[modeller_usage] Oligomer Missing Loop Residue Restrained Modeling, Broken Loop Issue

[Joel Subach <>]

Hi, I loop missing residue MODELLER modeled a heptamer both
unrestrained and restrained with the former exhibiting an RMSD
of 0.295 while the restrained exhibited an RMSD of 0.0.

The restrained model´s missing residue loops, however, are too
dynamic and seem to be broken when visualized via Pymol.
Accordingly, is there a way to generate the restrained version to
exhibit intact loops so that I may keep this version because of its
0.0 RMSD?

Thanks if you can help:)

Below is the code I used:



















*from modeller import *from modeller.automodel import *    # Load the
AutoModel classlog.verbose()env = Environ()# directories for input atom
filesenv.io.atom_files_directory = ['.', '../atom_files']class
MyModel(AutoModel):    def select_atoms(self):        return
Selection(self.residue_range('89:A', '99:A'))a = MyModel(env, alnfile =
'alignment.ali',            knowns = '7dwb', sequence =
'7dwb_fill')a.starting_model= 1a.ending_model  = 1a.make()*

Hi, I loop missing residue MODELLER modeled a heptamer both unrestrained and restrained with the former exhibiting an RMSD  of 0. 295 while the restrained exhibited an RMSD of 0. 0.   The restrained model´s missing residue loops, however, are

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Hi, I loop missing residue MODELLER modeled a heptamer both unrestrained and restrained with the former exhibiting an RMSD 

of 0.295 while the restrained exhibited an RMSD of 0.0. 

The restrained model´s missing residue loops, however, are too 

dynamic and seem to be broken when visualized via Pymol. 

Accordingly, is there a way to generate the restrained version to 

exhibit intact loops so that I may keep this version because of its 

0.0 RMSD?

Thanks if you can help:)

Below is the code I used:

from modeller import *
from modeller.automodel import *    # Load the AutoModel class

log.verbose()
env = Environ()

# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']

class MyModel(AutoModel):
    def select_atoms(self):
        return Selection(self.residue_range('89:A', '99:A'))

a = MyModel(env, alnfile = 'alignment.ali',
            knowns = '7dwb', sequence = '7dwb_fill')
a.starting_model= 1
a.ending_model  = 1

a.make()