Hi Edward,
Just wanted to update you on the status of my runs. I had 2 potential dimer
structures. I ran Chain A and B for one of them, and Chain B for the other.
All the results were all very similar. There was missing data though
throughout (i.e. I had data for some residues for Chain A that had no data
in Chain B, Or chain A for one pdb file and Chain B for the other pdb file
would have data, but Chain B for the other pdb file wouldn't). The data
that is there for all 3 though does make sense. Thank you so much for your
help
Sincerely,
Sam
On Sat, Oct 1, 2016 at 11:17 AM, Edward d'Auvergne <edward@xxxxxxxxxxxxx>
wrote:
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
Re: relax-users Digest, Vol 116, Issue 38