=================
Reliontomo plugin
=================
This plugin provide wrappers around several programs of `RELION <https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page>`_ software suite (version 3.0) 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
-----------
* **Extract coordinates from pseudo-subtomograms** : Protocol to extract a set of 3D coordinates from a set of pseudo-subtomograms.
* **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 maps** : 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).
* **Matching coordinates** : Protocol to generate a set of pseudosubtomograms taking into account the intersection of a set of 3D coordinates and a set of pseudosubtomograms as input.
**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 3.0, 4.0
References
----------
1. Scheres et al., JMB, 2012
2. Scheres et al., JSB, 2012
3. Kimanius et al., eLife, 2016
4. Zivanov et al., eLife, 2018
Buildbot status
---------------
Status devel version:
.. image:: http://scipion-test.cnb.csic.es:9980/badges/reliontomo_devel.svg
Status production version:
.. image:: http://scipion-test.cnb.csic.es:9980/badges/reliontomo_prod.svg
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"description": "=================\nReliontomo plugin\n=================\n\nThis plugin provide wrappers around several programs of `RELION <https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page>`_ software suite (version 3.0) for its use in Tomography.\n\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\n\nProtocols\n-----------\n\n* **Extract coordinates from pseudo-subtomograms** : Protocol to extract a set of 3D coordinates from a set of pseudo-subtomograms.\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 maps** : 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* **Matching coordinates** : Protocol to generate a set of pseudosubtomograms taking into account the intersection of a set of 3D coordinates and a set of pseudosubtomograms as input.\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. A complete list of tests can be displayed by executing ``scipion3 tests --grep reliontomo --show``\n\nSupported versions\n------------------\n\nRelion 3.0, 4.0\n\n\nReferences\n----------\n\n1. Scheres et al., JMB, 2012 \n2. Scheres et al., JSB, 2012 \n3. Kimanius et al., eLife, 2016 \n4. Zivanov et al., eLife, 2018\n\n\nBuildbot status\n---------------\n\nStatus devel version:\n\n.. image:: http://scipion-test.cnb.csic.es:9980/badges/reliontomo_devel.svg\n\n\nStatus production version:\n\n.. image:: http://scipion-test.cnb.csic.es:9980/badges/reliontomo_prod.svg\n\n\n\n",
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