Re: [modeller_usage] How to create a Pentameric Channel?
To: Michael Accardi <>
Subject: Re: [modeller_usage] How to create a Pentameric Channel?
From: Modeller Caretaker <>
Date: Mon, 17 May 2010 11:19:24 -0700
Cc: "" <>
On 5/16/10 1:50 PM, Michael Accardi wrote:
I am using the acetylcholine binding protein (PDB ID 1I9B) as a template
for my protein sequence. However, I appear to only ever produce a single
subunit. I have searched for command inputs to produce a pentameric
channel as the acetylcholine binding protein itself is a pentameric
channel. Unfortunately I have had no luck.
You don't have to do anything special - building a multi-chain protein
is exactly the same as a single chain, except that you have to put the
sequences for all the chains in your alignment file of course. Separate
each chain with a chain break (/) character. See
http://salilab.org/modeller/9v8/manual/node28.html for an example. Note
that that example also constrains the two chain to be symmetrical, since
it is a homodimer, but you can just use the regular automodel class
(rather than subclassing to 'MyModel') if you don't need symmetry.