Yet Uaniso's are multiplied by 10000 and stored as integers with no problem!
-- Ian On Thu, Oct 13, 2011 at 1:44 AM, James Holton <jmhol...@lbl.gov> wrote: > 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 >>> >> >
