Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS-INSERM-UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France.
Acta Crystallogr D Struct Biol. 2018 Jul 1;74(Pt 7):621-631. doi: 10.1107/S2059798318005764. Epub 2018 Jun 8.
TLS modelling was developed by Schomaker and Trueblood to describe atomic displacement parameters through concerted (rigid-body) harmonic motions of an atomic group [Schomaker & Trueblood (1968), Acta Cryst. B24, 63-76]. The results of a TLS refinement are T, L and S matrices that provide individual anisotropic atomic displacement parameters (ADPs) for all atoms belonging to the group. These ADPs can be calculated analytically using a formula that relates the elements of the TLS matrices to atomic parameters. Alternatively, ADPs can be obtained numerically from the parameters of concerted atomic motions corresponding to the TLS matrices. Both procedures are expected to produce the same ADP values and therefore can be used to assess the results of TLS refinement. Here, the implementation of this approach in PHENIX is described and several illustrations, including the use of all models from the PDB that have been subjected to TLS refinement, are provided.
TLS 模型是由 Schomaker 和 Trueblood 开发的，用于通过原子团的协调（刚体）谐运动来描述原子位移参数[Schomaker & Trueblood（1968）， Acta Cryst. B24, 63-76]。TLS 精修的结果是 T、L 和 S 矩阵，它们为属于该组的所有原子提供了各自的各向异性原子位移参数 (ADP)。这些 ADP 可以使用将 TLS 矩阵的元素与原子参数相关联的公式进行分析计算。或者，可以从与 TLS 矩阵对应的协调原子运动的参数中数值获得 ADP。这两种方法都有望产生相同的 ADP 值，因此可用于评估 TLS 精修的结果。本文介绍了 PHENIX 中对此方法的实现，并提供了几个示例，包括使用已进行 TLS 精修的 PDB 中的所有模型。
