Plugin to use cisTEM programs within the Scipion framework
Project description
This plugin provides wrappers for 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:
Stable version
scipion installp -p scipion-em-cistem
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
scipion tests cistem.tests.test_protocols_cistem_ts.TestCtffind4Ts
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
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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