The CCP4 file format is file generated by the
Collaborative Computational Project Number 4
The Collaborative Computational Project Number 4 in protein crystallography (CCP4) was set up in 1979 in the United Kingdom to support collaboration between researchers working in software development and assemble a comprehensive collection of so ...
in 1979. The file format for
electron density
In quantum chemistry, 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 va ...
has become industry standard in
X-ray crystallography
X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles ...
and
Cryo-electron microscopy
Cryogenic electron microscopy (cryo-EM) is a cryomicroscopy technique applied on samples cooled to cryogenic temperatures. For biological specimens, the structure is preserved by embedding in an environment of vitreous ice. An aqueous sample sol ...
where the result of the technique is a three-dimensional grid of
voxel
In 3D computer graphics, a voxel represents a value on a regular grid in three-dimensional space. As with pixels in a 2D bitmap, voxels themselves do not typically have their position (i.e. coordinates) explicitly encoded with their values. Ins ...
s each with a value corresponding to density of electrons (see
wave function
A wave function in quantum physics is a mathematical description of the quantum state of an isolated quantum system. The wave function is a complex-valued probability amplitude, and the probabilities for the possible results of measurements mad ...
) The CCP4 format is supported by almost every molecular graphics suite that supports volumetric data. The major packages include:
*
Visual molecular dynamics
Visual Molecular Dynamics (VMD) is a molecular modelling and visualization computer program. VMD is developed mainly as a tool to view and analyze the results of molecular dynamics simulations. It also includes tools for working with volumetric d ...
*
PyMOL
PyMOL is an open source but proprietary 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 ...
*
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, a ...
*
Bsoft {{Short description, Structural biology software
Bsoft is a collection of programs and a platform for development of software for image and molecular processing in structural biology. Problems in structural biology are approached with a highly modul ...
*
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 usually ...
*
MOE
Moe, MOE, MoE or m.o.e. may refer to:
In arts and entertainment Characters
* Moe Szyslak, from the animated television show ''The Simpsons''
* Moe, leader of The Three Stooges, played by Moe Howard
* Moe Higurashi, supporting character in ''Yash ...
See also
*
MTZ (file format) MTZ may refer to
*Manuel Turizo Zapata, Colombian singer also known as MTZ
* Minsk Tractor Works, or Minski Traktarny Zavod (MTZ / МТЗ)
*Mantle transition zone
The transition zone is part of the Earth's mantle, and is located between the lowe ...
*
MRC (file format)
MRC is a file format that has become an industry standard in cryo-electron microscopy (cryoEM) and electron tomography (ET), where the result of the technique is a three-dimensional grid of voxels each with a value corresponding to electron densi ...
*
EZD (file format)
*
Chemical file format
A chemical file format is a type of data file which is used specifically to 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. The PDB format accordingly provides for description and annotation of protein and nucleic acid ...
*
Voxel
In 3D computer graphics, a voxel represents a value on a regular grid in three-dimensional space. As with pixels in a 2D bitmap, voxels themselves do not typically have their position (i.e. coordinates) explicitly encoded with their values. Ins ...
- one way of presenting 3D densities
External links
Format technical details
Computational chemistry
Chemical file formats
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