<div dir="ltr">Hi<br>I try to model an heterodimer using this alignment<br><br>&gt;P1;1DZB2<br>structureX:1DZB2:1:A:107:B::::<br>QVKLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGNTKYDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCAR-----WDWYFDVWGQGTTVTVSSG/<br>
------------DIELTQSPSSMYTSLGERVTITCKASQDINSYLRWFQQKPGKSPKTLIYYATSLADGVPSRFSGSGSGQDYSLTISSLESDDTTTYYCLQHGESPYTFGGGTKLEIK---------*<br><br>&gt;P1;atc<br>sequence:::::::::<br>-VKLQQSGGGLVQPGGSLKLSCAASGFDFSRYWMSWVRQAPGKGLEWIGEINPDSSTINYTPSLKDTFIISRDNAKNTLYLQMSKVRSEDTALYYCARQGYDGYHWYFDVWGQGTTVTVSSE/<br>
SLDLGGGGGGGGDIQLTQSPSSLSASVGETVTLTCGASENIYGGLNWYQRKQGKSPQLLIYGATKLADGMSSRFSGGGSGRQYFLKITSLHPDDVATYYCQNVLSNPLTFGAGTKLELKRADAAPTVS*<br><br>each time it gives me this error message <br>define__595E&gt; Number of selected atoms in sets 2 &amp; 3 is not the same:      121      128<br>
<br>Can you tell me please what&#39;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 &#39;special_restraints&#39; and &#39;user_after_single_model&#39; 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[&#39;A&#39;]).only_atom_types(&#39;CA&#39;)<br>
            s2 = selection(self.chains[&#39;B&#39;]).only_atom_types(&#39;CA&#39;)<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 = &#39;./&#39;<br><br>a = MyModel(env,<br>            alnfile  = &#39;ali.pir&#39;,<br>
            knowns   = &#39;1DZB2&#39;,<br>            sequence = &#39;atc&#39;)<br>a.starting_model= 1<br>a.ending_model  = 1<br><br>a.make()<br><br></div>