Re: [modeller_usage] Modelling complexes

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

Chido Mpamhanga wrote:
> I'm new with modeller, I have used it to do simple models.. However I'm 
> now trying to model a tri-metric complex where the active site of the 
> complex is includes all three subunits. How do i go about this?

Building multi-chain models is straightforward, particularly if you have 
a multimeric template - just add chain breaks ('/') to your alignment 
where needed. See the example in the manual:
http://salilab.org/modeller/9v3/manual/node28.html

If you have ligands which interact with two or more chains, Modeller 
should handle them correctly, as the constraints are distance-based, not 
sequence-based.

	Ben Webb, Modeller Caretaker
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