CCP4 (The Collaborative Computational Project Number 4 in Protein Crystallography) is a suite of separate programs which communicate via standard data files, rather than all operations being integrated into one huge program. The programs range from coordinate file manipulations and dataset management to sequence alignment and structure validation.
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.
How to Use
There are multiple versions of CCP4 available. An easy way of selecting the version is to use modules. To see the modules available, typemodule avail CCP4
To select a module, typemodule load CCP4/[ver]
where [ver] is the version of choice. This will set a large number of environment variables, including $PATH, $LD_LIBRARY_PATH, and $MANPATH.
Then invoke the program using the appropriate options.
This example aligns 3ESZ onto 3F6R, based on the superposition of the A chains from both PDB entries.[helix]$ zcat /pdb/pdb/es/pdb3esz.ent.gz > 3esz.pdb [helix]$ zcat /pdb/pdb/f6/pdb3f6r.ent.gz > 3f6r.pdb [helix]$ superpose 3esz.pdb -s "A" 3f6r.pdb -s "A" 3esz_ON_3f6r.pdb
CCP4 also includes an interactive graphical interface. This application requires an X-Windows connection. First source the correct setup file (see above), then type 'ccp4i' at the prompt.