TEMPy2: a Python']Python library with improved 3D electron microscopy density-fitting and validation workflows

被引：23

作者：

Cragnolini, Tristan ^{[1
]}

Sahota, Harpal ^{[1
]}

Joseph, Agnel Praveen ^{[1
,5
]}

Sweeney, Aaron ^{[1
]}

Malhotra, Sony ^{[1
]}

Vasishtan, Daven ^{[2
]}

Topf, Maya ^{[1
,3
,4
]}

机构：

[1] Birkbeck Univ Coll London, Inst Struct & Mol Biol, London, England

[2] Univ Oxford, Oxford Particle Imaging Ctr, Wellcome Trust Ctr Human Genet, Div Struct Biol, Oxford, England

[3] Leibniz Inst Expt Virol, Heinrich Pette Inst, Ctr Struct Syst Biol, Hamburg, Germany

[4] Univ Klinikum Hamburg Eppendorf, Hamburg, Germany

[5] Res Complex Harwell, Sci & Technol Facil Council, Didcot, Oxon, England

来源：

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY | 2021年 / 77卷

基金：

英国惠康基金; 英国生物技术与生命科学研究理事会; 英国医学研究理事会;

关键词：

three-dimensional electron microscopy; model fitting; validation; fitting scores; model assessment; macromolecular complexes; TEMPy2; EM RECONSTRUCTIONS; RESOLUTION; MODEL; REFINEMENT; MAPS; FIT;

D O I：

10.1107/S2059798320014928

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Structural determination of molecular complexes by cryo-EM requires large, often complex processing of the image data that are initially obtained. Here, TEMPy2, an update of the TEMPy package to process, optimize and assess cryo-EM maps and the structures fitted to them, is described. New optimization routines, comprehensive automated checks and workflows to perform these tasks are described.

引用

页码：41 / 47

页数：7

共 50 条

[31] Study of Petrophysical Properties Using Nano-Scale Resolution Electron Microscopy and 3D to 2D Upscaling
Jin, Xu
Wang, Xiaoqi
Sun, Liang
Li, Jianming
Liu, Xiaodan
Yao, Zixiu
Meng, Fanli
Zhang, Shawn
JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY, 2016, 16 (09) : 9690 - 9698
[32] AN IMPROVED MACROSCOPIC MODEL FOR VISCOUS FINGERING AND ITS VALIDATION FOR 2D AND 3D FLOWS .3. INCLUSION OF EFFECTS OF HETEROGENEITIES
FAYERS, FJ
JOUAUX, F
IN SITU, 1995, 19 (04): : 393 - 425
[33] Correlative In Vivo 2-Photon Beam Scanning Electron Microscopy: 3D Analysis of Neuronal Ultrastructure
Maco, Bohumil
Holtmaat, Anthony
Jorstad, Anne
Fua, Pascal
Knott, Graham W.
CORRELATIVE LIGHT AND ELECTRON MICROSCOPY II, 2014, 124 : 339 - 361
[34] AN IMPROVED MACROSCOPIC MODEL FOR VISCOUS FINGERING AND ITS VALIDATION FOR 2D AND 3D FLOWS .2. FLOWS INFLUENCED BY GRAVITY
FAYERS, FJ
JOUAUX, F
TCHELEPI, HA
IN SITU, 1994, 18 (01): : 79 - 105
[35] 2D and 3D crystals of myosin-II tails analyzed by electron microscopy and X-ray crystallography
Turbedsky, KF
Yeager, M
Pollard, TD
BIOPHYSICAL JOURNAL, 2000, 78 (01) : 247A - 247A
[36] Many-beam dynamical scattering simulations for scanning and transmission electron microscopy modalities for 2D and 3D quasicrystals
Singh, Saransh
Lenthe, William C.
De Graef, Marc
PHILOSOPHICAL MAGAZINE, 2019, 99 (14) : 1732 - 1750
[37] Determination of 3D flame surface density variables from 2D measurements: Validation using direct numerical simulation
Chakraborty, Nilanjan
Hawkes, Evatt R.
PHYSICS OF FLUIDS, 2011, 23 (06)
[38] Kondo effect at low electron density and high particle-hole asymmetry in 1D, 2D, and 3D
Zitko, Rok
Horvat, Alen
PHYSICAL REVIEW B, 2016, 94 (12)
[39] Statistical Reconstruction of 3D Paper Structure Using Simulated Annealing Algorithm Based on 2D Scanning Electron Microscopy Image
Xu, Jie
Liu, Yin
Li, Jiaqin
Shen, Wenhao
Corriou, Jean-Pierre
JOURNAL OF NATURAL FIBERS, 2022, 19 (16) : 13815 - 13830
[40] Reconstruction of Stochastic 3D Signals With Symmetric Statistics From 2D Projection Images Motivated by Cryo-Electron Microscopy
Xu, Nan
Doerschuk, Peter C.
IEEE TRANSACTIONS ON IMAGE PROCESSING, 2019, 28 (11) : 5479 - 5494

← 1 2 3 4 5 →