(Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries used for macromolecular structure determination by X-ray crystallography.
Usage Notes
All SBGrid members must complete the CCP4 license and return the executed document directly to The Science and Technology Facilities Council as specified on the CCP4 licensing page located here: http://legacy.ccp4.ac.uk/ccp4license.php.
Version 0.9 of coot contains a bug in hardware stereo display mode. To re-enable hardware stereo, run
echo "(set-display-lists-for-maps 0)" >> ~/.coot
Installation
Use the following command to install this title with the CLI client: $ sbgrid-cli install ccp4
Primary Citation*
M. D. Winn, C. C. Ballard, K. D. Cowtan, E. J. Dodson, P. Emsley, P. R. Evans, R. M. Keegan, E. B. Krissinel, A. G. Leslie, A. McCoy, S. J. McNicholas, G. N. Murshudov, N. S. Pannu, E. A. Potterton, H. R. Powell, R. J. Read, A. Vagin, and K. S. Wilson. 2011. Overview of the CCP4 suite and current developments. Acta crystallographica Section D: Biological crystallography. 67(4): 235-242.
*Full citation information available through
Citation Note
Any publication arising from use of the CCP4 software suite should include both references to the specific programs used (see subprograms) and the primary citation for the CCP4 suite. Additional citations can be found on the CCP4 website.
Sit down in front of a newly installed copy of CCP4 today, and you will
find approximately 250 computer programs for solving protein structures.
The list of programs includes several with catchy names, such as beast (for
molecular replacement), dimple (for ligand identification in difference
maps), crank (for experimental phasing) and buccaneer (for model building),
and some cryptic, such as seqwt and npo. Nearly two dozen applications
support file manipulations and format conversions. Still more are
riders-on, either deprecated or unsupported.
The seeming mishmash is so by design. "CCP4 has always been a very loose
collaboration," says Phil Evans, a structural biologist at the Medical
Research Council Laboratory of Molecular Biology in Cambridge, UK, and one
of the earliest members of the team that created CCP4 in 1979. …
Back in the mid-1970s, the British government funded several collaborative
computing projects. Among them (14 in all) was Collaborative Computing
Project 4, known by structural biologists as CCP4. "The idea was that
computers were so expensive, you'd probably only have one in London and
maybe one in Manchester, so everybody would have to collaborate on using
the hardware and developing software," says Eleanor Dodson, Professor
Emeritus at the York Structural Biology Laboratory and a contributor to
CCP4 from the beginning.
By then, Dodson had already been involved in structural biology for over a
decade. With just a bachelor's degree, she began working in the lab of
protein crystallography pioneer and Nobel Laureate Dorothy Hodgkin, who
solved structures for penicillin, Vitamin B12 and insulin. "Dorothy needed
a technician …
Topic: PanDDA: extracting ligand-bound protein states from conventionally uninterpretable crystallographic electron density
Presenter: Nicholas Pearce, Postdoctoral Researcher, Utrecht University, The Netherlands
Recorded on: December 4th, 2018 Host: Jason Key
Topic: AMPLE: a pipeline for unconventional Molecular Replacement Presenter: Daniel Rigden, Ph.D., Reader in Post-Genome Bioinformatics, University of Liverpool, UK
Host: Jason Key Recorded on April 26, 2016
Topic: Automated macromolecular structure solution from SAD and MR-SAD experiments with Crank2 Presenter: Navraj Pannu, Assistant Professor Leiden University, The Netherlands
Host: Jason Key Recorded on March 8, 2016
Topic: Assembling data from multiple crystals with BLEND Presenter: James Foadi, Postdoctoral Research Associate, Diamond Synchrotron, Oxfordshire
Host: Jason Key Recorded on February 9th, 2016
Presenter: Phil Evans, MRC Laboratory of Molecular Biology Topic: MOSFLM and FRIENDS: Data Processing in the CCP4 Suite
SBGrid/NE-CAT 2014: Data Processing in Crystallography June 5-6, 2014
Topic: What's new in CCP4 6.3.0 Presenter: Ronan Keegan, Ph.D., Senior Computation Scientist, CCP4 group, STFC Rutherford Appleton Laboratory
SBGrid Host: Piotr Sliz Recorded on November 1, 2012
Topic: Extending the reach of molecular replacement in Phaser Presenter: Randy Read, Wellcome Trust Principal Research Fellow in the Department of Haematology at University of Cambridge.
