Well, I guess I was thinking to make the b-factor such a preposterous value that no one would possibly believe it. Setting occupancies to zero effectively places a stumbling block, because people see the residues and think they are actually supported by data. So to counter-balance this, I thought putting up a high-b-factor flag would prevent people from tripping over the stumbling block. Look, you could even set the b-factor to 10000 if you want--just something so people totally discount those coordinates.
Jacob On Thu, Mar 31, 2011 at 9:55 AM, Nat Echols <[email protected]> wrote: > On Thu, Mar 31, 2011 at 7:42 AM, Jacob Keller > <[email protected]> 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 -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: [email protected] *******************************************
