I think the PDB decided to store "B" instead of "U" because unless the B factor was > 80, there would always be a leading "0." in that column, and that would just be a pitiful waste of two bytes. At the time the PDB was created, I understand bytes cost about $100 each! (But that could be a slight exaggeration)
-James Holton MAD Scientist On Wed, Oct 12, 2011 at 2:56 PM, Phil Evans <p...@mrc-lmb.cam.ac.uk> wrote: > 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 <p...@mrc-lmb.cam.ac.uk> 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 >> >
