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

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