On Wed, 2006-10-11 at 18:57 +1000, Edward d'Auvergne wrote:
3.5.3 The 'spin' user function class
This new user function class could contain functions such as:
spin.add()
spin.copy() # Copy the spin info (name and num) from another pipe.
spin.delete()
spin.display()
spin.read()
spin.sort()
spin.write()
These functions could be applied selectively using the 'mol_num',
'mol_name', 'res_num', or 'res_name' arguments.
One extension to the current model which might have value is the idea of
a spin group. This would describe a group of spins for which relaxation
has been measured which are believed to undergo the same relaxation
causing dynamic process. This idea is less relevant to classic
model-free analyses due to the timescales involved, but might be more
important for studying ns motions by extended MF or slower motions by
relaxation-dispersion type approaches. To make it clear what I mean,
imagine a single peptide bond where you have both NH and Ca relaxation
and where there is evidence that ns motions are involved (or
equivalently a nucleobase with several relaxation probes). You might
hypothesise that the motion involved is coordinated motion of a peptide
plane which is essentially rigid on this timescale. I seems to me that
relax could be well placed to formulate and test such an hypothesis.
Mathematically, it implies that the spectral densities for the
respective spins are related by Wigner rotation terms that relate the
relative orientation of the respective DD and CSA vectors. Of course all
of the requisite maths would need to be coded before this was of any
use, but the spin-group concept would be a first step.
Given its lack of immediate applications in relax, it might be deemed a
complication too far, but its worth considering in the context of a big
re-write.
Chris
Re: Redesign of the relax data model: 3. Molecules, residues, and spins