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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 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 Ext ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 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 (physics), 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 the square ... [...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 Resolution (electron density), 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 plot, 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 hav ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 scientific data (e.g. geographic information systems (GIS)). Voxels also have technical and artistic applications in video games, largely originating with surface rendering in ''Outcast (video game), Outcast'' (1999). ''Minecraft'' (2011) makes use of an entirely voxelated world to allow for a fully destructable and constructable environment. Voxel art, of the sort used in ''Minecraft'' and elsewhere, is a style and format of 3D art analogous to pixel art. 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 (computer graphics), rendering systems infer the position of a voxel based upon its position relative to other voxels (i.e., its pos ... [...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, now succeeded by the Macromolecular Crystallographic Information File, mmCIF format. 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 has kept data on biological macromolecules in the newer Macromolecular Crystallographic Information File, PDBx/mmCIF file format since 2014. History The PDB file format was invented in 1972 as a human-readable file that would allow researchers to exchange the atomic coordinates in a given protein through a database system. Its fixed-column width format is limited to 80 or 140 columns, which was based on the width of the computer punch ... [...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 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 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] |
EZD (file Format)
EZD can refer to: * Philippines AirAsia, a low-cost airline from the Philippines, by ICAO code * AirAsia Zest, a now-defunct low-cost airline from the Philippines that merged into Philippines AirAsia in 2015, by ICAO code * Zduńska Wola County __NOTOC__ Zduńska Wola County () is a unit of territorial administration and local government (powiat) in Łódź Voivodeship, central Poland. It came into being on January 1, 1999, as a result of the Polish local government reforms passed in 1998 ..., a county in central Poland, by car plate code * EZ-D, prototype name of Flexplay, a disposable home video format {{disambiguation ... [...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 t ... References External links MRC specification Computational chemistry Structural biology Computer file formats {{Bioph ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MTZ (file Format)
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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, 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 *Martinez station, an Amtrak station stop in Martinez, California Martinez (Spanish language, Spanish: ''Martínez'') is a city in and the county seat of Contra Costa County, California, United States, in the East Bay region of the San Francisco Bay Area. Located on the southern shore of the Carquinez Strai ... [...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 macOS, previously OS&nb ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bsoft
Bsoft is a collection of programs and a platform for development of software for image and molecular processing in structural biology.{{Cite journal , last1=Heymann , first1=J. Bernard , last2=Belnap , first2=David M. , date=2007-01-01 , title=Bsoft: Image processing and molecular modeling for electron microscopy , url=https://www.sciencedirect.com/science/article/abs/pii/S1047847706001997 , journal=Journal of Structural Biology , series=Software tools for macromolecular microscopy , volume=157 , issue=1 , pages=3–18 , doi=10.1016/j.jsb.2006.06.006 , pmid=17011211 , issn=1047-8477, url-access=subscription 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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 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 (BBSRC). The project is coordinated at Daresbury Laboratory, CCLRC Daresbury Laboratory. The results of this effort gave rise to the CCP4 program suite,M.D. Winn, C.C. Ballard, K.D. Cowtan, E.J. Dodson, P. Emsley, P.R. Evans, R.M. Keegan, E.B. Krissinel, A.G.W. Leslie, A. McCoy, S.J. McNicholas, G.N. Murshudov, N.S. Pannu, E.A. Potterton, H.R. Powell, R.J. Read, A. Vagin, K.S. W ... [...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). Chimera is no longer actively developed and is superseded by 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 cent ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
