modeller\automodel\automodel.py", line 427, in homcsr self.mkhomcsr(selection(self), aln) File "C:\Program Files\Modeller9v1\modlib\modeller\automodel\automodel.py", line 537, in mkhomcsr self.special_restraints(aln) File "model-ca.py", line 19, in special_restraints atoms = [self.atoms[j] for j in ids1] File "C:\Program Files\Modeller9v1\modlib\modeller\coordinates.py", line 127, in __getitem__ (self.offset, self.length, self.suffix)) File "C:\Program Files\Modeller9v1\modlib\modeller\util\modutil.py", line 76, in handle_seq_indx int_indx = lookup_func(*args) File "C:\Program Files\Modeller9v1\modlib\modeller\coordinates.py", line 40, in _indxatm newindx = _modeller.indxatm2(indx+suffix, self.modpt) - 1 - offset _modeller.error: indxatm_278E> No ":" in ATOM:RESID[:CHAINID] atom identifier: O ---------------------------------------------------------------------------------------------
I am using python for the first time so that must be some problem with the script. Do you have any suggestions? Thank you!