Dear all, I have just made a model according to the tutorial for missing residues for Modeller. I wanted all atoms not to move so i used the script at the bottom of the tutorial. It seems to work but when i do match align i can still see a very very slight misalignment in certain areas that are not supposed to be touched. I used residue ranges from the alignment window by just clicking on residues and reading their positions at the bottom of the alignment window (might be an issue with numbering?). As a starting structure i used the structure i wanted to take the loops from and as a template structure i used the structure in which i wanted to fill the loops (100% same, difference is in states). I edited the script in chimera as follows: from modeller import * from modeller.automodel import * namelist = open( 'namelist.dat', 'r' ).read().split('\n') tarSeq = namelist[0] template = tuple( [ x.strip() for x in namelist[1:] if x != '' ] ) log.verbose() env = environ() env.io.atom_files_directory = ['.', './template_struc'] class MyModel(automodel): def select_atoms(self): return selection(self.residue_range('312', '315'), self.residue_range('630', '642'), self.residue_range('668', '674')) #code overrides the special_restraints method #def special_restraints(self, aln): #code overrides the special_patches method. # e.g. to include the addtional disulfides. #def special_patches(self, aln): a = MyModel(env, sequence = tarSeq, # alignment file with template codes and target sequence alnfile = 'alignment.ali', # PDB codes of the templates knowns = template) a.starting_model = 1 a.ending_model = 1 loopRefinement = False a.assess_methods = (assess.GA341, assess.normalized_dope) a.make() Link to tutorial: https://salilab.org/modeller/wiki/Missing%20residues