Indeed that paper does lay out clearly the various definitions, thank you, but I note that you do explicitly discourage use of B (= 8 pi^2 U), and don't explain why the factor is 8 rather than 2 (ie why it multiplies (d*/2)^2 rather than d*^2). I think James Holton's reminder that the definition dates from 1914 answers my question.
So why do we store B in the PDB files rather than U? :-)
Phil
On 12 Oct 2011, at 21:19, Pavel Afonine wrote:
> This may answer some of your questions or at least give pointers:
>
> Grosse-Kunstleve RW, Adams PD:
> On the handling of atomic anisotropic displacement parameters.
> Journal of Applied Crystallography 2002, 35, 477-480.
>
> http://cci.lbl.gov/~rwgk/my_papers/iucr/ks0128_reprint.pdf
>
> Pavel
>
> On Wed, Oct 12, 2011 at 6:55 AM, Phil Evans <[log in to unmask]> wrote:
> I've been struggling a bit to understand the definition of B-factors, particularly anisotropic Bs, and I think I've finally more-or-less got my head around the various definitions of B, U, beta etc, but one thing puzzles me.
>
> It seems to me that the natural measure of length in reciprocal space is d* = 1/d = 2 sin theta/lambda
>
> but the "conventional" term for B-factor in the structure factor expression is exp(-B s^2) where s = sin theta/lambda = d*/2 ie exp(-B (d*/2)^2)
>
> Why not exp (-B' d*^2) which would seem more sensible? (B' = B/4) Why the factor of 4?
>
> Or should we just get used to U instead?
>
> My guess is that it is a historical accident (or relic), ie that is the definition because that's the way it is
>
> Does anyone understand where this comes from?
>
> Phil
>
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