Python-based Helix Indexer: A graphical user interface program for finding symmetry of helical assembly through Fourier-Bessel indexing of electron microscopic data.
Python-based Helix Indexer: A graphical user interface program for finding symmetry of helical assembly through Fourier-Bessel indexing of electron microscopic data.
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基于 Python 的螺旋索引器：一种图形用户界面程序，用于通过电子显微镜数据的傅里叶贝塞尔索引来查找螺旋组件的对称性。
DOI：
10.1002/pro.4186
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发表时间：
2022
期刊：
影响因子：
--
通讯作者：
Zhang,Xuewu
中科院分区：
文献类型：
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作者：
Zhang,Xuewu
许多大分子形成螺旋组装体以执行其功能。从电子显微镜图像的螺旋重建是解决这种组件的高分辨率结构的强大方法。螺旋装配体对称性参数的确定是螺旋重构的前提。推导对称性的最广泛使用的方法是通过傅立叶-贝塞尔指数的螺旋组件的衍射图案。然而，这种方法，往往会导致不正确的解决方案，由于内在的模糊性索引螺旋衍射图案。在这里，我们介绍了基于Python的Hacking Indexer（PyHI），它提供了一个图形用户界面（GUI）来指导用户完成对称性确定的过程。衍射图可以直接读入程序，也可以根据螺旋组件的二维类平均值实时计算。PyHI允许通过使用衍射数据的振幅和相位来推导衍射峰的贝塞尔阶。基于两个单位向量的Bessel阶，构造了具有最小用户输入的Fourier空间格。然后，该程序使用一种细化算法来优化傅立叶空间晶格，并随后在真实的空间中生成螺旋组件。该程序提供了螺旋装配的出版质量图形表示和后续螺旋重建步骤所需的对称参数。
Many macromolecules form helical assemblies to carry out their functions. Helical reconstruction from electron microscopic images is a powerful approach for solving high‐resolution structures of such assemblies. Determination of the symmetry parameters of the helical assemblies is a prerequisite step in helical reconstruction. The most widely used method for deducing the symmetry is through Fourier–Bessel indexing the diffraction pattern of the helical assemblies. This method, however, often leads to incorrect solutions, due to intrinsic ambiguities in indexing helical diffraction patterns. Here, we present Python‐based Helix Indexer (PyHI), which provides a graphical user interface (GUI) to guide the users through the process of symmetry determination. Diffraction patterns can be read into the program directly or calculated on the fly from two‐dimensional class averages of helical assemblies. PyHI allows deducing the Bessel orders of diffraction peaks by using both the amplitudes and phases of the diffraction data. Based on the Bessel orders of two unit vectors, the Fourier space lattice is constructed with minimal user inputs. The program then uses a refinement algorithm to optimize the Fourier space lattice, and subsequently generate the helical assembly in real space. The program provides both a publication‐quality graphic representation of the helical assembly and the symmetry parameters required for subsequent helical reconstruction steps.