On Fri, May 28, 2021, Hughes, Jonathan wrote:
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".
Two points that haven't yet been raised: 1. Crystallographers have a half-century of experience in "seeing the B factor as a number", and many have a good intuitive feeling for how these numbers are affected by secondary structure, resolution, and so on. 2. B-factors are really refinement parameters, and can serve to account for errors or uncertainties in other parts of data processing or refinement. Stated in another way: the simple atomic model of xyz coordinates + ADPs is generally not sufficient to represent what is really going on at the atomic level. The connection to <u2> is a rough one: especially for large B-factors (relative to the average) using the simple formula to estimate <u2> often underestimates the atomic fluctuations that are actually present. ....dac ######################################################################## 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/
