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Plugin to use cryoEF program within the Scipion framework
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README.rst . May 4, 2019

Cryoef plugin

This plugin provide a wrapper around cryoEF program.

build status


You will need to use 2.0 version of Scipion to be able to run these protocols. To install the plugin, you have two options:

a) Stable version

scipion installp -p scipion-em-cryoef

b) Developer's version

  • download repository
 git clone
  • install
 scipion installp -p path_to_scipion-em-cryoef --devel

CryoEF binaries will be installed automatically with the plugin, but you can also link an existing installation. Default installation path assumed is software/em/cryoEF-1.1.0, if you want to change it, set CRYOEF_HOME in scipion.conf file to the folder where the cryoEF is installed. To check the installation, simply run the following Scipion test:

scipion test cryoef.tests.test_protocols_cryoef.TestCryoEF

Supported versions



Detailed manual can be found in software/em/cryoEF-1.1.0/cryoEF_v1.1.0_manual.pdf


1. Naydenova, K and Russo, CJ "Measuring the effects of particle orientation to improve the efficiency of electron cryomicroscopy" Nature Communications (2017).

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