Re: [modeller_usage] How to create a Pentameric Channel?

[Modeller Caretaker <modeller-care@ucsf.edu>]

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.

If you can't figure it out, post your current alignment file.

	Ben Webb, Modeller Caretaker
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