On 05/04/2010 03:16 PM, Spencer Bliven wrote: > I have produced a number of circular permutations for IL-1b. There are > several structures available for the wild type protein, so I would like > to model how the circular permutation effects the structure. Is MODELLER > able to process circular permutations? If so, how would I encode this in > my alignment file? It doesn't seem like the PIR format is well suited to > this. Thanks in advance for your advice to a new modeller user.

Yes, I think this would be hard to encode in a typical alignment file. My suggestion is to write a short script in your favorite scripting language to take the template PDB, do the permutation by simple cut-and-pasting in that file, and then use that as your template for modeling.

Ben Webb, Modeller Caretaker