scipion-em-emantomo 3.1.0

Plugin to use EMAN2 tomography programs within the Scipion framework

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

stable:

devel: |

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-emantomo

2. Developer’s version

   • download repository

   git clone https://github.com/scipion-em/scipion-em-emantomo.git

   • install

   scipion installp -p path_to_scipion-em-emantomo --devel

EMAN2 binaries will be installed automatically with the plugin using a Conda environment.

• Default installation path assumed is software/em/eman-2.91, if you want to change it, set EMANTOMO_HOME in scipion.conf file pointing to the folder where the EMANTOMO is installed.

To check the installation, simply run one of the following Scipion tests:

scipion3 tests emantomo.tests.test_protocols_emantomo.TestEmanTomoTempMatch
scipion3 tests emantomo.tests.test_protocols_emantomo.TestEmanTomoSubtomogramRefinement
scipion3 tests emantomo.tests.test_protocols_emantomo.TestEmanTomoReconstruction
scipion3 tests emantomo.tests.test_protocols_emantomo.TestEmanTomoInitialModel
scipion3 tests emantomo.tests.test_protocols_emantomo.TestEmanTomoExtraction

A complete list of tests can also be seen by executing scipion test --show --grep emantomo

Supported versions

• 2.9

• 2.91 (Default version)

Protocols

• boxer (new interactive e2spt_boxer.py)

• Template Matching

• Initial model SGD

• Tomogram reconstruction

• Subtomogram extraction

• Subtomogram refinement

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