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Re: [modeller_usage] Modeling circular permutation

On 2/16/11 5:23 AM, bharat lal wrote:

I am trying to model circular permutation in my protein which is a beta
barrel and I modeled it the following way--

AAAA-----BBB
--------CCC-------

If this is really your alignment, Modeller will try to use structural 
information from both B and C for two residues (and nothing at all for 
the linker between A and B). That's probably not going to work. You 
might want to manually perform the mutation first in one of your 
template PDB files, and give Modeller that modified template.

	Ben Webb, Modeller Caretaker
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