ccp4

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 and Fortran 77.
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.