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CCP4 (file Format)
The CCP4 file format is file generated by the Collaborative Computational Project Number 4 in 1979. The file format for electron density has become industry standard in X-ray crystallography and Cryo-electron microscopy where the result of the technique is a three-dimensional grid of voxels each with a value corresponding to density of electrons (see wave function) The CCP4 format is supported by almost every molecular graphics suite that supports volumetric data. The major packages include: *Visual molecular dynamics *PyMOL *UCSF Chimera *Bsoft *Coot *MOE See also *MTZ (file format) *MRC (file format) * EZD (file format) *Chemical file format **Protein Data Bank (file format) *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 Externa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 variables and is typically denoted as either \rho(\textbf r) or n(\textbf r). The density is determined, through definition, by the normalised N-electron wavefunction which itself depends upon 4N variables (3N spatial and N spin coordinates). Conversely, the density determines the wave function modulo up to a phase factor, providing the formal foundation of density functional theory. According to quantum mechanics, due to the uncertainty principle on an atomic scale the exact location of an electron cannot be predicted, only the probability of its being at a given position; therefore electrons in atoms and molecules act as if they are "smeared out" in space. For one-electron systems, the electron density at any point is proportional to th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Coot (program)
The program Coot (Crystallographic Object-Oriented Toolkit) is used to display and manipulate atomic models of macromolecules, typically of proteins or nucleic acids, using 3D computer graphics. It is primarily focused on building and validation of atomic models into three-dimensional electron density maps obtained by X-ray crystallography methods, although it has also been applied to data from electron microscopy. Overview Coot displays electron density maps and atomic models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, and Ramachandran idealization. The software is designed to be easy-to-learn for novice users, achieved by ensuring that tools for common tasks are 'discoverable' through familiar user interface elements (menus and toolbars), or by intuitive behaviour (mouse controls). Recent developments have enhanced the usability of the software for expe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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. Instead, rendering systems infer the position of a voxel based upon its position relative to other voxels (i.e., its position in the data structure that makes up a single volumetric image). In contrast to pixels and voxels, polygons are often explicitly represented by the coordinates of their vertices (as points). A direct consequence of this difference is that polygons can efficiently represent simple 3D structures with much empty or homogeneously filled space, while voxels excel at representing regularly sampled spaces that are non-homogeneously filled. Voxels are frequently used in the visualization and analysis of medical and scientific data (e.g. geographic information systems (GIS)). Some volumetric displays use voxels to describe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 structures including atomic coordinates, secondary structure assignments, as well as atomic connectivity. In addition experimental metadata are stored. The PDB format is the legacy file format for the Protein Data Bank which now keeps data on biological macromolecules in the newer mmCIF file format. History The PDB file format was invented in 1976 as a human-readable file that would allow researchers to exchange protein coordinates through a database system. Its fixed-column width format is limited to 80 columns, which was based on the width of the computer punch cards that were previously used to exchange the coordinates.Berman, Helen M. "The protein data bank: a historical perspective." Acta Crystallographica Section A 64.1 (2007): 88-9 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 that represent multiple chemical structure records and associated data fields. The XYZ file format is a simple format that usually gives the number of atoms in the first line, a comment on the second, followed by a number of lines with atomic symbols (or atomic numbers) and cartesian coordinates. The Protein Data Bank Format is commonly used for proteins but is also used for other types of molecules. There are many other types which are detailed below. Various software systems are available to convert from one format to another. Distinguishing formats Chemical information is usually provided as files or streams and many formats have been created, with varying degrees of documentation. The format is indicated in three ways:(see ) * ''f ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 density or electric potential. It was developed by the MRC ( Medical Research Council, UK) Laboratory of Molecular Biology. In 2014, the format was standardised. The format specification is available on thCCP-EM website The MRC format is supported by many of the software packages listed in b:Software Tools For Molecular Microscopy. See also *CCP4 (file format) The CCP4 file format is file generated by the Collaborative Computational Project Number 4 in 1979. The file format for electron density has become industry standard in X-ray crystallography and Cryo-electron microscopy where the result of the ... References External links MRC specification Computational chemistry Structural biology Computer file formats {{Biophy ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MTZ (file Format) , a black hole solution for (3+1)-dimensional gravity with a minimally coupled self-interacting scalar field, named after Cristian Martinez, Ricardo Troncoso and Jorge Zanelli
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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 See also *MTZ-RIPO, Belarusian football club established in 2002, later renamed Partizan-MTZ Minsk and nw now renamed FC Partizan Minsk *MTZ black hole The MTZ black hole, named after Cristian Martinez, Ricardo Troncoso and Jorge Zanelli, is a black hole solution for (3+1)-dimensional gravity with a minimally coupled self-interacting scalar field. The event horizon is a surface of constant negativ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chemical Computing Group
Chemical Computing Group is a software company specializing in research software for computational chemistry, bioinformatics, cheminformatics, docking, pharmacophore searching and molecular simulation. The company's main customer base consists of pharmaceutical and biotechnology companies, as well as academic research groups. It is a private company that was founded in 1994; it is based in Montreal, Quebec, Canada. Its main product, Molecular Operating Environment (MOE), is written in a self-contained programming system, the Scientific Vector Language (SVL). Products * MOE (Molecular Operating Environment) MOE is a drug discovery software platform that integrates visualization, modeling, and simulations, as well as methodology development. MOE scientific applications are used by biologists, medicinal chemists and computational chemists in pharmaceutical, biotechnology and academic research. MOE runs on Windows, Linux, Unix, and MAC OS X. Main application areas: Structur ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 modular design, allowing fast development of new algorithms without the burden of issues such as file I/O. It provides an easily accessible interface, a resource that can be and has been used in other packages. Several workflows such as for single particle analysis and tomography are supported with parameter exchange as well as the ability to do distributed processing across heterogeneous clusters of computers. Technical details Version: 1.8.8 OS support: Unix (Mac OS X, IRIX, Linux, AIX, Solaris, Tru64), OpenVMS Format support: * Images: BioRad, Brix, CCP4, Digital Instruments, Digital Micrograph, DSN6, EM, Goodford, GRD, Imagic, JPEG, MFF, Image Magick, MRC, PIC, PIF, PNG, Spider, Suprim, TIFF, RAW * Micrograph parameters: STAR (Bsoft ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 software for structural biology. The CCP4 core team is located at the Research Complex at Harwell (RCaH) at Rutherford Appleton Laboratory (RAL) in Didcot, near Oxford, UK. CCP4 was originally supported by the UK Science and Engineering Research Council (SERC), and is now supported by the Biotechnology and Biological Sciences Research Council Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation, is a non-departmental public body (NDPB), and is the largest UK public funder of non-medical bioscience. It predominantly funds scientific rese ... (BBSRC). The project is coordinated at CCLRC Daresbury Laboratory. The results of this effort gave rise to the CCP4 program suite,M.D. Winn, C.C. Balla ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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, and conformational ensembles. High-quality images and movies can be created. Chimera includes complete documentation and can be downloaded free of charge for noncommercial use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics (RBVI) at the University of California, San Francisco. Development is partially supported by the National Institutes of Health (NIGMS grant P41-GM103311). The next-generation program is UCSF ChimeraX. General structure analysis * automatic identification of atom * hydrogen addition and partial charge assignment * high-quality hydrogen bond, contact, and clash detection * measurements: distances, angles, surface area, volume * calculation of centroids, axes, planes and associate ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
