Academic Journal
Python-based Helix Indexer: A graphical user interface program for finding symmetry of helical assembly through Fourier-Bessel indexing of electron microscopic data.
| Title: | 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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| Authors: | Zhang X; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas.; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas. |
| Source: | Protein science : a publication of the Protein Society [Protein Sci] 2022 Jan; Vol. 31 (1), pp. 107-117. Date of Electronic Publication: 2021 Sep 22. |
| Publication Type: | Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't |
| Language: | English |
| Journal Info: | Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9211750 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1469-896X (Electronic) Linking ISSN: 09618368 NLM ISO Abbreviation: Protein Sci Subsets: MEDLINE |
| Imprint Name(s): | Publication: 2001- : Woodbury, NY : Cold Spring Harbor Laboratory Press Original Publication: New York, N.Y. : Cambridge University Press, c1992- |
| MeSH Terms: | Algorithms* , Image Processing, Computer-Assisted* , Microscopy, Electron* , Models, Molecular* , Programming Languages* , User-Computer Interface* |
| Abstract: | 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. (© 2021 The Protein Society.) |
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| Grant Information: | R01 CA220283 United States CA NCI NIH HHS |
| Contributed Indexing: | Keywords: cryo-EM; helical reconstruction; helical symmetry; indexing |
| Entry Date(s): | Date Created: 20210916 Date Completed: 20220203 Latest Revision: 20230102 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC8740834 |
| DOI: | 10.1002/pro.4186 |
| PMID: | 34529294 |
| Database: | MEDLINE |
| ISSN: | 1469-896X |
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| DOI: | 10.1002/pro.4186 |