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-ccp4OR
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.gitInstall:
scipion installp -p path_to_scipion-em-ccp4 --develBinary 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
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.
Examples
Buildbot status
Status devel version:
Status production version:
Version in Pypi
1 maintainer
Metadata
1 maintainer
Release files for scipion-em-ccp4 3.2.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| scipion-em-ccp4-3.2.0.tar.gz | 46.8 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| scipion_em_ccp4-3.2.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 107.3 kB
Release files / scipion-em-ccp4-3.2.0.tar.gz
| Download URL | scipion-em-ccp4-3.2.0.tar.gz |
|---|---|
| Size | 46.8 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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|
|
BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.8.17
|
Release files / scipion_em_ccp4-3.2.0-py3-none-any.whl
| Download URL | scipion_em_ccp4-3.2.0-py3-none-any.whl |
|---|---|
| Size | 60.5 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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|
|
BLAKE2b-256 checksum How to use checksums |
6ef166153f89a8dc754f881cf256f4b89cc80788620078320b897ca043beb054
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.8.17
|
