[modeller_usage] Re: Modelling based on two templates - one oligomer and one monomer

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

On 3/19/24 11:12 AM, hmad3--- via modeller_usage wrote:
> Maybe I'm being a bit over-cautious, but if I'd like all of my
> subunits to be aligned according to the AF model(s), would there need to
> be n (where n = number of subunits) templates in the .ali file alongside
> the template corresponding to the pentameric .pdb file?

Yes, absolutely. Modeller will use exactly the alignment you provide it, 
so if you want your monomer to be used to model every chain, you should 
provide multiple copies; Modeller will not assume that otherwise. The 
alternative would be to add a symmetry restraint to force every chain to 
look alike: https://salilab.org/modeller/10.5/manual/node29.html

	Ben Webb, Modeller Caretaker
-- 
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