scipion-em-atsas

Plugin to use ATSAS programs within the Scipion framework


Keywords
scipion, electron-microscopy, cryo-em, structural-biology, image-processing, scipion-3, 0, atom
License
GPL-3.0
Install
pip install scipion-em-atsas==1.0.2

Documentation

ATSAS plugin

This plugin provides a wrapper for ATSAS - a program suite for small-angle scattering data analysis from biological macromolecules.

PyPI release License Supported Python versions SonarCloud quality gate Downloads

Installation

You will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:

  1. Stable version
scipion installp -p scipion-em-atsas
  1. Developer's version

    • download repository
    git clone -b devel https://github.com/scipion-em/scipion-em-atsas.git
    
    • install
    scipion installp -p /path/to/scipion-em-atsas --devel
    

Important: ATSAS binaries is free for academic users, but you will have to register, download and install them yourself from https://www.embl-hamburg.de/biosaxs/download.html

Configuration variables

ATSAS_HOME: Installation path to ATSAS. Default is software/em/atsas-3.2.0

Supported versions

3.0.1, 3.2.0

Protocols

  • convert PDB to SAXS curve

References

  1. Manalastas-Cantos, K., Konarev, P.V., Hajizadeh, N.R., Kikhney, A.G., Petoukhov, M.V., Molodenskiy, D.S., Panjkovich, A., Mertens, H.D.T., Gruzinov, A., Borges, C., Jeffries, C.M., Svergun, D.I., Franke, D. (2021). ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis J. Appl. Cryst. 54, 343-355
  2. Svergun, D., Barberato, C., and Koch, M. H. J. (1995). CRYSOL - a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates. Journal of Applied Crystallography, 28(6): 768–773.