Re: relax-users Digest, Vol 116, Issue 38 -- October 01, 2016 - 20:18

On 1 October 2016 at 20:14, Mahdi, Sam <sam.mahdi.846@xxxxxxxxxxx> wrote:
> Hi Edward,
>
> Oh ok. Thank you for your help, I was able to resolve the problems I had
> with both proteins, and now they are both running. Since there is symmetry
> within the dimer, both chain A and chain B will give me the same S^2 results
> correct?

Hi Sam,

That depends.  If you superimpose A and B and have an RMSD of
0.000000000000000000000, then the S2 values will be identical.  But if
the docking software changed the monomer structures slightly so the
RMSD is not exactly zero, then the S2 values will be slightly
different for some residues.  You can use relax to superimpose
structures and determine the RMSD to very high precision, if you like,
but I'll leave that to you as a learning exercise ;)

Regards,

Edward