[modeller_usage] MUTATE MODEL [OPTIMIZATION]

["Mahesh Velusamy" <>]

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