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Plugin to use cisTEM programs within the Scipion framework

Project description

This plugin provides wrappers for several programs of cisTEM software suite.

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-cistem
  1. Developer’s version

    • download repository

    git clone -b devel https://github.com/scipion-em/scipion-em-cistem.git
    • install

    scipion installp -p /path/to/scipion-em-cistem --devel

Important: Starting from plugin v3.9, the config variables have been renamed. See: scipion3 config -p cistem

cisTEM and CTFFind binaries will be installed automatically with the plugin, but you can also link an existing installation.

  • Default cisTEM installation path assumed is software/em/cistem-1.0.0-beta, if you want to change it, set CISTEM_HOME in scipion.conf file pointing to the folder where the cisTEM is installed.

  • Default CTFFind installation path assumed is software/em/ctffind-5.0.2,if you want to change it, set CTFFIND_HOME in scipion.conf file pointing to the folder where CTFFind is installed.

A complete list of tests can be seen by executing scipion test --show --grep cistem

Supported versions

  • 1.0.0-beta (cistem)

  • 4.1.14 (ctffind4)

  • 5.0, 5.0.2 (ctffind5)

Licenses

Protocols

  • ctffind

  • import tomo CTFs

  • tilt-series ctffind

  • unblur

  • find particles

  • classify 2D

References

  1. Johannes Elferich, Lingli Kong, Ximena Zottig, Nikolaus Grigorieff. (2024) CTFFIND5 provides improved insight into quality, tilt and thickness of TEM samples. bioRxiv 2024.02.26.582023; doi: https://doi.org/10.1101/2024.02.26.582023

  2. Timothy Grant and Alexis Rohou and Nikolaus Grigorieff. (2018) cisTEM, user-friendly software for single-particle image processing. eLife 7:e35383.

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