On 30 September 2016 at 17:31, Mahdi, Sam <sam.mahdi.846@xxxxxxxxxxx> wrote:
Hi Gary,
There is only a monomer version of it on pdb, so if you mean it in that
sense, yes. I obtained results from it; however the S^2 were very high, but
I attributed this to having data for a dimer, but using a monomer pdb file.
Hi Sam,
This cannot be the case. The S2 values are often very similar in a
monomer and homodimer case. Or a trimer, tetramer, etc. The only
difference is that the global tumbling - the diffusion tensor - is
slower in the dimer/trimer/tetramer/etc. (and the tensor type and
shape will be different due to the different hydrodynamic+water shell
shape).
If you mean have I tried to just delete set B from the pdb file I uploaded,
I have not attempted that.
With relax, you should never modify the PDB files - relax can do that
for you much better and to the PDB standard via the PDB user
functions.
So I am a bit confused here, so if I add read_mol=1 instead of my
read_mol=0, it'll only read set A?
Sorry, I meant "read_mol=0" for PDB chain ID A. The argument
read_mol=1 will pull out chain ID B.
Assuming symmetry, relax will
automatically calculate and determine set B?
Assuming symmetry, you will get the identical results for read_mol=0
and read_mol=1. There might be slight differences in bond orientation
if the symmetry is not perfect.
If there is no symmetry, the relaxation data for monomer A and monomer
B will be different, but it will be averaged to a single value. If
this is the case, as I said before there is no theory on the planet
for properly handling such averaged data, and you cannot perform any
model-free, reduced spectral density mapping (J(w) mapping), or other
analysis on it.
I hope this clarifies the situation a little better.
Regards,
Edward
Re: relax-users Digest, Vol 116, Issue 38