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

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:

----/----/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
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage