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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.