# Loop refinement of an existing model
from modeller.automodel import *
log.verbose()
env = environ()
# directories for input atom files
env.io.atom_files_directory = './'
# Create a new class based on 'loopmodel' so that we can redefine
# select_loop_atoms (necessary)
class myloop(loopmodel):
# This routine picks the residues to be refined by loop modeling
def select_loop_atoms(self):
self.pick_atoms(selection_segment=('200:A', '205:A'),
selection_status='INITIALIZE')
m = myloop(env,
inimodel='dimer_Cloop_STR_fakeprot_full.pdb', # initial model of the target
sequence='dimer_Cloop_STR_fakeprot_full') # code of the target
m.loop.starting_model= 1 # index of the first loop model
m.loop.ending_model = 500 # index of the last loop model
m.loop.md_level = refine.slow_large # loop refinement method
m.make()
Problem 1:
Is is possible in Modeller to fully optimize the specified loop but also to allow a little bit of "adjustment freedom" to the loop end residues (here 199 and 206)? If so, how should I modify the script?
Problem 2:
Could anyone advise on the m.loop.md_level? How should I judge what's best for my loop?
tons of thanks for help and comments
Agnieszka