Plugin to use EMAN2 programs within the Scipion framework
Project description
This plugin provide wrappers around several programs of EMAN2 software suite.
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:
Stable version
scipion installp -p scipion-em-eman2
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
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-2.3, if you want to change it, set EMAN2_HOME in scipion.conf file pointing to the folder where the EMAN2 is installed.
IMPORTANT: From plugin version 1.0.5 EMAN2DIR was renamed to EMAN2_HOME. Please update your scipion.conf file!
If you need to pass special options to mpirun (like a hostfile), you can use the EMANMPIOPTS shell variable, but most users should not need this. A typical usage would be export EMANMPIOPTS="-hostfile myhosts.txt". You should only do this if necessary, though (note that then when supplying the parameter –parallel=mpi:n:scratch_directory, ‘n’ is no longer the number of cpus to use, but rather the number of nodes listed in myhosts.txt).
The default scratch directory is assumed /tmp/. You can change it by setting EMAN2SCRATCHDIR in 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
2.21, 2.3
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.
Protocols
boxer auto (fully automated new boxer in >=2.21)
ctf auto
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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