<div dir="ltr">Hi<br>I try to model an heterodimer using this alignment<br><br>>P1;1DZB2<br>structureX:1DZB2:1:A:107:B::::<br>QVKLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGNTKYDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCAR-----WDWYFDVWGQGTTVTVSSG/<br>
------------DIELTQSPSSMYTSLGERVTITCKASQDINSYLRWFQQKPGKSPKTLIYYATSLADGVPSRFSGSGSGQDYSLTISSLESDDTTTYYCLQHGESPYTFGGGTKLEIK---------*<br><br>>P1;atc<br>sequence:::::::::<br>-VKLQQSGGGLVQPGGSLKLSCAASGFDFSRYWMSWVRQAPGKGLEWIGEINPDSSTINYTPSLKDTFIISRDNAKNTLYLQMSKVRSEDTALYYCARQGYDGYHWYFDVWGQGTTVTVSSE/<br>
SLDLGGGGGGGGDIQLTQSPSSLSASVGETVTLTCGASENIYGGLNWYQRKQGKSPQLLIYGATKLADGMSSRFSGGGSGRQYFLKITSLHPDDVATYYCQNVLSNPLTFGAGTKLELKRADAAPTVS*<br><br>each time it gives me this error message <br>define__595E> Number of selected atoms in sets 2 & 3 is not the same: 121 128<br>
<br>Can you tell me please what's wrong in my alignment file<br><br>script used:<br># Homology modeling by the automodel class<br>#<br># Demonstrates how to build multi-chain models, and symmetry restraints<br>#<br>from modeller import *<br>
from modeller.automodel import * # Load the automodel class<br>log.verbose()<br># Override the 'special_restraints' and 'user_after_single_model' methods:<br>class MyModel(automodel):<br> def special_restraints(self, aln):<br>
# Constrain the A and B chains to be identical (but only restrain<br> # the C-alpha atoms, to reduce the number of interatomic distances<br> # that need to be calculated):<br> s1 = selection(self.chains['A']).only_atom_types('CA')<br>
s2 = selection(self.chains['B']).only_atom_types('CA')<br> self.restraints.symmetry.append(symmetry(s1, s2, 1.0))<br> def user_after_single_model(self):<br> # Report on symmetry violations greater than 1A after building<br>
# each model:<br> self.restraints.symmetry.report(1.0)<br>env = environ()<br># directories for input atom files<br>env.io.atom_files_directory = './'<br><br>a = MyModel(env,<br> alnfile = 'ali.pir',<br>
knowns = '1DZB2',<br> sequence = 'atc')<br>a.starting_model= 1<br>a.ending_model = 1<br><br>a.make()<br><br></div>