===================
CCP4 scipion plugin
===================
This plugin allows to use CCP4 programs within the Scipion framework. **You need to install the CCP4 suite before installing the plugin**, see section "Binary Files" for details.
CCP4, from Collaborative Computational Project Number 4, is a software suite that allows model building of macromolecule structures obtained by X-ray crystallography, and that has been extended to other techniques like cryo-EM (see `CCP4 home page <http://www.ccp4.ac.uk/>`_ for details).
Programs from CCP4 included in the Scipion framework for model building:
* coot
* refmac
===================
Install this plugin
===================
You will need to use `3.0.0 <https://github.com/I2PC/scipion/releases/tag/v3.0>`_ version of Scipion (o latter) to run these protocols. To install the plugin, you have two options:
- **Stable version**
.. code-block::
scipion installp -p scipion-em-ccp4
OR
- 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-ccp4.git
2. Install:
.. code-block::
scipion installp -p path_to_scipion-em-ccp4 --devel
- **Binary files**
CCP4 binaries will *NOT* be installed automatically with the plugin. The independent installation of CCP4 software suite by the user is required before running the programs. Default installation path assumed is */usr/local/ccp4-7.0*; this path or any other of your preference has to be set in *CCP4_HOME* in *scipion.conf*. We recommend to install CCP4 version 7.0.056 or higher. (see http://www.ccp4.ac.uk/download/#os=linux)
- **Tests**
Tested with CCP4 versions: 7.0.056 and 7.0.066.
To check the installation, simply run the following Scipion test:
* scipion test ccp4.tests.test_protocol_coot_refmac
- **Supported versions of CCP4**
7.0.056 or higher.
- **Additional Instruction**
see https://github.com/scipion-em/scipion-em-ccp4/wiki
=========
Protocols
=========
* coot refinement: Molecular interactive graphics application used for flexible fitting, refinement, model completion, and validation of structures of macromolecules regarding electron density maps. See the `details <https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/>`_ of *Coot* utilities.
* refmac: Automatic refinement program in Fourier space of macromolecule structures regarding electron density maps. See ` <http://www.ccp4.ac.uk/html/refmac5/description.html>`_ of *Refmac* utilities.
========
Examples
========
See `Model Building Tutorial <https://scipion-em.github.io/docs/release-3.0.0/docs/user/user-documentation.html#model-building>`_
===============
Buildbot status
===============
Status devel version:
.. image:: http://scipion-test.cnb.csic.es:9980/badges/ccp4_devel.svg
Status production version:
.. image:: http://scipion-test.cnb.csic.es:9980/badges/ccp4_prod.svg
Version in Pypi
.. image:: https://img.shields.io/pypi/v/scipion-em-ccp4.svg
:target: https://pypi.python.org/pypi/scipion-em-ccp4
:alt: PyPI release
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"description": "===================\nCCP4 scipion plugin\n===================\n\nThis plugin allows to use CCP4 programs within the Scipion framework. **You need to install the CCP4 suite before installing the plugin**, see section \"Binary Files\" for details.\n\nCCP4, from Collaborative Computational Project Number 4, is a software suite that allows model building of macromolecule structures obtained by X-ray crystallography, and that has been extended to other techniques like cryo-EM (see `CCP4 home page <http://www.ccp4.ac.uk/>`_ for details).\n\nPrograms from CCP4 included in the Scipion framework for model building:\n\n * coot\n * refmac\n\n===================\nInstall this plugin\n===================\n\nYou will need to use `3.0.0 <https://github.com/I2PC/scipion/releases/tag/v3.0>`_ version of Scipion (o latter) to run these protocols. To install the plugin, you have two options:\n\n- **Stable version** \n\n.. code-block:: \n\n scipion installp -p scipion-em-ccp4\n\nOR\n\n - 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-ccp4.git\n\n2. Install:\n\n.. code-block::\n\n scipion installp -p path_to_scipion-em-ccp4 --devel\n\n\n\n- **Binary files** \n\nCCP4 binaries will *NOT* be installed automatically with the plugin. The independent installation of CCP4 software suite by the user is required before running the programs. Default installation path assumed is */usr/local/ccp4-7.0*; this path or any other of your preference has to be set in *CCP4_HOME* in *scipion.conf*. We recommend to install CCP4 version 7.0.056 or higher. (see http://www.ccp4.ac.uk/download/#os=linux)\n\n\n\n- **Tests**\n\nTested with CCP4 versions: 7.0.056 and 7.0.066.\n\nTo check the installation, simply run the following Scipion test: \n\n* scipion test ccp4.tests.test_protocol_coot_refmac\n\n\n\n- **Supported versions of CCP4**\n\n7.0.056 or higher.\n\n- **Additional Instruction**\n\nsee https://github.com/scipion-em/scipion-em-ccp4/wiki\n\n=========\nProtocols\n=========\n\n* coot refinement: Molecular interactive graphics application used for flexible fitting, refinement, model completion, and validation of structures of macromolecules regarding electron density maps. See the `details <https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/>`_ of *Coot* utilities. \n* refmac: Automatic refinement program in Fourier space of macromolecule structures regarding electron density maps. See ` <http://www.ccp4.ac.uk/html/refmac5/description.html>`_ of *Refmac* utilities.\n\n\n\n========\nExamples\n========\n\nSee `Model Building Tutorial <https://scipion-em.github.io/docs/release-3.0.0/docs/user/user-documentation.html#model-building>`_\n\n\n\n===============\nBuildbot status\n===============\n\nStatus devel version: \n\n.. image:: http://scipion-test.cnb.csic.es:9980/badges/ccp4_devel.svg\n\nStatus production version: \n\n.. image:: http://scipion-test.cnb.csic.es:9980/badges/ccp4_prod.svg\n\nVersion in Pypi\n\n.. image:: https://img.shields.io/pypi/v/scipion-em-ccp4.svg\n :target: https://pypi.python.org/pypi/scipion-em-ccp4\n :alt: PyPI release\n\n\n",
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