hi ian, yes, that aspect was in my mind, a bit, but i wanted to keep it simple. my point wasn't really how the "uncertainty" parameter is derived but rather its units. i can imagine that uncertainty in 3D could be expressed in ų (without helping the naïve user much) or in Å (which to me at least seems useful), but Ų (i.e. the B factor) seems neither logical nor helpful in this context, irrespective of its utility elsewhere. if you just see the B factor as a number, ok, you can do the √ in your head, but if it's visualized as in pymol/putty larger uncertainties become exaggerated – which is another word for "misrepresented". cheers j
Von: Ian Tickle <[email protected]> Gesendet: Freitag, 28. Mai 2021 12:10 An: Hughes, Jonathan <[email protected]> Cc: [email protected] Betreff: Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS Hi Jonathan On Thu, 27 May 2021 at 18:34, Hughes, Jonathan <[email protected]<mailto:[email protected]>> wrote: "B = 8π2<u2> where u is the r.m.s. displacement of a scattering center, and <...> denotes time averaging" Neither of those statements is necessarily correct: u is the _instantaneous_ displacement which of course is constantly changing (on a timescale of the order of femtoseconds) and cannot be measured. So u2 is the squared instantaneous displacement, <u2> is the mean-squared displacement, and so the root-mean-squared displacement (which of course is amenable to measurement) is sqrt(<u2>), not the same thing at all as u. Incidentally, the 8π2 constant factor comes from Fourier-transforming the Debye-Waller factor expression I mentioned earlier. Also for crystals at least, the averaging is not only over time, it's over all unit cells, i.e. the displacements are not only thermal in origin but also due to spatial static disorder (instantaneous differences between unit cells). it would seem to me that we would be able to interpret things MUCH more easily with u rather than anything derived from u². So then I think what you mean is sqrt(<u2>) rather than <u2>, which seems not unreasonable. Cheers -- Ian ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
