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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.