On 30 September 2016 at 17:31, Mahdi, Sam <sam.mahdi....@my.csun.edu> 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

> 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

> 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.



relax (http://www.nmr-relax.com)

This is the relax-users mailing list

To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at

Reply via email to