[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [modeller_usage] Modeling Circular Permutations

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