ArticleProtein science : a publication of the Protein Society2022
Python-based Helix Indexer: A graphical user interface program for finding symmetry of helical assembly through Fourier-Bessel indexing of electron microscopic data.
Article in Protein science : a publication of the Protein Society, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- Structure of core assembly of the Clostridioides difficile germinosome.Nature communications · 2026Article
- Auto-crosslinking sporesilk fibers promote endospore and Cry toxin clustering.Nature communications · 2026Article
- Structural basis for ACT1 oligomerization induced by IL-17 receptor hetero-tetramer.Nature communications · 2025Article
- DiameTR: A cryo-EM tool for diameter sorting of tubular samples.Journal of structural biology: X · 2025Article
- The bacterial ESCRT-III PspA rods thin lipid tubules and increase membrane curvature through helix α0 interactions.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Curvature Generation and Engineering Principles fromACS nano · 2025Article
- Structural basis for Vipp1 membrane binding: from loose coats and carpets to ring and rod assemblies.Nature structural & molecular biology · 2025Article
- The Asgard archaeal ESCRT-III system forms helical filaments and remodels eukaryotic-like membranes.The EMBO journal · 2025Article
- Structural plasticity of bacterial ESCRT-III protein PspA in higher-order assemblies.Nature structural & molecular biology · 2025Article
- Purification and Cryo-Electron Microscopy Analysis of Bacterial Appendages.Bio-protocol · 2024Article
- Helical reconstruction, again.Current opinion in structural biology · 2024Review
- Helical reconstruction of VP39 reveals principles for baculovirus nucleocapsid assembly.Nature communications · 2024Article
- Helical reconstruction of VP39 reveals principles for baculovirus nucleocapsid assembly.bioRxiv : the preprint server for biology · 2023Article
- DNA-origami-directed virus capsid polymorphism.Nature nanotechnology · 2023Article
- Helical ordering of envelope-associated proteins and glycoproteins in respiratory syncytial virus.The EMBO journal · 2022Article
- 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 : a publication of the Protein Society · 2022Article
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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.
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