scipion-em-eman2 3.5

Plugin to use EMAN programs within the Scipion framework

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:

1. Stable version

scipion installp -p scipion-em-eman2

2. 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

EMAN software will be installed automatically with the plugin but you can also use an existing installation by providing EMAN_ENV_ACTIVATION (see below).

Important: you need to have conda (miniconda3 or anaconda3) pre-installed to use this program.

Configuration variables

CONDA_ACTIVATION_CMD: If undefined, it will rely on conda command being in the PATH (not recommended), which can lead to execution problems mixing scipion python with conda ones. One example of this could can be seen below but depending on your conda version and shell you will need something different: CONDA_ACTIVATION_CMD = eval “$(/extra/miniconda3/bin/conda shell.bash hook)”

EMAN_ENV_ACTIVATION (default = conda activate eman-2.99.47): Command to activate the EMAN environment.

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

2.99.47

Protocols

• boxer

• boxer auto

• 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