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Title: From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation

Abstract

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. B 24 , 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.

Authors:
ORCiD logo; ;
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1441078
Grant/Contract Number:  
AC02-05CH11231; ANR-10-INSB-05-01
Resource Type:
Journal Article: Published Article
Journal Name:
Acta Crystallographica Section D Structural Biology
Additional Journal Information:
Journal Name: Acta Crystallographica Section D Structural Biology Journal Volume: 74 Journal Issue: 7; Journal ID: ISSN 2059-7983
Publisher:
International Union of Crystallography (IUCr)
Country of Publication:
United Kingdom
Language:
English

Citation Formats

Afonine, Pavel V., Adams, Paul D., and Urzhumtsev, Alexandre. From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation. United Kingdom: N. p., 2018. Web. doi:10.1107/S2059798318005764.
Afonine, Pavel V., Adams, Paul D., & Urzhumtsev, Alexandre. From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation. United Kingdom. doi:10.1107/S2059798318005764.
Afonine, Pavel V., Adams, Paul D., and Urzhumtsev, Alexandre. Fri . "From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation". United Kingdom. doi:10.1107/S2059798318005764.
@article{osti_1441078,
title = {From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation},
author = {Afonine, Pavel V. and Adams, Paul D. and Urzhumtsev, Alexandre},
abstractNote = {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. B 24 , 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.},
doi = {10.1107/S2059798318005764},
journal = {Acta Crystallographica Section D Structural Biology},
number = 7,
volume = 74,
place = {United Kingdom},
year = {Fri Jun 08 00:00:00 EDT 2018},
month = {Fri Jun 08 00:00:00 EDT 2018}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1107/S2059798318005764

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