Open AccessDealing with structural variability in molecular replacement and crystallographic refinement through normal‐mode analysis
Author(s) -
Delarue Marc
Publication year - 2008
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s0907444907053516
Subject(s) - normal mode , degrees of freedom (physics and chemistry) , amplitude , molecular replacement , mode (computer interface) , statistical physics , molecular dynamics , sample (material) , computer science , biological system , crystal structure , physics , algorithm , crystallography , chemistry , thermodynamics , computational chemistry , vibration , biology , quantum mechanics , operating system
Normal‐mode analysis (NMA) can be used to generate multiple structural variants of a given template model, thereby increasing the chance of finding the molecular‐replacement solution. Here, it is shown that it is also possible to directly refine the amplitudes of the normal modes against experimental data (X‐ray or cryo‐EM), generalizing rigid‐body refinement methods by adding just a few additional degrees of freedom that sample collective and large‐amplitude movements. It is also argued that the situation where several (conformations of) models are present simultaneously in the crystal can be studied with adjustable occupancies using techniques derived from statistical thermodynamics and already used in molecular modelling.