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