Dear Modeller users, I'm refining a conformation of a 6-residue long loop and use the script: # 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