Plugin to use EMAN2 programs within the Scipion framework
Project description
This plugin provides wrappers around several programs of EMAN software suite.
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:
Stable version
scipion installp -p scipion-em-eman2
Developer’s version
download repository
git clone -b devel https://github.com/scipion-em/scipion-em-eman2.git
install
scipion installp -p /path/to/scipion-em-eman2 --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-2.99, 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
2.91, 2.99 (continuous build)
Protocols
boxer
boxer auto
ctf auto
initial model
initial model SGD
reconstruct
refine 2d
refine 2d bispec
refine easy
tilt validate
References
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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