[modeller_usage] Modeling Circular Permutations

[Spencer Bliven <sbliven AT ucsd.edu>]

Hello,

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.

-Spencer Bliven