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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
Thanks if you can help:)
Below is the code I used:
from modeller import *
from modeller.automodel import * # Load the AutoModel class
env = Environ()
# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']
return Selection(self.residue_range('89:A', '99:A'))
a = MyModel(env, alnfile = 'alignment.ali',
knowns = '7dwb', sequence = '7dwb_fill')
a.ending_model = 1