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Plugin to use Eman2 programs within the Scipion framework
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LICENSE Create LICENSE Jul 29, 2018

EMAN2 plugin

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

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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-eman

b) Developer's version

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

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-2.21, if you want to change it, set EMAN2DIR in scipion.conf file to the folder where the EMAN2 is installed. 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.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

In 2018 the plugin was updated to support the latest (at that moment) EMAN2: 2.21. This required a lot of code refactoring and the support of old EMAN2 version 2.11 had to be discontinued. Several new protocols were added: 2D refinements, tilt validation, ctf-auto and new e2boxer. The full changelog since Scipion-1.x is available here. In the following releases we plan to deprecate 2.12 support as well.



  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
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