=================================== Scipion plugin for EMAN2 Tomography

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This plugin provide wrappers around several programs of EMAN2 <https://blake.bcm.edu/emanwiki/EMAN2>_ tomography software suite.

============ Installation

The plugin can be installed in user (stable) or developer (latest, may be unstable) mode:

1. User (stable) version::

.. code-block::

scipion3 installp -p scipion-em-emantomo

2. Developer (latest, may be unstable) version::

• Clone the source code repository:

.. code-block::

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

• Move to devel branch:

.. code-block::

git checkout devel

• Install:

.. code-block::

scipion3 installp -p local/path/to/scipion-em-emantomo --devel

========= Protocols

The integrated protocols are:

1. Tilt series alignment and tomograms reconstruction.

2. CTF estimation.

3. Tomogram clipping.

4. Subtomograms manual picking.

5. Template matching picking.

6. Average subtomograms.

7. Subtomograms extraction from the tomograms.

8. Subtomograms extraction from the tilt series.

9. Initial model.

10. New initial model (from particles extracted from the tilt series).

11. Subtomograms refinement.

12. New subtomograms refinement (from particles extracted from the tilt series).

13. New multi-reference classification of subtomograms (from particles extracted from the tilt series).

===== Tests

The installation can be checked out running some tests. To list all of them, execute:

.. code-block::

 scipion3 tests --grep emantomo

To run all of them, execute:

.. code-block::

 scipion3 tests --grep emantomo --run

To run a specific test, for example, the tests to check the protocol for averaging subtomograms (the following command can be copied from the test list displayed when listing the tests, as explained above):

.. code-block::

scipion3 tests emantomo.tests.test_protocols_sta_classic_workflow.TestEmanTomoAverageSubtomogramsStaClassic

======== Tutorial

The workflow test generates a emantomo workflow that offers an overview of how to use emantomo.

.. code-block::

scipion3 tests emantomo.tests.test_protocols_sta_classic_workflow

========== References

• Single particle tomography in EMAN2. <https://doi.org/10.1016/j.jsb.2015.04.016>_ Jesús G. Galaz-Montoya et al., Journal of Structural Biology, 2015.

• High resolution single particle refinement in EMAN2.1. <https://doi.org/10.1016/j.ymeth.2016.02.018>_ James M. Bell et al., Methods, 2016.

=================== Contact information

If you experiment any problem, please contact us here: scipion-users@lists.sourceforge.net or open an issue_.

We'll be pleased to help.

Scipion Team

.. _issue: https://github.com/scipion-em/scipion-em-emantomo/issues