ATTENTION: This plugin replaces grigoriefflab plugin. You cannot use both of them simultaneously.

This plugin provide wrappers around several programs of cisTEM software suite.

stable: stable

devel: | devel

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 https://github.com/scipion-em/scipion-em-cistem.git

    • install

    scipion installp -p path_to_scipion-em-cistem --devel

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

  • Default 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.

  • It’s possible to use CTFFIND4 installed separately from cisTEM by defining CTFFIND4_HOME variable in scipion.conf.

To check the installation, simply run one of the following Scipion tests:

scipion test cistem.tests.test_protocols_cistem_movies.TestUnblur
scipion test cistem.tests.test_protocols_cistem.TestCtffind4
scipion test cistem.tests.test_protocols_cistem.TestFindParticles
scipion test cistem.tests.test_protocols_cistem.TestRefine2D

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

Supported versions

1.0.0-beta

Protocols

  • ctffind4

  • unblur

  • find particles

  • classify 2D

References

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

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (3.10.1)

2 maintainers

PyPI data
Data sourced directly from PyPI's database.
Avatar for azazello from gravatar.com azazello Avatar for scipion from gravatar.com scipion

Credits

Author: Grigory Sharov

License

GNU General Public License v3 (GPLv3)

Tags

scipion electron-microscopy cryo-em structural-biology image-processing scipion-3.0

Classifiers

Report project as malware

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