====================================
Scipion plugin for Relion Tomography
====================================
.. image:: https://img.shields.io/pypi/v/scipion-em-reliontomo.svg
:target: https://pypi.python.org/pypi/scipion-em-reliontomo
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:target: https://pypi.python.org/pypi/scipion-em-reliontomo
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.. image:: https://img.shields.io/pypi/pyversions/scipion-em-reliontomo.svg
:target: https://pypi.python.org/pypi/scipion-em-reliontomo
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.. image:: https://img.shields.io/pypi/dm/scipion-em-reliontomo
:target: https://pypi.python.org/pypi/scipion-em-reliontomo
:alt: Downloads
This plugin provide wrappers around several programs of `RELION <https://relion.readthedocs.io/en/release-5.0/index.html>`_ software suite for its use in Tomography.
Installation
------------
You will need to use `3.0 <https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html>`_ version of Scipion to be able to run these protocols.
Protocols
-----------
VERSION 4.0:
* **Import coordinates 3D from a star file** : Protocol to import a set of 3D coordinates from a star file.
* **Import subtomograms from a star file** : Protocol to import a set of subtomograms from a star file.
* **3D Classification of subtomograms** : 3D Classification of subtomograms.
* **Tomo CTF refine** : Tomo CTF refine
* **De novo 3D initial model** : Generate a de novo 3D initial model from the pseudo-subtomograms.
* **Apply operation to Relion particles** : Operate on the particles star file.
* **Make pseudo-subtomograms** : Make pseudo-subtomograms.
* **Sharpen a 3D reference map** : Sharpen a 3D reference map and estimate the gold-standard FSC curves for subtomogram averaging.
* **Prepare data for Relion 4** : Prepare data for Relion 4
* **Reconstruct particle from tilt series** : Reconstruct particle from the original tilt series images.
* **Auto-refinement of subtomograms** : Auto-refinement of subtomograms.
* **Rec. particle averaging subtomograms** : This protocol reconstructs a volume using Relion. Reconstruct a volume from a given set of particles. The alignment parameters will be converted to a Relion star file and used as direction projections to reconstruct.
* **Tomo frame align** : Tomo frame align
* **Reconstruct tomograms from prepare data prot** : This protocol reconstructs a single tomogram using Relion. It is very useful to check if the protocol "Prepare data" has been applied correctly (in terms of flip options, for example).
VERSION 5.0:
* **Import subtomograms from a star file** : Protocol to import a set of subtomograms from a star file.
* **3D Classification of subtomograms** : 3D Classification of subtomograms.
* **Tomo CTF refine** : apply the refinement of the different parameters related to the CTF estimation.
* **De novo 3D initial model** : Generate a de novo 3D initial model from the pseudo-subtomograms.
* **Apply operation to Relion particles** : Operate on the particles star file: re-center and duplicates removal.
* **Sharpen a 3D reference map** : Sharpen a 3D reference map and estimate the gold-standard FSC curves for subtomogram averaging.
* **Extract subtomos** : extract the subtomograms from the tilt-series.
* **Reconstruct particle** : generate a reference map from a particle set by averaging the particles using their positions and orientations
* **Auto-refinement of subtomograms** : Auto-refinement of subtomograms.
* **Bayesian polishing** : refine the projections that map 3D space onto the images of the tilt series.
* **Tomogram reconstruction** : reconstruct tomograms.
* **Motion correction** : motion correction of the angular frame stacks using Relion's own implementation.
**Latest plugin versions**
==========================
If you want to check the latest version and release history go to `CHANGES <https://github.com/scipion-em-reliotomo/reliontomo/blob/master/CHANGES.txt>`_
**Installing the plugin**
=========================
In order to install the plugin follow these instructions:
.. code-block::
scipion installp -p scipion-em-reliontomo
or through the **plugin manager** by launching Scipion and following **Configuration** >> **Plugins**
**To install in development mode**
Clone or download the plugin repository
.. code-block::
git clone https://github.com/scipion-em/scipion-em-reliontomo.git
Install the plugin in developer mode.
.. code-block::
scipion installp -p local/path/to/scipion-em-reliontomo --devel
To check the installation, simply run one of the tests. A complete list of tests can be displayed by executing ``scipion3 tests --grep reliontomo --show``
Supported versions
------------------
Relion 4.0, 5.0
References
----------
1. Zivanov et al., eLife, 2022
2. Burt et al., bioRxiv, 2024
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"description": "====================================\nScipion plugin for Relion Tomography\n====================================\n\n.. image:: https://img.shields.io/pypi/v/scipion-em-reliontomo.svg\n :target: https://pypi.python.org/pypi/scipion-em-reliontomo\n :alt: PyPI release\n\n.. image:: https://img.shields.io/pypi/l/scipion-em-reliontomo.svg\n :target: https://pypi.python.org/pypi/scipion-em-reliontomo\n :alt: License\n\n.. image:: https://img.shields.io/pypi/pyversions/scipion-em-reliontomo.svg\n :target: https://pypi.python.org/pypi/scipion-em-reliontomo\n :alt: Supported Python versions\n\n.. image:: https://img.shields.io/pypi/dm/scipion-em-reliontomo\n :target: https://pypi.python.org/pypi/scipion-em-reliontomo\n :alt: Downloads\n\nThis plugin provide wrappers around several programs of `RELION <https://relion.readthedocs.io/en/release-5.0/index.html>`_ software suite for its use in Tomography.\n\n\nInstallation\n------------\n\nYou will need to use `3.0 <https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html>`_ version of Scipion to be able to run these protocols.\n\n\nProtocols\n-----------\n\nVERSION 4.0:\n\n* **Import coordinates 3D from a star file** : Protocol to import a set of 3D coordinates from a star file.\n* **Import subtomograms from a star file** : Protocol to import a set of subtomograms from a star file.\n* **3D Classification of subtomograms** : 3D Classification of subtomograms.\n* **Tomo CTF refine** : Tomo CTF refine\n* **De novo 3D initial model** : Generate a de novo 3D initial model from the pseudo-subtomograms.\n* **Apply operation to Relion particles** : Operate on the particles star file.\n* **Make pseudo-subtomograms** : Make pseudo-subtomograms.\n* **Sharpen a 3D reference map** : Sharpen a 3D reference map and estimate the gold-standard FSC curves for subtomogram averaging.\n* **Prepare data for Relion 4** : Prepare data for Relion 4\n* **Reconstruct particle from tilt series** : Reconstruct particle from the original tilt series images.\n* **Auto-refinement of subtomograms** : Auto-refinement of subtomograms.\n* **Rec. particle averaging subtomograms** : This protocol reconstructs a volume using Relion. Reconstruct a volume from a given set of particles. The alignment parameters will be converted to a Relion star file and used as direction projections to reconstruct.\n* **Tomo frame align** : Tomo frame align\n* **Reconstruct tomograms from prepare data prot** : This protocol reconstructs a single tomogram using Relion. It is very useful to check if the protocol \"Prepare data\" has been applied correctly (in terms of flip options, for example).\n\nVERSION 5.0:\n\n* **Import subtomograms from a star file** : Protocol to import a set of subtomograms from a star file.\n* **3D Classification of subtomograms** : 3D Classification of subtomograms.\n* **Tomo CTF refine** : apply the refinement of the different parameters related to the CTF estimation.\n* **De novo 3D initial model** : Generate a de novo 3D initial model from the pseudo-subtomograms.\n* **Apply operation to Relion particles** : Operate on the particles star file: re-center and duplicates removal.\n* **Sharpen a 3D reference map** : Sharpen a 3D reference map and estimate the gold-standard FSC curves for subtomogram averaging.\n* **Extract subtomos** : extract the subtomograms from the tilt-series.\n* **Reconstruct particle** : generate a reference map from a particle set by averaging the particles using their positions and orientations\n* **Auto-refinement of subtomograms** : Auto-refinement of subtomograms.\n* **Bayesian polishing** : refine the projections that map 3D space onto the images of the tilt series.\n* **Tomogram reconstruction** : reconstruct tomograms.\n* **Motion correction** : motion correction of the angular frame stacks using Relion's own implementation.\n\n\n**Latest plugin versions**\n==========================\n\nIf you want to check the latest version and release history go to `CHANGES <https://github.com/scipion-em-reliotomo/reliontomo/blob/master/CHANGES.txt>`_\n\n\n**Installing the plugin**\n=========================\n\nIn order to install the plugin follow these instructions:\n\n.. code-block::\n\n scipion installp -p scipion-em-reliontomo\n\n\nor through the **plugin manager** by launching Scipion and following **Configuration** >> **Plugins**\n\n\n**To install in development mode**\n\nClone or download the plugin repository\n\n.. code-block::\n\n git clone https://github.com/scipion-em/scipion-em-reliontomo.git\n\nInstall the plugin in developer mode.\n\n.. code-block::\n\n scipion installp -p local/path/to/scipion-em-reliontomo --devel\n\n\nTo check the installation, simply run one of the tests. 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