scipion-em-eman2 1.0.7

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 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 (old and new interactive e2boxer.py)

• boxer auto (fully automated new boxer in >=2.21)

• ctf auto

• initial model

• initial model SGD

• reconstruct

• refine 2d

• refine 2d bispec

• refine easy

• sparx picker

• 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