Mark, alternative conformations and associated with them occupancies are to describe the larger scale disorder (the one that goes beyond the B-factor's capability to cope with). Multi-model PDB files is another option. Best, Pavel.
On Wed, Mar 30, 2011 at 2:15 PM, VAN RAAIJ , MARK JOHAN < [email protected]> wrote: > 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] > >
