Supported Applications

CCP4

Description

(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: https://www.ccp4.ac.uk/?page_id=657.

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 at https://www.ccp4.ac.uk/?page_id=878.
Tales

Unstructured

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. …
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Stop, Collaborate and Listen

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 …
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Webinars

Topic: CCP4 Cloud in a nutshell and automated structure solution

Presenter: Eugene Krissinel, Ph.D., Science and Technology Facilities Council

Host: Jason Key
Recorded on February 1, 2022

Topic: CCP4 Cloud advanced: interactive MR, EP and model building
Presenter: Eugene Krissinel, Ph.D., Science and Technology Facilities Council

Hosted by Jason Key
Recorded on Feb 8, 2022

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: 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.

Host: Piotr Sliz
Recorded on April 23, 2012

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

CCP4 website: http://www.ccp4.ac.uk