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EMAN2 plugin

This plugin provide wrappers around several programs of EMAN2 software suite.

PyPI release License Supported Python versions SonarCloud quality gate Downloads
stable: stable devel: | devel


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-eman2
  1. Developer's version

    • download repository
    git clone
    • install
    scipion installp -p path_to_scipion-em-eman2 --devel

Important: starting from the plugin v3.2 all tomo protocols have been removed, they are now in

EMAN2 binaries will be installed automatically with the plugin, but you can also link an existing installation.

  • Default installation path assumed is software/em/eman-2.91, if you want to change it, set EMAN2_HOME in scipion.conf file pointing to the folder where the EMAN2 is installed.
  • The default scratch directory is assumed /tmp/. You can change it by setting EMAN2SCRATCHDIR in scipion.conf or your shell environment.

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

scipion test eman2.tests.test_protocols_eman.TestEmanTiltValidate
scipion test eman2.tests.test_protocols_eman.TestEmanRefineEasy
scipion test eman2.tests.test_protocols_eman.TestEmanRefine2DBispec
scipion test eman2.tests.test_protocols_eman.TestEmanRefine2D
scipion test eman2.tests.test_protocols_eman.TestEmanReconstruct
scipion test eman2.tests.test_protocols_eman.TestEmanInitialModelMda
scipion test eman2.tests.test_protocols_eman.TestEmanInitialModelGroel
scipion test eman2.tests.test_protocols_eman.TestEmanInitialModelSGD
scipion test eman2.tests.test_protocols_eman.TestEmanCtfAuto
scipion test eman2.tests.test_protocols_eman.TestEmanAutopick

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

Supported versions

2.31, 2.9, 2.91


  • boxer (new interactive
  • boxer auto (fully automated new boxer in EMAN >= 2.21)
  • ctf auto
  • initial model
  • initial model SGD
  • reconstruct
  • refine 2d
  • refine 2d bispec
  • refine easy
  • tilt validate


  1. G. Tang, L. Peng, P.R. Baldwin, D.S. Mann, W. Jiang, I. Rees & S.J. Ludtke. (2007) EMAN2: an extensible image processing suite for electron microscopy. J Struct Biol. 157, 38-46. PMID: 16859925


Plugin to use Eman2 SPA programs within the Scipion framework





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