> An important question is how would you define 'auto'? A number of
> algorithms would be required. Would you loop over all atoms of all
> residues and pick the atom furthest away from the centre of mass?
Probably the easiest would be to scale relative to the molecular mass,
though a maximum dimension as you suggest, or a radius of gyration might
be more robust. I can do a bit of playing to see what works. Tensor
seems to do a good job of it, so it cant be too hard.
There are functions within the file 'generic_fns/pdb.py' which would
help with the molecular mass. The function 'self.center_of_mass()'
loops over all the atoms while the function 'self.atomic_mass()' will
give you the atomic mass (of unlabelled atoms, 1H, 12C, 14N, etc.).
The scale argument value could be set to 'mass' to select this
behaviour.
> How
> would you handle multi-domain systems? If there are multiple tensors,
> then they will have to be all scaled by the same amount. Or what
> about complexes?
>
For these rarer and more complicated systems, the user might have to
take some responsibility for getting a good result.
Having a default rotational diffusion rate of 5.55e6 s^-1 per Angstrom
(scale = 1.8e-6) which can then be adjusted by hand should alleviate
these problems. As long as the diffusion rate per Angstrom is
included in figure legends, comparisons between publications should be
a lot easier.
Edward
Re: PyMOL is now supported.