ddg_monomer with -ddg::local_opt_only true, will it affect other chains that are close?

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    • December 26, 2014 at 9:11 pm #2118
      Anonymous

        I have a .pdb file containing two chains. I do a mutation on one residue on one of the chains, using ddg_monomer. If I set the flag “-ddg::local_opt_only true” in the ddg_monomer run, and if some residues on the OTHER chain (the one I didn’t mutate) are very close to the mutated chain (less than 8 angstroms), does that mean that the residues on the other chain are optimized too?

        Thanks.

      • January 2, 2015 at 6:25 pm #10731
        Anonymous

          Yes, the local optimization is based on through-space distance only, without consideration for chain membership.

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