On Thu, Mar 31, 2011 at 7:42 AM, Jacob Keller < j-kell...@fsm.northwestern.edu> wrote:
> Why not have the "b-factors take care of it" until some magic cutoff > number? When they reach the cutoff, two things happen: > > 1. Occupancies are set to zero for those side chains, to represent our > lack of ability to model the region, > > 2. B-factors are set to exactly 500, as a "flag" allowing casual > b-factor-savvy users to identify suspicious regions, since they will > probably not see occupancies, but *will* see b-factors. Therefore, all > 0-occupancy atoms will automatically have b-factors = 500. I believe > it is true that if the occupancies are zero, the b-factors are totally > irrelevant for all calculations? > > Doesn't this satisfy both parties? No, because now you're not only presenting the user with made-up coordinates, you're giving them a made-up B-factor as well, so there is effectively no property of those atoms that is based on experimental data rather than subjective criteria. Regardless of any problems inherent in letting the B-factors take care of all forms of disorder, they are nonetheless a refined parameter. -Nat
