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Molekel
Molekel is a free software multiplatform molecular visualization program. It was originally developed at the University of Geneva by Peter F. Flükiger in the 1990s for Silicon Graphics Computers. In 1998, Stefan Portmann took over responsibility and released Version 3.0. Version 4.0 was a nearly platform independent version. Further developments lead to version 4.3, before Stefan Portmann moved on and ceased to develop the codes. In 2006, the Swiss National Supercomputing Centre (CSCS) restarted the project and version 5.0 was released on 21 December 2006. Molekel uses and Qwt and therefore as well [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Orbital
In chemistry, a molecular orbital is a mathematical function describing the location and wave-like behavior of an electron in a molecule. This function can be used to calculate chemical and physical properties such as the probability of finding an electron in any specific region. The terms ''atomic orbital'' and ''molecular orbital'' were introduced by Robert S. Mulliken in 1932 to mean ''one-electron orbital wave functions''. At an elementary level, they are used to describe the ''region'' of space in which a function has a significant amplitude. In an isolated atom, the orbital electrons' location is determined by functions called atomic orbitals. When multiple atoms combine chemically into a molecule, the electrons' locations are determined by the molecule as a whole, so the atomic orbitals combine to form molecular orbitals. The electrons from the constituent atoms occupy the molecular orbitals. Mathematically, molecular orbitals are an approximate solution to the Schrödin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of Free And Open-source Software Packages
This is a list of free and open-source software packages, computer software licensed under free software licenses and open-source licenses. Software that fits the Free Software Definition may be more appropriately called free software; the GNU project in particular objects to their works being referred to as open-source. For more information about the philosophical background for open-source software, see free software movement and Open Source Initiative. However, nearly all software meeting the Free Software Definition also meets ''the Open Source Definition'' and vice versa. A small fraction of the software that meets either definition is listed here. Some of the open-source applications are also the basis of commercial products, shown in the List of commercial open-source applications and services. Artificial intelligence General AI *OpenCog – A project that aims to build an artificial general intelligence (AGI) Software framework, framework. OpenCog Prime is a specific ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of Molecular Graphics Systems
This is a list of notable software systems that are used for visualizing macromolecules. Key The tables below indicate which types of data can be visualized in each system: See also * Biological data visualization * Comparison of nucleic acid simulation software * Comparison of software for molecular mechanics modeling * List of microscopy visualization systems * List of open-source bioinformatics software * Molecular graphics * Molecule editor A molecule editor is a computer program for creating and modifying representations of chemical structures. Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or three-dimensional space, v ... References External links * A rather detailed, objective, and technical assessment of about 20 tools. * * * {{Chemistry software Chemistry software molecular graphics systems Molecular modelling ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Isosurface
An isosurface is a three-dimensional analog of an isoline. It is a surface that represents points of a constant value (e.g. pressure, temperature, velocity, density) within a volume of space; in other words, it is a level set of a continuous function whose domain is 3-space. The term ''isoline'' is also sometimes used for domains of more than 3 dimensions. Applications Isosurfaces are normally displayed using computer graphics, and are used as data visualization methods in computational fluid dynamics (CFD), allowing engineers to study features of a fluid flow (gas or liquid) around objects, such as aircraft wings. An isosurface may represent an individual shock wave in supersonic flight, or several isosurfaces may be generated showing a sequence of pressure values in the air flowing around a wing. Isosurfaces tend to be a popular form of visualization for volume datasets since they can be rendered by a simple polygonal model, which can be drawn on the screen very quic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SAMSON
Samson (; , '' he, Šīmšōn, label= none'', "man of the sun") was the last of the judges of the ancient Israelites mentioned in the Book of Judges (chapters 13 to 16) and one of the last leaders who "judged" Israel before the institution of the monarchy. He is sometimes considered as an Israelite version of the popular Near Eastern folk hero also embodied by the Sumerian Enkidu and the Greek Heracles. The biblical account states that Samson was a Nazirite, and that he was given immense strength to aid him against his enemies and allow him to perform superhuman feats, including slaying a lion with his bare hands and massacring an entire army of Philistines using only the jawbone of a donkey. However, if Samson's long hair were cut, then his Nazirite vow would be violated and he would lose his strength. Samson is betrayed by his lover Delilah, who, sent by the Philistines officials to entice him, orders a servant to cut his hair while he is sleeping and turns him over to hi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of Software For Molecular Mechanics Modeling
This is a list of computer programs that are predominantly used for molecular mechanics calculations. See also *Car–Parrinello molecular dynamics *Comparison of force-field implementations *Comparison of nucleic acid simulation software *List of molecular graphics systems *List of protein structure prediction software *List of quantum chemistry and solid-state physics software *List of software for Monte Carlo molecular modeling *List of software for nanostructures modeling *Molecular design software *Molecular dynamics *Molecular modeling on GPUs *Molecule editor A molecule editor is a computer program for creating and modifying representations of chemical structures. Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or three-dimensional space, v ... Notes and references External linksSINCRIS [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Graphics
Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device". Ever since Dalton's atoms and Kekulé's benzene, there has been a rich history of hand-drawn atoms and molecules, and these representations have had an important influence on modern molecular graphics. Colour molecular graphics are often used on chemistry journal covers artistically. History Prior to the use of computer graphics in representing molecular structure, Robert Corey and Linus Pauling developed a system for representing atoms or groups of atoms from hard wood on a scale of 1 inch = 1 angstrom connected by a clamping device to maintain the molecular configuration. These early models also established the CPK coloring scheme that is still used today to differentiate the different types of atoms in molecular models (e.g. carbon = black, oxygen = red, nitrogen = blue ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molden
Molden is a general molecular and electronic structure processing program. Major features * Reads output from the ab initio packages GAMESS (US), Gaussian, MOLPRO, PySCF and from semi-empirical packages such as MOPAC, and supports a number of other formats. * Displays molecular orbitals or electron density as contour plots or 3D grid plots and output to a number of graphical formats. * Animates reaction paths and molecular vibrations. * A Z-matrix editor. Molden program has been tested on different platforms, namely Linux, Windows NT, Windows95, Windows2000, WindowsXP, MacOSX, Silicon Graphics IRIX, Sun SunOS and Solaris. Ambfor, the main force field module of Molden, is an external program that can be initialized from Molden. Ambfor admits protein force field Amber and GAFF (General Amber Force Field). Use of Ambfor is automatic when a protein is studied with Molden. The GAFF force field is used only small molecules. Both Amber and GAFF are based on atomic charges. The di ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gabedit
Gabedit is a graphical user interface to GAMESS (US), Gaussian, MOLCAS, MOLPRO, MPQC, OpenMopac, PC GAMESS, ORCA and Q-Chem computational chemistry packages. Major features * Builds molecules by atom, ring, group, amino acid and nucleoside. * Creates an input file for computational chemistry packages. * Reads output from the ab initio packages, and supports a number of other formats. * Displays molecular orbitals or electron density as contour plots or 3D grid plots and output to a number of graphical formats. * Animates molecular vibrations, contours, isosurfaces and rotation. See also * List of molecular graphics systems * PC GAMESS * ORCA * Quantum chemistry computer programs * SAMSON Samson (; , '' he, Šīmšōn, label= none'', "man of the sun") was the last of the judges of the ancient Israelites mentioned in the Book of Judges (chapters 13 to 16) and one of the last leaders who "judged" Israel before the institution o ... External links Gabedit official ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tagged Image File Format
Tag Image File Format, abbreviated TIFF or TIF, is an image file format for storing raster graphics images, popular among graphic artists, the publishing industry, and photographers. TIFF is widely supported by scanning, faxing, word processing, optical character recognition, image manipulation, desktop publishing, and page-layout applications. The format was created by the Aldus Corporation for use in desktop publishing. It published the latest version 6.0 in 1992, subsequently updated with an Adobe Systems copyright after the latter acquired Aldus in 1994. Several Aldus or Adobe technical notes have been published with minor extensions to the format, and several specifications have been based on TIFF 6.0, including TIFF/EP (ISO 12234-2), TIFF/IT (ISO 12639), TIFF-F (RFC 2306) and TIFF-FX (RFC 3949). History TIFF was created as an attempt to get desktop scanner vendors of the mid-1980s to agree on a common scanned image file format, in place of a multitude of proprietary for ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PostScript
PostScript (PS) is a page description language in the electronic publishing and desktop publishing realm. It is a dynamically typed, concatenative programming language. It was created at Adobe Systems by John Warnock, Charles Geschke, Doug Brotz, Ed Taft and Bill Paxton from 1982 to 1984. History The concepts of the PostScript language were seeded in 1976 by John Gaffney at Evans & Sutherland, a computer graphics company. At that time Gaffney and John Warnock were developing an interpreter for a large three-dimensional graphics database of New York Harbor. Concurrently, researchers at Xerox PARC had developed the first laser printer and had recognized the need for a standard means of defining page images. In 1975-76 Bob Sproull and William Newman developed the Press format, which was eventually used in the Xerox Star system to drive laser printers. But Press, a data format rather than a language, lacked flexibility, and PARC mounted the Interpress effort to create a succ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Van Der Waals Radius
The van der Waals radius, ''r'', of an atom is the radius of an imaginary hard sphere representing the distance of closest approach for another atom. It is named after Johannes Diderik van der Waals, winner of the 1910 Nobel Prize in Physics, as he was the first to recognise that atoms were not simply points and to demonstrate the physical consequences of their size through the van der Waals equation of state. van der Waals volume The van der Waals volume, ''V'', also called the atomic volume or molecular volume, is the atomic property most directly related to the van der Waals radius. It is the volume "occupied" by an individual atom (or molecule). The van der Waals volume may be calculated if the van der Waals radii (and, for molecules, the inter-atomic distances, and angles) are known. For a single atom, it is the volume of a sphere whose radius is the van der Waals radius of the atom: V_ = \pi r_^3. For a molecule, it is the volume enclosed by the van der Waals surfac ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
