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