Dear Modeller-Usage group, I have a problem with my structure. It is lacking 9 amino acids from a loop next to its active center. I've tried to refill it using the loopmodel class script from this tutorial: http://salilab.org/modeller/wiki/Missing%20residues. My script looks like this: # Ab-initio modeling by the loopmodel class from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] a = loopmodel(env, alnfile = 'sEH_AN_A.ali', knowns = 'sEH_AN_A', sequence = 'sEH_AN_A_fill', assess_methods=(assess.DOPE, assess.GA341), loop_assess_methods=(assess.DOPE, assess.normalized_dope, assess.GA341)) a.starting_model= 1 a.ending_model = 10 a.loop.starting_model = 1 a.loop.ending_model = 10 a.loop.md_level = refine.fast a.make() I've also find a homologous structure with a complete amino acid sequence but its sequence has only 34% identity with my structure. So I just cut the loop from the homologous and use it as a template. I think that the loop from my structure will be similar to the loop from the homologous structure. My second script looks like that # Homology modeling by the automodel class from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] a = automodel(env, alnfile = 'sEH_AN-homolog.ali', knowns = ('homologue', 'sEH_AN_A'), sequence = 'sEH_AN_A_fill', assess_methods=(assess.DOPE, assess.normalized_dope, assess.GA341)) a.starting_model= 1 a.ending_model = 100 a.make() Then I compared all the models I've build by Z-score (normalized.DOPE) value and by calculating the RMSD of the created models and homologous structure. The RMSD is very high (1,55 to even 5,48) so I think the models are not so good. Which method will give me more accurate and native-like models? Best regards, Karolina Markowska Silesian University of Technology