============
FSC3D plugin
============
This plugin provides a wrapper for `3DFSC <https://github.com/nysbc/Anisotropy/>`_ program developed at Salk Institute and NYSBC.
.. image:: https://img.shields.io/pypi/v/scipion-em-fsc3d.svg
:target: https://pypi.python.org/pypi/scipion-em-fsc3d
:alt: PyPI release
.. image:: https://img.shields.io/pypi/l/scipion-em-fsc3d.svg
:target: https://pypi.python.org/pypi/scipion-em-fsc3d
:alt: License
.. image:: https://img.shields.io/pypi/pyversions/scipion-em-fsc3d.svg
:target: https://pypi.python.org/pypi/scipion-em-fsc3d
:alt: Supported Python versions
.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-fsc3d?server=https%3A%2F%2Fsonarcloud.io
:target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-fsc3d
:alt: SonarCloud quality gate
.. image:: https://img.shields.io/pypi/dm/scipion-em-fsc3d
:target: https://pypi.python.org/pypi/scipion-em-fsc3d
:alt: Downloads
Installation
-------------
You will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:
a) Stable version
.. code-block::
scipion installp -p scipion-em-fsc3d
b) Developer's version
* download repository
.. code-block::
git clone -b devel https://github.com/scipion-em/scipion-em-fsc3d.git
* install
.. code-block::
scipion installp -p /path/to/scipion-em-fsc3d --devel
FSC3D software will be installed automatically with the plugin but you can also use an existing installation by providing *FSC3D_HOME* (see below).
**Important:** you need to have conda (miniconda3 or anaconda3) pre-installed to use this program.
Configuration variables
-----------------------
*CONDA_ACTIVATION_CMD*: If undefined, it will rely on conda command being in the
PATH (not recommended), which can lead to execution problems mixing scipion
python with conda ones. One example of this could can be seen bellow but
depending on your conda version and shell you will need something different:
CONDA_ACTIVATION_CMD = eval "$(/extra/miniconda3/bin/conda shell.bash hook)"
*FSC3D_HOME* (default = software/em/fsc3D-3.0):
Path where the 3DFSC is installed.
*FSC3D_ENV_ACTIVATION* (default = conda activate fsc3D-3.0):
Command to activate the 3DFSC environment.
Verifying
---------
To check the installation, simply run the following Scipion test:
``scipion test fsc3d.tests.test_protocols_3dfsc.Test3DFSC``
Supported versions
------------------
3.0 (modified for Scipion, see https://github.com/azazellochg/fsc3D)
Protocols
----------
* resolution estimation
References
-----------
1. Yong Zi Tan, Philip R Baldwin, Joseph H Davis, James R Williamson, Clinton S Potter, Bridget Carragher & Dmitry Lyumkis. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nature Methods volume 14, pages 793–796 (2017).
Raw data
{
"_id": null,
"home_page": "https://github.com/scipion-em/scipion-em-fsc3d",
"name": "scipion-em-fsc3d",
"maintainer": "",
"docs_url": null,
"requires_python": "",
"maintainer_email": "",
"keywords": "scipion electron-microscopy cryo-em structural-biology image-processing scipion-3.0",
"author": "Grigory Sharov",
"author_email": "sharov.grigory@gmail.com",
"download_url": "https://files.pythonhosted.org/packages/52/45/22d9cef135e7479a2de7c2f20e8f978524d64d7db7591e52d5d61c550969/scipion-em-fsc3d-3.2.1.tar.gz",
"platform": null,
"description": "============\nFSC3D plugin\n============\n\nThis plugin provides a wrapper for `3DFSC <https://github.com/nysbc/Anisotropy/>`_ program developed at Salk Institute and NYSBC.\n\n.. image:: https://img.shields.io/pypi/v/scipion-em-fsc3d.svg\n :target: https://pypi.python.org/pypi/scipion-em-fsc3d\n :alt: PyPI release\n\n.. image:: https://img.shields.io/pypi/l/scipion-em-fsc3d.svg\n :target: https://pypi.python.org/pypi/scipion-em-fsc3d\n :alt: License\n\n.. image:: https://img.shields.io/pypi/pyversions/scipion-em-fsc3d.svg\n :target: https://pypi.python.org/pypi/scipion-em-fsc3d\n :alt: Supported Python versions\n\n.. image:: https://img.shields.io/sonar/quality_gate/scipion-em_scipion-em-fsc3d?server=https%3A%2F%2Fsonarcloud.io\n :target: https://sonarcloud.io/dashboard?id=scipion-em_scipion-em-fsc3d\n :alt: SonarCloud quality gate\n\n.. image:: https://img.shields.io/pypi/dm/scipion-em-fsc3d\n :target: https://pypi.python.org/pypi/scipion-em-fsc3d\n :alt: Downloads\n\n\nInstallation\n-------------\n\nYou will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have two options:\n\na) Stable version\n\n.. code-block::\n\n scipion installp -p scipion-em-fsc3d\n\nb) Developer's version\n\n * download repository\n\n .. code-block::\n\n git clone -b devel https://github.com/scipion-em/scipion-em-fsc3d.git\n\n * install\n\n .. code-block::\n\n scipion installp -p /path/to/scipion-em-fsc3d --devel\n\nFSC3D software will be installed automatically with the plugin but you can also use an existing installation by providing *FSC3D_HOME* (see below).\n\n**Important:** you need to have conda (miniconda3 or anaconda3) pre-installed to use this program.\n\nConfiguration variables\n-----------------------\n*CONDA_ACTIVATION_CMD*: If undefined, it will rely on conda command being in the\nPATH (not recommended), which can lead to execution problems mixing scipion\npython with conda ones. One example of this could can be seen bellow but\ndepending on your conda version and shell you will need something different:\nCONDA_ACTIVATION_CMD = eval \"$(/extra/miniconda3/bin/conda shell.bash hook)\"\n\n*FSC3D_HOME* (default = software/em/fsc3D-3.0):\nPath where the 3DFSC is installed.\n\n*FSC3D_ENV_ACTIVATION* (default = conda activate fsc3D-3.0):\nCommand to activate the 3DFSC environment.\n\n\nVerifying\n---------\nTo check the installation, simply run the following Scipion test:\n\n``scipion test fsc3d.tests.test_protocols_3dfsc.Test3DFSC``\n\nSupported versions\n------------------\n\n3.0 (modified for Scipion, see https://github.com/azazellochg/fsc3D)\n\nProtocols\n----------\n\n* resolution estimation\n\nReferences\n-----------\n\n1. Yong Zi Tan, Philip R Baldwin, Joseph H Davis, James R Williamson, Clinton S Potter, Bridget Carragher & Dmitry Lyumkis. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nature Methods volume 14, pages 793\u2013796 (2017).\n\n\n",
"bugtrack_url": null,
"license": "",
"summary": "Plugin to use 3DFSC within the Scipion framework",
"version": "3.2.1",
"project_urls": {
"Bug Reports": "https://github.com/scipion-em/scipion-em-fsc3d/issues",
"Homepage": "https://github.com/scipion-em/scipion-em-fsc3d",
"Source": "https://github.com/scipion-em/scipion-em-fsc3d/"
},
"split_keywords": [
"scipion",
"electron-microscopy",
"cryo-em",
"structural-biology",
"image-processing",
"scipion-3.0"
],
"urls": [
{
"comment_text": "scipion-3.0",
"digests": {
"blake2b_256": "1a54c77e9e4b3d1b2ca4d480a07cd8439a6cac18c3fcfa6783973b0c71e501fc",
"md5": "34c064bfacc0821fdf542d5258db8286",
"sha256": "61b3d159689e579a16adffe5b3b961a988b2b86c54a202921f8c1dbc26b5c097"
},
"downloads": -1,
"filename": "scipion_em_fsc3d-3.2.1-py3-none-any.whl",
"has_sig": false,
"md5_digest": "34c064bfacc0821fdf542d5258db8286",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": null,
"size": 58882,
"upload_time": "2023-11-19T13:43:45",
"upload_time_iso_8601": "2023-11-19T13:43:45.765258Z",
"url": "https://files.pythonhosted.org/packages/1a/54/c77e9e4b3d1b2ca4d480a07cd8439a6cac18c3fcfa6783973b0c71e501fc/scipion_em_fsc3d-3.2.1-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "scipion-3.0",
"digests": {
"blake2b_256": "524522d9cef135e7479a2de7c2f20e8f978524d64d7db7591e52d5d61c550969",
"md5": "e01b89b763da213fc367e1a5074237f9",
"sha256": "cc52e2c8479a4f1aae8d4f7ec600a88f8ab6ff723d4c3cefd50aa10b88f5a35e"
},
"downloads": -1,
"filename": "scipion-em-fsc3d-3.2.1.tar.gz",
"has_sig": false,
"md5_digest": "e01b89b763da213fc367e1a5074237f9",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 60708,
"upload_time": "2023-11-19T13:43:47",
"upload_time_iso_8601": "2023-11-19T13:43:47.783638Z",
"url": "https://files.pythonhosted.org/packages/52/45/22d9cef135e7479a2de7c2f20e8f978524d64d7db7591e52d5d61c550969/scipion-em-fsc3d-3.2.1.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-11-19 13:43:47",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "scipion-em",
"github_project": "scipion-em-fsc3d",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"lcname": "scipion-em-fsc3d"
}
JSON
