plmallip@mail.uh.edu wrote: > I want to model a pentamer. I have two templates. One of the > templates is arranged anti-clockwise in the order ABCDE. The other > template runs clockwise (AEDCB) and has identical chains. Thus if I > overlap the two templates, subunit B overlaps with subunit E and so on.
Probably the easiest way to do this is to manually edit your clockwise template to put the chains in the same order as in the desired anti-clockwise model. It will be essentially impossible to align the two sequences correctly otherwise. You imply that you tried this already, but I can't tell why it didn't work for you without more information.
(I'm assuming that your alignment between the two templates is C-terminus to C-terminus, N-terminus to N-terminus for each chain. If the sequence in the template is reversed, i.e. C-terminus in template aligns with N-terminus in model, you would have to manually edit the PDB to reverse the sequence.)
Ben Webb, Modeller Caretaker