A collection of tools for cryo-EM analysis of helical structures.
Li, D., Zhang, X., and Jiang, W. (2025). Helicon: Helical indexing and 3D reconstruction from one image. bioRxiv, 2025.04.05.647385. doi:10.1101/2025.04.05.647385.
Run this command in a terminal:
pip install "helicon[all] @ git+https://github.com/jianglab/helicon"
Run this command in a terminal and follow the help message:
helicon --help
- cryosparc: A command line tool that interacts with a CryoSPARC server and performs image analysis tasks
- ctfSimulation: A Web app that simulates 1D/2D TEM contrast transfer function (CTF)
- denovo3D: A Web app for de novo helical indexing and 3D reconstruction from a single 2D image
- denovo3DBatch: A command line tool for de novo helical indexing and 3D reconstruction from a single 2D image
- helicalLattice: A Web app that illustrates the interconversion of 2D Lattice ⇔ Helical Lattice
- helicalPitch: A Web app that helps you determine helical pitch/twist using 2D Classification info
- helicalProjection: A Web app that helps you compare 2D images with helical structure projections
- hi3d: A Web app for helical indexing using the cylindrical projection of a 3D map
- hill: A Web app for helical indexing using Fourier layer lines of 2D images
- images2star: A command line tool that analyzes/transforms dataset(s) and saves the dataset in RELION star file
- map2seq: A Web app that identifies the best protein sequence explaining a 3D density map
- proc3d: A command line tool that anaylzes/transforms 3D maps
- procart: A Web app that plots cartoon illustration of the residue properties of amyloid atomic models
- whereIsMyClass: A Web app that maps 2D classes to helical tube/filament images
- HOMcontainer: A command line tool for looking at the consistency of helical assignments. Open github issue to update WISHLIST_HOMcontainer.md.
- Helicon@readthedocs: for users
- Helicon@DeepWiki: for developers