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