# 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