> What do we gain? As Dale pointed out, we are already abusing either occupancy, B-factor or delete the side chain to compensate for our inability to tell the user that the side chain is disordered. With your proposal, we would fudge both occupancy and B-factor, which in my eyes is even worse as fudging just one of the two.
We gain clarity to the non-crystallographer user: a b-factor of 278.9
sounds like possibly something real. A b-factor of exactly 1000 does
not. Both probably have the same believability, viz., ~zero. Also,
setting occupancy = zero is not fudging but rather respectfully
declining to comment based on lack of data. I think it is exactly the
same as omitting residues one cannot see in the density.
> Also, who should decide on the magic number: the all-knowing gurus at the protein data bank? Maybe we should really start using cif files, which allow to specify coordinate uncertainties.
I think a reasonable number could be derived and agreed upon, and
would not be surprised if there is such a derivation or analysis in
the literature answering the question:
"At what b-factor does modelling an atom become insignificant with
respect to explaining/predicting/fitting the data?"
That point would be the b-factor/occupancy cutoff.