Helicon

A collection of tools for cryo-EM analysis of helical structures.

Installation

Run this command in a terminal:

pip install "helicon[all] @ git+https://github.com/jianglab/helicon"

Usage

Run this command in a terminal and follow the help message:

helicon --help

Commands included in helicon

• 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
• 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

Disclaimer

Helicon is at a very early stage of development, and we are releasing it to promote open science. However, it might be very unstable/buggy, and the support will be very limited.