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README.rst

CCP4 scipion plugin

This plugin allows to use CCP4 programs within the Scipion framework.

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 2.0.0 version of Scipion to run these protocols. To install the plugin, you have two options:

  • Stable version
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:
git clone https://github.com/scipion-em/scipion-em-ccp4.git
  1. 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.

  • 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 the details of Refmac utilities.

Examples

See Model Building Tutorial

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