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Python-based Helix Indexer: A graphical user interface program for finding symmetry of helical assembly through Fourier–Bessel indexing of electron microscopic data
Protein Science ( IF 8 ) Pub Date : 2021-09-16 , DOI: 10.1002/pro.4186
Xuewu Zhang 1, 2
Affiliation  

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.

中文翻译:

基于 Python 的 Helix Indexer:一种图形用户界面程序,用于通过电子显微数据的傅里叶-贝塞尔索引找到螺旋组装的对称性

许多大分子形成螺旋组装体来执行它们的功能。电子显微图像的螺旋重建是解决此类组件的高分辨率结构的有效方法。螺旋组件对称参数的确定是螺旋重建的先决条件。最广泛使用的推导对称性的方法是通过傅里叶-贝塞尔索引螺旋组件的衍射图案。然而,由于索引螺旋衍射图案的内在模糊性,这种方法通常会导致不正确的解决方案。在这里,我们介绍了基于 Python 的螺旋索引器 (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过程。衍射图案可以直接读入程序或根据螺旋组件的二维类平均值即时计算。PyHI 允许通过使用衍射数据的振幅和相位来推导出衍射峰的贝塞尔阶。基于两个单位向量的贝塞尔阶,傅里叶空间格是用最少的用户输入构建的。该程序然后使用细化算法优化傅里叶空间格,随后在实空间中生成螺旋组件。该程序提供了螺旋组件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。PyHI 允许通过使用衍射数据的振幅和相位来推导出衍射峰的贝塞尔阶。基于两个单位向量的贝塞尔阶,傅里叶空间格是用最少的用户输入构建的。该程序然后使用细化算法优化傅里叶空间格,随后在实空间中生成螺旋组件。该程序提供了螺旋组件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。PyHI 允许通过使用衍射数据的振幅和相位来推导出衍射峰的贝塞尔阶。基于两个单位向量的贝塞尔阶,傅里叶空间格是用最少的用户输入构建的。该程序然后使用细化算法优化傅里叶空间格,随后在实空间中生成螺旋组件。该程序提供了螺旋组件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。
更新日期:2021-09-16
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