To whom this may concern,
I am new to MODELLER 9v7 and, as such, am having difficulty creating a pentameric channel.
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.
I have very basic computer language skills.
If anyone has any advice or useful tutorials I could review in order to produce a pentamer, it would be greatly appreciated!
Thanks in advance, Mike
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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Michael Accardi -
Modeller Caretaker