Open AccessFrom deep TLS validation to ensembles of atomic models built from elemental motions
Author(s) -
Urzhumtsev Alexandre,
Afonine Pavel V.,
Van Benschoten Andrew H.,
Fraser James S.,
Adams Paul D.
Publication year - 2015
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s1399004715011426
Subject(s) - libration (molecule) , matrix (chemical analysis) , computer science , translation (biology) , molecular dynamics , decomposition , algorithm , computational chemistry , statistical physics , physics , chemistry , mathematics , geometry , biochemistry , point (geometry) , organic chemistry , chromatography , messenger rna , gene
The translation–libration–screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because the T , L and S matrices describe a combination of atomic vibrations and librations, TLS models can also potentially shed light on molecular mechanisms involving correlated motions. However, this use of TLS models in mechanistic studies is hampered by the difficulties in translating the results of refinement into molecular movement or a structural ensemble. To convert the matrices into a constituent molecular movement, the matrix elements must satisfy several conditions. Refining the T , L and S matrix elements as independent parameters without taking these conditions into account may result in matrices that do not represent concerted molecular movements. Here, a mathematical framework and the computational tools to analyze TLS matrices, resulting in either explicit decomposition into descriptions of the underlying motions or a report of broken conditions, are described. The description of valid underlying motions can then be output as a structural ensemble. All methods are implemented as part of the PHENIX project.