I'm trying to apply a restraint to keep fixed the CA of a specific residue using a Gaussian form. This mathematical form of restraints accept four arguments:

forms.Gaussian(group, feature, mean, stdev)

mean and stdev are defined by me according to my system. In the `feature` I could use features.ZCoordinate(*atom_ids).

But I`m struggling with the group argument. I think the group is a physical restraints type and I have defined the type `z_coord_type', but I always get an error from MODELLER/10.4.

rsr.add(forms.Gaussian(group=physical.z_coordinate,
AttributeError: 'module' object has no attribute 'z_coordinate'

Am I doing this right? Below I include my script file.

Thank you in advance.

from modeller import *
from modeller.automodel import *
from modeller.physical import PhysicalType
z_coord_type = PhysicalType(99, 'z_coordinate')
import sys
log.verbose()
env = Environ()

class MyModel(AutoModel):
def special_restraints(self, aln):
rsr = self.restraints
at = self.atoms

rsr.add(forms.Gaussian(group=physical.z_coordinate,
feature=features.ZCoordinate(at['CA:25:A']),
mean=193.8, stdev=0.1))

a = MyModel(env,
alnfile='multi-co.ali',
knowns=('HPI1_fit'),
sequence='multi',
assess_methods=(assess.DOPE,assess.GA341))
a.starting_model = 1
a.ending_model = 10
a.make()

Frederico José de S. Pontes

PDRA at LICAMM

University of Leeds