RT Journal Article
SR Electronic
T1 From deep TLS validation to ensembles of atomic models built from elemental motions
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 012930
DO 10.1101/012930
A1 Alexre Urzhumtsev
A1 Pavel V. Afonine
A1 Andrew H. Van Benschoten
A1 James S. Fraser
A1 Paul D. Adams
YR 2015
UL http://biorxiv.org/content/early/2015/01/02/012930.abstract
AB The widely used Translation Libration Screw (TLS) approximation describes concerted motions of atomic groups in X-ray refinement. TLS refinement often provides a better interpretation of diffraction data and the resulting rigid body motions may subsequently be assigned biochemical significance. In TLS refinement, three matrices (T, L and S) describe harmonic vibration, libration and their correlation. Because these matrices describe specific motions, they impose a number of conditions on their elements. Ignoring these conditions while refining the matrix elements may result in matrices that cannot be interpreted in terms of physically realistic motions. We describe a mathematical framework and the computational tools to analyze refined TLS matrices through their decomposition into descriptors of underlying motions. This allows for straightforward validation and identification of implausible TLS parameters. An algorithm for the generation of structural ensembles that are consistent with given TLS parameters, implemented as a part of the Phenix project, is also described.Synopsis Procedures for the decomposition of TLS matrices into elementary vibrations and librations indicates possible errors in the definition of these matrices and corrects them when possible. The program outputs the corresponding vibration-libration parameters and generates structural ensembles.