jvini98/scipion-em-cistem

Plugin to use cisTEM programs within the Scipion framework

cisTEM plugin

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

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

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

2. 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. Setting this value will have the priority over Ctffind inside cisTEM.

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
• tilt-series 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.