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用于在相互连接的刚性单元网络中发现协同刚性单元旋转的软件。

The software for discovering cooperative rigid-unit rotations in networks of interconnected rigid units.

作者信息

Campbell Branton J, Stokes Harold T, Averett Tyler B, Machlus Shae, Yost Christopher J

机构信息

Physics and Astronomy, Brigham Young University, Provo, Utah 84602, USA.

出版信息

J Appl Crystallogr. 2021 Nov 2;54(Pt 6):1847-1856. doi: 10.1107/S1600576721009353. eCollection 2021 Dec 1.

DOI:10.1107/S1600576721009353
PMID:34963771
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8662972/
Abstract

A user-friendly web-based software tool called '' is introduced for detecting cooperative rigid-unit modes (RUMs) in networks of interconnected rigid units ( molecules, clusters or polyhedral units). This tool implements a recently described algorithm in which symmetry-mode patterns of pivot-atom rotation and displacement vectors are used to construct a linear system of equations whose null space consists entirely of RUMs. The symmetry modes are first separated into independent symmetry-mode blocks and the set of equations for each block is solved separately by singular value decomposition. is the newest member of the . Here, it is shown how to prepare structural and symmetry-mode information for use in , how to use each of 's input fields and options, and how to use and interpret output.

摘要

介绍了一种名为“ ”的用户友好型基于网络的软件工具，用于检测相互连接的刚性单元（分子、簇或多面体单元）网络中的协同刚性单元模式（RUMs）。该工具实现了一种最近描述的算法，其中枢轴原子旋转和位移矢量的对称模式用于构建一个线性方程组，其零空间完全由RUMs组成。对称模式首先被分离成独立的对称模式块，每个块的方程组通过奇异值分解单独求解。 是 的最新成员。在此，展示了如何准备用于 的结构和对称模式信息，如何使用 的每个输入字段和选项，以及如何使用和解释 输出。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bb8a/8662972/b15d9c710a21/j-54-01847-fig11.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bb8a/8662972/47d8c54721c1/j-54-01847-fig1.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bb8a/8662972/06be67908d04/j-54-01847-fig7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bb8a/8662972/ced2d0affa5d/j-54-01847-fig8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bb8a/8662972/eb893c99d42c/j-54-01847-fig9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bb8a/8662972/4c8ac1efb6dd/j-54-01847-fig10.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bb8a/8662972/b15d9c710a21/j-54-01847-fig11.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bb8a/8662972/47d8c54721c1/j-54-01847-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bb8a/8662972/542a01474ffe/j-54-01847-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bb8a/8662972/000cd406df1c/j-54-01847-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bb8a/8662972/e14f44db2839/j-54-01847-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bb8a/8662972/d22e703c856d/j-54-01847-fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bb8a/8662972/cf566fc77499/j-54-01847-fig6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bb8a/8662972/06be67908d04/j-54-01847-fig7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bb8a/8662972/ced2d0affa5d/j-54-01847-fig8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bb8a/8662972/eb893c99d42c/j-54-01847-fig9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bb8a/8662972/4c8ac1efb6dd/j-54-01847-fig10.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/bb8a/8662972/b15d9c710a21/j-54-01847-fig11.jpg

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