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