Re: [modeller_usage] Post - problem with modelling a chain using another chain as template

plmallip@mail.uh.edu wrote: > Is it possible to re-orient chains in a pentameric way after using one of > > those chains as template to build others?

This is so similar to the post you just sent to CCL that I'll duplicate my answer to that post here ;)

Why don't you just combine steps 1 and 2 into a single step? Modeller can build models using multiple templates, and will sort out the orientation for you. So your alignment would look something like:

AAAA/BBBB/CC-C/DDDD/EEEE (template 1) ----/----/EEEE/----/---- (template 2) aaaa/bbbb/cccc/dddd/eeee (target sequence)

Here 'template 2' is just another copy of the first pentameric template, using only the E chain, to fill in the missing residues in the C chain.

Ben Webb, Modeller Caretaker