I have modeled a homopentamer using automodel with enforcing pentameric
symmetry, and everything looks fine. There are two regions of each
subunit that have 3 and 5 residue long loops that aren't in the
templates. When I do loop modeling of all 10 of these loops at the same
time using a script based on the one in the Advanced tutorial, I get a
set of models where the loops are no longer symmetric.
I then introduced the same symmetry constraints in the loop modeling
that I used in the original model, and it produced models with the
appropriate symmetry. However, it took much longer (765 seconds of cpu
time to generate 5 loop models without the symmetry , but 8629 seconds
to generate 2 loop models with symmetry). I don't mind letting things
run overnight to generate models, but the hugh increase in computational
time suggests that I might not be doing this right.