scipion-em-ccp4 3.1.1 on PyPI

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 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 version of Scipion (o latter) to run these protocols. To install the plugin, you have two options:

Stable version

scipion installp -p scipion-em-ccp4

through the plugin manager GUI by launching Scipion and following Configuration >> Plugins

Developer's version

Download repository:

git clone https://github.com/scipion-em/scipion-em-ccp4.git

Install:

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 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.