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()*