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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

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-eman2
  1. Developer's version

    • download repository
    git clone https://github.com/scipion-em/scipion-em-eman2.git
    
    • 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 https://github.com/scipion-em/scipion-em-emantomo

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

Protocols

  • boxer (new interactive e2boxer.py)
  • 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

References

  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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Plugin to use Eman2 SPA programs within the Scipion framework

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