Manalastas-Cantos Karen, Konarev Petr V, Hajizadeh Nelly R, Kikhney Alexey G, Petoukhov Maxim V, Molodenskiy Dmitry S, Panjkovich Alejandro, Mertens Haydyn D T, Gruzinov Andrey, Borges Clemente, Jeffries Cy M, Svergun Dmitri I, Franke Daniel
European Molecular Biology Laboratory, Hamburg Site, Notkestrasse 85, Building 25 A, Hamburg, 22607, Germany.
A.V. Shubnikov Institute of Crystallography, Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of Sciences, Leninsky prospekt 59, Moscow, 119333, Russian Federation.
J Appl Crystallogr. 2021 Feb 1;54(Pt 1):343-355. doi: 10.1107/S1600576720013412.
The software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small-angle scattering data, with a focus on the data measured from biological macromolecules. Here, new developments in the package are described. They include , for simulating isotropic 2D scattering patterns; , to perform operations on 2D images and masks; , a method for variance estimation of structural invariants through parametric resampling; , which computes the pair distance distribution function by a direct Fourier transform of the scattering data; , to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in for Bayesian consensus-based concentration-independent molecular weight estimation; , an shape analysis method that optimizes the search model directly against the scattering data; , an application to set up the initial search volume for multiphase modelling of membrane proteins; , to perform quasi-atomistic modelling of liposomes with elliptical shapes; , which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; , which reconstructs the shape of an unknown intermediate in an evolving system; and and , for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the graphical interface to Qt5, updating - a plugin to run a subset of tools - to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future releases. All these features are implemented in , freely available for academic users at https://www.embl-hamburg.de/biosaxs/software.html.
该软件套件包含许多用于小角散射数据处理、可视化、分析和建模的程序,重点是从生物大分子测量的数据。本文描述了该软件包的新进展。它们包括,用于模拟各向同性二维散射图案;,用于对二维图像和掩码执行操作;,一种通过参数重采样估计结构不变量方差的方法;,通过散射数据的直接傅里叶变换计算对距离分布函数;,用于从对距离分布函数计算散射数据,以便与实验数据进行比较;中的一个新模块,用于基于贝叶斯共识的浓度无关分子量估计;,一种直接针对散射数据优化搜索模型的形状分析方法;,一种用于设置膜蛋白多相建模初始搜索体积的应用程序;,用于对椭圆形脂质体进行准原子建模;,通过扭转角空间中的正常模式分析对核酸结构的构象变化进行建模;,用于重建演化系统中未知中间体的形状;以及和,分别用于对多层和不对称脂质囊泡进行建模。此外,还进行了技术更新以促进软件包的可维护性,包括将图形界面移植到Qt5,更新 - 一个运行工具子集的插件 - 以兼容Python 2和3,并添加实用程序以促进未来版本中的mmCIF兼容性。所有这些功能都在中实现,学术用户可在https://www.embl-hamburg.de/biosaxs/software.html免费获取。