Molekel
Encyclopedia
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 Portman 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.
Free software
Free software, software libre or libre software is software that can be used, studied, and modified without restriction, and which can be copied and redistributed in modified or unmodified form either without restriction, or with restrictions that only ensure that further recipients can also do...
multiplatform molecular
Molecule
A molecule is an electrically neutral group of at least two atoms held together by covalent chemical bonds. Molecules are distinguished from ions by their electrical charge...
visualization program. It was originally developed at the University of Geneva
University of Geneva
The University of Geneva is a public research university located in Geneva, Switzerland.It was founded in 1559 by John Calvin, as a theological seminary and law school. It remained focused on theology until the 17th century, when it became a center for Enlightenment scholarship. In 1873, it...
by Peter F. Flükiger in the 1990s for Silicon Graphics
Silicon Graphics
Silicon Graphics, Inc. was a manufacturer of high-performance computing solutions, including computer hardware and software, founded in 1981 by Jim Clark...
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 Portman moved on and ceased to develop the codes. In 2006, the Swiss National Supercomputing Centre
Swiss National Supercomputing Centre
The Swiss National Supercomputing Centre develops and supports technical computing for the Swiss scientific research community. It provides high-performance computing infrastructure that enables world-class simulation-based science....
(CSCS) restarted the project and version 5.0 was released on 21 December 2006.
Major features
- Visualization of residuesResidue (chemistry)In chemistry, residue is the material remaining after a distillation or an evaporation, or to a portion of a larger molecule, such as a methyl group. It may also refer to the undesired byproducts of a reaction....
(ribbon or schematic) - Complete control over the generation of molecular surfaces (bounding boxMinimum bounding boxThe minimum or smallest bounding or enclosing box for a point set in N dimensions is the box with the smallest measure within which all the points lie...
and resolutionDisplay resolutionThe display resolution of a digital television or display device is the number of distinct pixels in each dimension that can be displayed. It can be an ambiguous term especially as the displayed resolution is controlled by all different factors in cathode ray tube , flat panel or projection...
) - Visualization of the following surfaces:
- orbitalsMolecular orbitalIn chemistry, a molecular orbital is a mathematical function describing the 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 term "orbital" was first...
- IsosurfaceIsosurfaceAn isosurface is a three-dimensional analog of an isoline. It is a surface that represents points of a constant value within a volume of space; in other words, it is a level set of a continuous function whose domain is 3D-space.Isosurfaces are normally displayed using computer graphics, and are...
from electron densityElectron densityElectron density is the measure of the probability of an electron being present at a specific location.In molecules, regions of electron density are usually found around the atom, and its bonds...
data - Isosurface from GaussianGAUSSIANGaussian is a computational chemistry software program initially released in 1970 by John Pople and his research group at Carnegie-Mellon University as Gaussian 70. It has been continuously updated since then...
cube grid data - Solvent-accesible surface (SAS)Accessible surface areaThe accessible surface area is the surface area of a biomolecule that is accessible to a solvent. The ASA is usually quoted in square ångstrom . ASA was first described by Lee & Richards in 1971 and is sometimes called the Lee-Richards molecular surface...
- Solvent excluded surface (SES)
- Van del Waals radiiVan der Waals radiusThe van der Waals radius, r, of an atom is the radius of an imaginary hard sphere which can be used to model the atom for many purposes. 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 had a finite size and to...
- Animation of molecular surfaces
- Export to PostScriptPostScriptPostScript is a dynamically typed concatenative programming language created by John Warnock and Charles Geschke in 1982. It is best known for its use as a page description language in the electronic and desktop publishing areas. Adobe PostScript 3 is also the worldwide printing and imaging...
or TIFFTagged Image File FormatTIFF is a file format for storing images, popular among graphic artists, the publishing industry, and both amateur and professional photographers in general. As of 2009, it is under the control of Adobe Systems...
See also
- GabeditGabeditGabedit is a Graphical User Interface to GAMESS , GAUSSIAN, MOLCAS, MOLPRO, MPQC, OpenMopac, PC GAMESS, and Q-Chem computational chemistry packages.- Major features :* builds molecules by atom, ring, group, amino acid and nucleoside....
- List of molecular graphics systems
- MoldenMoldenMolden is a general molecular and electronic structure processing program.- Major features :* Reads output from the ab initio packages GAMESS , Gaussian, MOLPRO and from semi-empirical packages such as MOPAC, and supports a number of other formats....
- Molecular graphicsMolecular graphicsMolecular 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"...