yet, apart from (and additionally to) modelling two conformations of the side-chain, the B-factor is the only tool we have (now).
Quoting Pavel Afonine: > Hi Quyen, > > > (...) And if B-factor is an estimate of thermo-motion (or static disorder), >> then would it not be reasonable to accept that building the side-chain and >> let B-factor sky rocket might reflect reality more so than not building it? >> > > NO. Your B-factors are valid within a harmonic (small) approximation of > atomic vibrations. Larger scale motions you are talking about go beyond the > harmonic approximation, and using the B-factor to model them is abusing the > corresponding mathematical model. > http://www.phenix-online.org/newsletter/CCN_2010_07.pdf > > Pavel. > Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoléculas Centro Nacional de Biotecnología - CSIC c/Darwin 3, Campus Cantoblanco 28049 Madrid tel. 91 585 4616 email: [email protected]
