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 <[log in to unmask]> wrote:
> On Thu, Mar 31, 2011 at 7:42 AM, Jacob Keller
> <[log in to unmask]> 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: [log in to unmask]
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