Re: relax-users Digest, Vol 116, Issue 38 -- September 30, 2016 - 19:20

Hi Edward,

I'm a bit confused to that. If the protein is a dimer, and the tumbling
decreases, will that not results in altered  relaxation data? Won't the
relaxation data average be higher, since it is relaxing slower due to its
increased size (tumbler slower in solution=slower relaxation back to
equilibrium)? Also, doesn't S^2 take into account the overall shape of the
molecule (as well as tensor type) in it's calculations? So won't a dimer
versus a monomer change the results just due to that?
So should I input both, read_mol=0 and read_mol=1? So
structure.read_pdb(file='cluster1_12.pdb', dir=None,
 read_mol=None, set_mol_name='hRGS4',
read_model=None,set_model_num=0,set_mol_num=1, alt_loc=None, verbosity=1,
merge=False)
So mol_num=0 will be for chain A and mol_num=1 for chain B?

Sincerely,
Sam

On Fri, Sep 30, 2016 at 9:17 AM, Edward d'Auvergne <edward@xxxxxxxxxxxxx>
wrote:

> 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