> 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. JPK
