ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis,Journal of Applied Crystallography

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ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis
Journal of Applied Crystallography ( IF 5.2 ) Pub Date : 2021-02-01 , DOI: 10.1107/s1600576720013412
Karen Manalastas-Cantos ₁ , Petr V Konarev ₂ , Nelly R Hajizadeh ₁ , Alexey G Kikhney ₁ , Maxim V Petoukhov ₂ , Dmitry S Molodenskiy ₁ , Alejandro Panjkovich ₁ , Haydyn D T Mertens ₁ , Andrey Gruzinov ₁ , Clemente Borges ₁ , Cy M Jeffries ₁ , Dmitri I Svergun ₁ , Daniel Franke ₁

Affiliation

The ATSAS 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 ATSAS 3.0 package are described. They include IMSIM, for simulating isotropic 2D scattering patterns; IMOP, to perform operations on 2D images and masks; DATRESAMPLE, a method for variance estimation of structural invariants through parametric resampling; DATFT, which computes the pair distance distribution function by a direct Fourier transform of the scattering data; PDDFFIT, to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in DATMW for Bayesian consensus-based concentration-independent molecular weight estimation; DATMIF, an ab initio shape analysis method that optimizes the search model directly against the scattering data; DAMEMB, an application to set up the initial search volume for multiphase modelling of membrane proteins; ELLLIP, to perform quasi-atomistic modelling of liposomes with elliptical shapes; NMATOR, which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; DAMMIX, which reconstructs the shape of an unknown intermediate in an evolving system; and LIPMIX and BILMIX, for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the PRIMUS graphical interface to Qt5, updating SASpy – a PyMOL plugin to run a subset of ATSAS tools – to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future ATSAS releases. All these features are implemented in ATSAS 3.0, freely available for academic users at https://www.embl-hamburg.de/biosaxs/software.html.

中文翻译：

ATSAS 3.0：用于小角度散射数据分析的扩展功能和新工具

ATSAS 软件套件包含许多用于小角度散射数据的处理、可视化、分析和建模的程序，重点关注生物大分子测量的数据。这里描述了 ATSAS 3.0 软件包的新发展。它们包括 IMSIM，用于模拟各向同性 2D 散射图案；IMOP，对2D图像和掩模进行操作；DATRESAMPLE，一种通过参数重采样对结构不变量进行方差估计的方法；DATFT，通过散射数据的直接傅立叶变换来计算对距离分布函数；PDDFFIT，根据一对距离分布函数计算散射数据，以便与实验数据进行比较；DATMW 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；DATMIF，一种从头开始形状分析方法，直接针对散射数据优化搜索模型；DAMEMB，用于设置膜蛋白多相建模初始搜索体积的应用程序；ELLLIP，对椭圆形脂质体进行准原子建模；NMATOR，通过扭转角空间中的正态模式分析来模拟核酸结构的构象变化；DAMMIX，在不断演化的系统中重建未知中间体的形状；LIPMIX 和 BILMIX，分别用于模拟多层和不对称脂质囊泡。此外，还部署了技术更新以促进软件包的可维护性，其中包括将 PRIMUS 图形界面移植到 Qt5、更新 SASpy（一个用于运行 ATSAS 工具子集的 PyMOL 插件）以兼容 Python 2 和 3，以及添加实用程序以促进未来 ATSAS 版本中的 mmCIF 兼容性。所有这些功能均在 ATSAS 3.0 中实现，学术用户可免费使用 https://www.embl-hamburg.de/biosaxs/software.html。

更新日期：2021-02-01

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