# Loop refinement of an existing model from modeller import * from modeller.automodel import * #from modeller import soap_loop log.verbose() env = Environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] # 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): # One loop in chain A from residue 19 to 28 inclusive return Selection(self.residue_range('19:A', '28:A')) # Two loops simultaneously #return Selection(self.residue_range('19:A', '28:A'), # self.residue_range('38:A', '42:A')) m = MyLoop(env, inimodel='1fdx.B99990001.pdb', # initial model of the target sequence='1fdx', # code of the target loop_assess_methods=assess.DOPE) # assess loops with DOPE # loop_assess_methods=soap_loop.Scorer()) # assess with SOAP-Loop m.loop.starting_model= 20 # index of the first loop model m.loop.ending_model = 23 # index of the last loop model m.loop.md_level = refine.very_fast # loop refinement method m.make()