[modeller_usage] missing loop

[Qinghua Liao <>]

    Hello, 
    
    In my protein, there is one missing loop, 15 residues.
    I used the script from the tutorials to add the missing residues
    while keeping other coordinates: 
    #
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('133', '135'),
                         self.residue_range('217', '230'))

a = MyModel(env, alnfile = 'alignment.ali',
            knowns = '1qg8', sequence = '1qg8_fill')
a.starting_model= 1
a.ending_model  = 1

a.make()
    #
    
    However, the loops added are too extended, even have bad contacts
    with the other parts of the protein.
    As the figure in the Dropbox:
    https://www.dropbox.com/s/3obtrrvc9c9w8df/image.png?dl=0
    
    Could someone guide me how to add the loop more properly? Thanks a
    lot!
    
    
    All the best,
    Qinghua