[modeller_usage] Specification of restraints

[Fred Pontes <>]

Hi
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 PhysicalTypez_coord_type = PhysicalType(99,
'z_coordinate')import syslog.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 =
1a.ending_model = 10a.make()*


-- 
Frederico José de S. Pontes
PDRA at LICAMM
University of Leeds

Hi

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