I want to define restraints while modeling with ligand and I want to
define different restraints.
I use the following script
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...
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
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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