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Plugin to use Eman2 programs within the Scipion framework
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eman2
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LICENSE Create LICENSE Jul 29, 2018
MANIFEST.in
README.md
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README.md

EMAN2 plugin

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

build status

Installation

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 https://github.com/scipion-em/scipion-em-eman.git
  • 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.

Protocols

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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