Hi,
I'm trying to add 3 loops to a crystal structure (loops are missing) without making any changes to the original X-Ray. I base the script on the existing example script 'examples/automodel/loop.py'.
My script:
##########################################################
from modeller import *
from modeller.automodel import * # Load the AutoModel class
log.verbose()
env = Environ()
code = '5uv1'
# directories for input atom files
env.io.atom_files_directory = ['.']
# Override the regular LoopModel class to select our own loops
class MyLoop(LoopModel):
# This routine picks the residues to be refined by loop modeling
def select_loop_atoms(self):
# Select gaps for loop modeling
return Selection(self.residue_range('157:A', '163:A'),
self.residue_range('434:A', '439:A'),
self.residue_range('507:A', '517:A'))
a = MyLoop(env,
inimodel='5uv1_fill.B99990001.pdb', #code+'.pdb', # initial model of the target
sequence=code, # code of the target
loop_assess_methods=assess.DOPE) # assess loops with DOPE
a.loop.starting_model = 1 # First loop model
a.loop.ending_model = 4 # Last loop model
a.loop.md_level = refine.very_fast # Loop model refinement level
a.make()
##########################################################
In the inimodel ('5uv1_fill.B99990001.pdb'), the missing residues have been added and simply appear as a straight line and are only connected to one end. When I try do loop modeling using the above script, the loop atoms hardly move and don't reconnect to the other endpoint. How can I model the loops without making any change to the other atoms.
Thanks,
Dan
