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It seems to me that the best solution here would be to model what is actually going on: disorder. For the example of a lysine where there is limited or poor electron density beyond the C-beta, the best representation of the physical model would be an ensemble of all possible rotamers of what is physically present in the crystal. Having "N" sidechains (alternate conformers) with occupancies of 1/N would be extremely clear to all users (novice and expert alike) as well as most if not all software. -Tom
I am actually of the same opinion...I think that a representation like this is supported fairly well by theory. But the idea of modeling more when you observe less is scary to me. What does this mean in the limit.... Should we use a kinematics approach to build all possible conformations for a disordered loop and assign occupancies by the density of the Ramachandran plot? or Should a 3.5 Angstrom structure with little sidechain density really have several alternate conformations? -bob
