CCP4 exists to produce and support a world-leading, integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques. CCP4 aims to develop and support the development of cutting edge approaches to experimental determination and analysis of protein structure, and integrate these approaches into the suite. CCP4 is a community based resource that supports the widest possible researcher community, embracing academic, not for profit, and for profit research. CCP4 aims to play a key role in the education and training of scientists in experimental structural biology. It encourages the wide dissemination of new ideas, techniques and practice.
Referencing CCP4 and individual programs
Any publication arising from use of the CCP4 software suite should include both references to the specific programs used (see the References section of the distributed documentation) and the following reference to the CCP4 suite:
M. D. Winn et al. Acta. Cryst. D67 , 235-242 (2011)
– “Overview of the CCP4 suite and current developments” [doi:10.1107/S0907444910045749]
reprint in PDF format Copyright © International Union of Crystallography
Such citations are vital to the CCP4 project, and individual program authors, in maintaining funding and thus being able to develop CCP4 further.
Many relevant articles can be found in the proceedings of the 2010 Study Weekend, published as a special issue of Acta Cryst D.
Philosophy of the CCP4 suite
Unlike many other packages, particularly for small molecule crystallography, the CCP4 suite is a set of separate programs which communicate via standard data files, rather than all operations being integrated into one huge program. This has some disadvantages in that it is less easy for programs to make decisions about what operation to do next – though it is seldom a problem in practice – and that the programs are less consistent with each other (although much work has been done to improve this). However the great advantage arising from such loose organisation is that it is very easy to add new programs or to modify existing ones without upsetting other parts of the suite. Converting a program to use the standard CCP4 file formats is generally straightforward, and the philosophy of the collection has been to be inclusive, so that several programs may be available to do the same task. The components of the whole system are thus a collection of programs using a standard software library to access standard format files (and a set of examples files and documentation) available for most operating systems (including Linux, Windows and Mac OS X). Programs are mostly written in C, C++, Fortran and Python.
To use the programs the user must assign input and output files, and run the programs. Often an output file becomes the input to the next step, and system parameter substitution may be used to create filenames in a systematic way. Most crystallographic calculations involve a series of steps in which no decisions need be made until the end, and a command file provides an easy way of chaining calculations.
Standard file formats are defined for the principal data types used in crystallography: reflection data; density maps; and atom coordinates. In defining these formats, a number of trade-offs are made between efficiency (in space and access time), flexibility, portability, and simplicity of use.
There is a policy of continual technical and scientific updates to the suite. Where existing programs have been incorporated into the suite they have often subsequently undergone considerable modification above that needed to use the CCP4 file formats.
Bug reports and/or problems running the programs should be sent to firstname.lastname@example.org. We will endeavour to
help where we can (but note that no warranty for the software is given or implied). But remember that we are not psychic and cannot solve problems without the necessary information (so send input script, entire log file and relevant data files).
Individual program documentation is available, together with a PostScript version of the CCP4 manual with content distinct from the program documentation (about 1.5 MB). The corresponding files are distributed with the suite.
Tutorials, examples and test data sets
A set of tutorials is distributed with the program suite, see the examples/tutorial subdirectory. There are also a large number of individual examples, see the examples/unix/runnable subdirectory. The tutorials and examples use distributed test data.
Email distribution lists
CCP4 organises and/or sponsors several meetings a year, see the Courses page. The most important of these is the two-day Study Weekend held each year on a chosen subject, just after the New Year. Back copies of the proceedings to these meetings are available.