Hi Sam,

Please see below:

> 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)?

No.  R2 will be higher.  R1 could go anywhere.  The NOE may not be
affected too much, but it may decrease (maybe).  You need to
understand how the diffusion tensor affects the J(w) spectral density
curves to understand how R1 and the NOE will be affected.

> Also, doesn't S^2 take into account the overall shape of the
> molecule (as well as tensor type) in it's calculations?

No.  The S2 value is the internal motions of the residue.  It is 100%
independent of the global tumbling.

> So won't a dimer
> versus a monomer change the results just due to that?

Not at all.  The optimised diffusion tensor should change, and the S2
value stay the same.

> So should I input both, read_mol=0 and read_mol=1?

No, only one.  You can, however, perform a second analysis later with
read_mol=1 (for comparison).

> 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?

This will have the same IndexError as before - relax will not handle
two identical molecules in a model-free analysis at the same time.
Again, this theory simply does not exist.  So I haven't added it to
relax.  You need to perform the analysis on a single monomer of the
homodimer.  But please check for symmetry - if you don't have
symmetry, nobody on the planet can currently analyse non-symmetric
homodimer data.



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

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