The CCP4 file format is file generated by the
Collaborative Computational Project Number 4
The Collaborative Computational Project Number 4 in protein crystallography, Protein Crystallography (CCP4) was set up in 1979 in the United Kingdom to support collaboration between researchers working in software development and assemble a compr ...
in 1979. The file format for
electron density
Electron density or electronic density is the measure of the probability of an electron being present at an infinitesimal element of space surrounding any given point. It is a scalar quantity depending upon three spatial variables and is typical ...
has become industry standard in
X-ray crystallography
X-ray crystallography is the experimental science of determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to Diffraction, diffract in specific directions. By measuring th ...
and
Cryo-electron microscopy
Cryogenic electron microscopy (cryo-EM) is a transmission electron microscopy technique applied to samples cooled to cryogenic temperatures. For biological specimens, the structure is preserved by embedding in an environment of vitreous ice. An ...
where the result of the technique is a three-dimensional grid of
voxel
In computing, a voxel is a representation of a value on a three-dimensional regular grid, akin to the two-dimensional pixel. Voxels are frequently used in the Data visualization, visualization and analysis of medical imaging, medical and scient ...
s each with a value corresponding to density of electrons (see
wave function
In quantum physics, a wave function (or wavefunction) is a mathematical description of the quantum state of an isolated quantum system. The most common symbols for a wave function are the Greek letters and (lower-case and capital psi (letter) ...
) The CCP4 format is supported by almost every molecular graphics suite that supports volumetric data. The major packages include:
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Visual molecular dynamics
Visual Molecular Dynamics (VMD) is a molecular modelling and Visualization (computer graphics), visualization computer program. VMD is developed mainly as a tool to view and analyze the results of molecular dynamics simulations. It also includes ...
*
PyMOL
PyMOL is a source-available molecular visualization system created by Warren Lyford DeLano. It was commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universall ...
*
UCSF Chimera
UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories ...
*
Bsoft
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Coot
Coots are medium-sized water birds that are members of the rail family, Rallidae. They constitute the genus ''Fulica'', the name being the Latin term for "coot". Coots have predominantly black plumage, and—unlike many rails—they are usual ...
*
MOE
See also
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MTZ (file format)
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MRC (file format)
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EZD (file format)
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Chemical file format
A chemical file format is a type of data file which is used specifically for depicting molecular data. One of the most widely used is the chemical table file format, which is similar to ''Structure Data Format'' (SDF) files. They are text files ...
**
Protein Data Bank (file format)
The Protein Data Bank (PDB) file format is a textual file format describing the three-dimensional structures of molecules held in the Protein Data Bank, now succeeded by the Macromolecular Crystallographic Information File, mmCIF format. The PDB f ...
*
Voxel
In computing, a voxel is a representation of a value on a three-dimensional regular grid, akin to the two-dimensional pixel. Voxels are frequently used in the Data visualization, visualization and analysis of medical imaging, medical and scient ...
- one way of presenting 3D densities
External links
Format technical details
Computational chemistry
Chemical file formats
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