Dear Sir,
 
I am trying to build a tetramer model for hERG based on the crystal structure KcsA (1BL8.pdb). The modeller did give me four chains, but not the correct symmetry. Since I am new to Modeller, I am wondering whether there is somebody can help me.
 
Thank you,
 
Lei Du-Cuny
 
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The following are the alignment file and python script I have used.
 
hERG-KcsA-multialign.ali
 
>P1;1BL8
structureX:1BL8:62: A:111: A:KcsA: : :
YPRALWWSVETATTVGYGDLYPVTLWGRCVAVVVMVAGITSFGLVTAALA*
 
>P1;hERG
sequence:hERG: : : : :hERG:human: :
VT-ALYFTFSSLTSVGFGNVSPNTNSEKIFSICVMLIGSLMYASIFGNV-/
VT-ALYFTFSSLTSVGFGNVSPNTNSEKIFSICVMLIGSLMYASIFGNV-/
VT-ALYFTFSSLTSVGFGNVSPNTNSEKIFSICVMLIGSLMYASIFGNV-/
VT-ALYFTFSSLTSVGFGNVSPNTNSEKIFSICVMLIGSLMYASIFGNV-*
 
model-multichain.py
 
# Homology modeling by the automodel class
#
# Demonstrates how to build multi-chain models, and symmetry restraints
#
from modeller import *
from modeller.automodel import * # Load the automodel class
 
log.verbose()
 
# Override the ’special_restraints’ and ’user_after_single_model’ methods:
class MyModel(automodel):
        def special_restraints(self, aln):
          # Constrain the A, B, C and D chains to be identical
          s1 = selection(self.chains['A']).only_atom_types('CA')
          s2 = selection(self.chains['B']).only_atom_types('CA')
          s3 = selection(self.chains['C']).only_atom_types('CA')
          s4 = selection(self.chains['D']).only_atom_types('CA')
          self.restraints.symmetry.append(symmetry(s1, s2, 1))
          self.restraints.symmetry.append(symmetry(s2, s3, 1))
          self.restraints.symmetry.append(symmetry(s3, s4, 1))
         
        def user_after_single_model(self):
          # Report on symmetry violations greater than 1A after building
          # each model:
          self.restraints.symmetry.report(1)
         
env = environ()
# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']
 
# Be sure to use ’MyModel’ rather than ’automodel’ here!
a = MyModel(env,
            alnfile = 'hERG-KcsA-multialign.ali' ,       # alignment filename
            knowns = '1BL8',             # codes of the templates
            sequence = 'hERG')           # code of the target
           
a.starting_model= 1                      # index of the first model
a.ending_model = 10                      # index of the last model
                                        # (determines how many models to calculate)
a.make()                                 # do homology modeling