[modeller_usage] MUTATE MODEL [OPTIMIZATION]

Dear All,

I have a couple of questions regarding optimization step of mutate_model script.

As mentioned in the script there is some optimization steps performed on mutated residue (the conformation of the mutant sidechain is optimized by conjugate gradient and refined using some MD).

Here my question is: can we include some neighbor residues (residues that are located around the mutated residue) for optimization ?

If yes,what is the reasonable size of neighbor residue region that we can use it for optimization? ( for ex: neighbor residues that are within 5Å/10Å of mutated residue)

Thanking you in advance

With Regards Mahesh V