Dear Ben,

I'm working on a project similar to the work you and Andrej Sali did in 2003 (comparative protein structure modeling by iterative alignment, model building and model assessment), Except that I'm using Scatter Search Heuristics rather than Genetic Algorithms. after running my algorithm and comparing the 3D structures obtained with the ones found in PDB, the results are showing good RMSD values, however using the superpose method of Modeller:

from modeller import *

env = environ()

env.io.atom_files_directory = ['']

mdl = model(env, file='3HLA')

mdl2 = model(env, file='3HLA.B99991001')

aln = alignment(env, file='superpose_alignment.ali', align_codes=('3HLA', 'ABCD'))

atmsel = selection(mdl).only_atom_types('CA')

r = atmsel.superpose(mdl2, aln, rms_cutoff =5, reference_distance = 10, refine_local=False, superpose_refine=False)

rms = r.rms

drms = r.drms

print("%d equivalent positions" % r.num_equiv_pos)

mdl2.write(file='superpose_alignment.txt')

I'm not getting such good overlaps within 5 angstroms. my question is that is there a way to refine my final comparative Model so that I'll get better (higher) native overlap values? Thank you.