===================================
Scipion plugin for EMAN2 Tomography
===================================
.. image:: https://img.shields.io/pypi/v/scipion-em-emantomo.svg
:target: https://pypi.python.org/pypi/scipion-em-emantomo
:alt: PyPI release
.. image:: https://img.shields.io/pypi/l/scipion-em-emantomo.svg
:target: https://pypi.python.org/pypi/scipion-em-emantomo
:alt: License
.. image:: https://img.shields.io/pypi/pyversions/scipion-em-emantomo.svg
:target: https://pypi.python.org/pypi/scipion-em-emantomo
:alt: Supported Python versions
.. image:: https://img.shields.io/pypi/dm/scipion-em-emantomo
:target: https://pypi.python.org/pypi/scipion-em-emantomo
:alt: Downloads
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
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"description": "===================================\nScipion plugin for EMAN2 Tomography\n===================================\n\n.. image:: https://img.shields.io/pypi/v/scipion-em-emantomo.svg\n :target: https://pypi.python.org/pypi/scipion-em-emantomo\n :alt: PyPI release\n\n.. image:: https://img.shields.io/pypi/l/scipion-em-emantomo.svg\n :target: https://pypi.python.org/pypi/scipion-em-emantomo\n :alt: License\n\n.. image:: https://img.shields.io/pypi/pyversions/scipion-em-emantomo.svg\n :target: https://pypi.python.org/pypi/scipion-em-emantomo\n :alt: Supported Python versions\n\n.. image:: https://img.shields.io/pypi/dm/scipion-em-emantomo\n :target: https://pypi.python.org/pypi/scipion-em-emantomo\n :alt: Downloads\n\nThis plugin provide wrappers around several programs of `EMAN2 <https://blake.bcm.edu/emanwiki/EMAN2>`_ tomography software suite.\n\n============\nInstallation\n============\nThe plugin can be installed in user (stable) or developer (latest, may be unstable) mode:\n\n**1. User (stable) version:**:\n\n.. code-block::\n\n scipion3 installp -p scipion-em-emantomo\n\n**2. Developer (latest, may be unstable) version:**:\n\n* Clone the source code repository:\n\n.. code-block::\n\n git clone https://github.com/scipion-em/scipion-em-emantomo.git\n\n* Move to devel branch:\n\n.. code-block::\n\n git checkout devel\n\n* Install:\n\n.. code-block::\n\n scipion3 installp -p local/path/to/scipion-em-emantomo --devel\n\n=========\nProtocols\n=========\nThe integrated protocols are:\n\n1. Tilt series alignment and tomograms reconstruction.\n\n2. CTF estimation.\n\n3. Tomogram clipping.\n\n4. Subtomograms manual picking.\n\n5. Template matching picking.\n\n6. Average subtomograms.\n\n7. Subtomograms extraction from the tomograms.\n\n8. Subtomograms extraction from the tilt series.\n\n9. Initial model.\n\n10. New initial model (from particles extracted from the tilt series).\n\n11. Subtomograms refinement.\n\n12. New subtomograms refinement (from particles extracted from the tilt series).\n\n13. New multi-reference classification of subtomograms (from particles extracted from the tilt series).\n\n\n=====\nTests\n=====\n\nThe installation can be checked out running some tests. To list all of them, execute:\n\n.. code-block::\n\n scipion3 tests --grep emantomo\n\nTo run all of them, execute:\n\n.. code-block::\n\n scipion3 tests --grep emantomo --run\n\nTo run a specific test, for example, the tests to check the protocol for averaging subtomograms (the following command\ncan be copied from the test list displayed when listing the tests, as explained above):\n\n.. code-block::\n\n scipion3 tests emantomo.tests.test_protocols_sta_classic_workflow.TestEmanTomoAverageSubtomogramsStaClassic\n\n========\nTutorial\n========\nThe workflow test generates a emantomo workflow that offers an overview of how to use emantomo.\n\n.. code-block::\n\n scipion3 tests emantomo.tests.test_protocols_sta_classic_workflow\n\n==========\nReferences\n==========\n\n* `Single particle tomography in EMAN2. <https://doi.org/10.1016/j.jsb.2015.04.016>`_\n Jes\u00fas G. Galaz-Montoya et al., Journal of Structural Biology, 2015.\n\n* `High resolution single particle refinement in EMAN2.1. <https://doi.org/10.1016/j.ymeth.2016.02.018>`_\n James M. Bell et al., Methods, 2016.\n\n\n===================\nContact information\n===================\n\nIf you experiment any problem, please contact us here: scipion-users@lists.sourceforge.net or open an issue_.\n\nWe'll be pleased to help.\n\n*Scipion Team*\n\n.. _issue: https://github.com/scipion-em/scipion-em-emantomo/issues\n\n\n",
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