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

[hmad3 AT cam.ac.uk]

Thanks a lot for your reply.

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? Something like:

temp1    AAAA./AAAA/BBBB./BBBB*
temp2    aaaa-/----/-----/----* (note the 5 dashes in the third "chain")
temp3    -----/aaaa/-----/----* (5 dashes in the 1st and 3rd "chain")
temp4    -----/----/bbbb./----* (5 dashes in the first "chain")
temp5    -----/----/-----/bbbb*
model    aaaa/aaaa/bbbb/bbbb/bbbb*