=======================
Localrec Scipion plugin
=======================
Cryogenic electron microscopy (cryoEM) can yield near-atomic resolution structures of highly ordered macromolecular complexes. Often however some subunits bind in a flexible manner, have different symmetry from the rest of the complex, or are present in sub-stoichiometric amounts, limiting the attainable resolution. We have developed a general method for the localized three-dimensional reconstruction of such subunits earlier (Ilca et al 2015 Nature Commun).
In this project we implement Localized Reconstruction as a plugin (Locarec) for Scipion.
If Localized Reconstruction is useful in your work, please cite:
Ilca SL, Kotecha A, Sun X, Poranen MM, Stuart DI & Huiskonen JT (2015). Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes. Nat Commun 6, 8843. doi:10.1038/ncomms9843
Abrishami V, Ilca SL, Gomez-Blanco J, Rissanen I, de la Rosa-Trevín JM, Reddy VS, Carazo JM, Huiskonen JT (2020). Localized reconstruction in Scipion expedites the analysis of symmetry mismatches in cryo-EM data. Prog. Biophys. Mol. Biol. doi:10.1016/j.pbiomolbio.2020.05.004.
===================
Install this plugin
===================
You will need to use `3.0.0 <https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html>`_ version of Scipion or later to run these protocols.
**Stable version**
Either use the following command
.. code-block::
scipion3 installp -p scipion-em-localrec
or
Install plugin through the plugin manager GUI by launching Scipion and following **Configuration** >> **Plugins**
**Developer's version**
1. Download repository:
.. code-block::
git clone https://github.com/scipion-em/scipion-em-localrec.git
2. Install:
.. code-block::
scipion3 installp -p path_to_scipion-em-localrec --devel
3. Test the plugin:
.. code-block::
scipion3 test localrec.tests.test_protocol_localized_reconstruction
=========
Protocols
=========
The following protocols have been implemented so far
* localrec - define subparticles: Determines the coordinates, orientations and defocus values of the sub-particles.
* localrec - filter subparticles: Excludes unwanted sub-particles based on alignment information.
* localrec - extract subparticles: Extracts sub-particle images from each particle image.
* localrec - set origin to subvolume: Fits a sub-volume back to it's original volume (larger volume).
* localrec - particles subset by subparticles: makes a subset of particles for which there is at least one sub-particle.
* localrec - stitch subvolumes: Assembles a full volume from the sub-volumes generated by localized reconstruction.
=====
Tests
=====
* scipion test localrec.tests.test_protocol_localized_reconstruction
===============
Buildbot status
===============
Status devel version:
.. image:: http://scipion-test.cnb.csic.es:9980/badges/localrec_devel.svg
Status production version:
.. image:: http://scipion-test.cnb.csic.es:9980/badges/localrec_prod.svg
================
Acknowledgements
================
The authors acknowledge funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (649053).
Raw data
{
"_id": null,
"home_page": "https://github.com/scipion-em/scipion-em-localrec",
"name": "scipion-em-localrec",
"maintainer": "",
"docs_url": null,
"requires_python": "",
"maintainer_email": "",
"keywords": "localizedreconstruction cryoem imageprocessing scipion-3.0",
"author": "Laboratory of Structural Biology",
"author_email": "grp-lsb-software@helsinki.fi",
"download_url": "https://files.pythonhosted.org/packages/85/2e/977d04a2971743ae1650ed3c5ba203c5c2912436a5fb6840cb3da5a771db/scipion-em-localrec-3.2.0.tar.gz",
"platform": null,
"description": "=======================\nLocalrec Scipion plugin\n=======================\n\nCryogenic electron microscopy (cryoEM) can yield near-atomic resolution structures of highly ordered macromolecular complexes. Often however some subunits bind in a flexible manner, have different symmetry from the rest of the complex, or are present in sub-stoichiometric amounts, limiting the attainable resolution. We have developed a general method for the localized three-dimensional reconstruction of such subunits earlier (Ilca et al 2015 Nature Commun).\n\nIn this project we implement Localized Reconstruction as a plugin (Locarec) for Scipion.\n\nIf Localized Reconstruction is useful in your work, please cite:\n\nIlca SL, Kotecha A, Sun X, Poranen MM, Stuart DI & Huiskonen JT (2015). Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes. Nat Commun 6, 8843. doi:10.1038/ncomms9843\n\nAbrishami V, Ilca SL, Gomez-Blanco J, Rissanen I, de la Rosa-Trev\u00edn JM, Reddy VS, Carazo JM, Huiskonen JT (2020). Localized reconstruction in Scipion expedites the analysis of symmetry mismatches in cryo-EM data. Prog. Biophys. Mol. Biol. doi:10.1016/j.pbiomolbio.2020.05.004.\n\n===================\nInstall this plugin\n===================\n\nYou will need to use `3.0.0 <https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html>`_ version of Scipion or later to run these protocols.\n\n**Stable version** \n\nEither use the following command\n\n.. code-block::\n\n scipion3 installp -p scipion-em-localrec\n\nor\n\nInstall plugin through the plugin manager GUI by launching Scipion and following **Configuration** >> **Plugins**\n\n**Developer's version** \n\n1. Download repository: \n\n.. code-block::\n\n git clone https://github.com/scipion-em/scipion-em-localrec.git\n\n2. Install:\n\n.. code-block::\n\n scipion3 installp -p path_to_scipion-em-localrec --devel\n\n3. Test the plugin:\n\n.. code-block::\n\n scipion3 test localrec.tests.test_protocol_localized_reconstruction\n\n=========\nProtocols\n=========\n\nThe following protocols have been implemented so far\n\n* localrec - define subparticles: Determines the coordinates, orientations and defocus values of the sub-particles.\n* localrec - filter subparticles: Excludes unwanted sub-particles based on alignment information.\n* localrec - extract subparticles: Extracts sub-particle images from each particle image.\n* localrec - set origin to subvolume: Fits a sub-volume back to it's original volume (larger volume).\n* localrec - particles subset by subparticles: makes a subset of particles for which there is at least one sub-particle.\n* localrec - stitch subvolumes: Assembles a full volume from the sub-volumes generated by localized reconstruction.\n\n=====\nTests\n=====\n\n* scipion test localrec.tests.test_protocol_localized_reconstruction\n\n===============\nBuildbot status\n===============\nStatus devel version: \n\n.. image:: http://scipion-test.cnb.csic.es:9980/badges/localrec_devel.svg\n\nStatus production version: \n\n.. image:: http://scipion-test.cnb.csic.es:9980/badges/localrec_prod.svg\n\n\n================\nAcknowledgements\n================\n\nThe authors acknowledge funding from the European Research Council under the European Union\u2019s Horizon 2020 research and innovation programme (649053).\n\n\n",
"bugtrack_url": null,
"license": "",
"summary": "Localrec ready to use in scipion.",
"version": "3.2.0",
"project_urls": {
"Homepage": "https://github.com/scipion-em/scipion-em-localrec"
},
"split_keywords": [
"localizedreconstruction",
"cryoem",
"imageprocessing",
"scipion-3.0"
],
"urls": [
{
"comment_text": "scipion-3.0",
"digests": {
"blake2b_256": "746d4f186b4e82e64802025cb37ad95e247bfd32368ef743dbb5cf318283100d",
"md5": "dc3faaa90b8caac4c66e64ec04ed0399",
"sha256": "2177559d2b850ec9ef169e4fb5a22ee6212f764f8624f675f1a5b12396e93ec2"
},
"downloads": -1,
"filename": "scipion_em_localrec-3.2.0-py3-none-any.whl",
"has_sig": false,
"md5_digest": "dc3faaa90b8caac4c66e64ec04ed0399",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": null,
"size": 533691,
"upload_time": "2023-11-21T11:26:20",
"upload_time_iso_8601": "2023-11-21T11:26:20.446188Z",
"url": "https://files.pythonhosted.org/packages/74/6d/4f186b4e82e64802025cb37ad95e247bfd32368ef743dbb5cf318283100d/scipion_em_localrec-3.2.0-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "scipion-3.0",
"digests": {
"blake2b_256": "852e977d04a2971743ae1650ed3c5ba203c5c2912436a5fb6840cb3da5a771db",
"md5": "b84b75faf98dbb5bdaf9233dbd283032",
"sha256": "27bd7955d17369fc7fbcf3b00709c443a6d0d85bc4f8551313c32319fad76ddb"
},
"downloads": -1,
"filename": "scipion-em-localrec-3.2.0.tar.gz",
"has_sig": false,
"md5_digest": "b84b75faf98dbb5bdaf9233dbd283032",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 522980,
"upload_time": "2023-11-21T11:26:22",
"upload_time_iso_8601": "2023-11-21T11:26:22.191458Z",
"url": "https://files.pythonhosted.org/packages/85/2e/977d04a2971743ae1650ed3c5ba203c5c2912436a5fb6840cb3da5a771db/scipion-em-localrec-3.2.0.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-11-21 11:26:22",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "scipion-em",
"github_project": "scipion-em-localrec",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"lcname": "scipion-em-localrec"
}
JSON
