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In biochemistry, a Ramachandran plot (also known as a Rama plot, a Ramachandran diagram or a [φ,ψ] plot), originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, [1] is a way to visualize energetically allowed regions for backbone dihedral angles ( also called as torsional angles , phi and psi angles ) ψ ...
PyMol allows you to save its current internal state, including all molecules you have loaded, all selections, objects, and representations, and all display settings in a PyMol session file, which has the file extension .pse. This is very useful for saving intermediate states of complex manipulations, especially since PyMol does not have a ...
The bond angles in the table below are ideal angles from the simple VSEPR theory (pronounced "Vesper Theory") [citation needed], followed by the actual angle for the example given in the following column where this differs. For many cases, such as trigonal pyramidal and bent, the actual angle for the example differs from the ideal angle, and ...
a torsion angle between ±90° and 180° is called anti (a) a torsion angle between 30° and 150° or between −30° and −150° is called clinal (c) a torsion angle between 0° and ±30° or ±150° and 180° is called periplanar (p) a torsion angle between 0° and ±30° is called synperiplanar (sp), also called syn-or cis-conformation
where J is the 3 J coupling constant, is the dihedral angle, and A, B, and C are empirically derived parameters whose values depend on the atoms and substituents involved. [3] The relationship may be expressed in a variety of equivalent ways e.g. involving cos 2φ rather than cos 2 φ —these lead to different numerical values of A , B , and C ...
PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. PyMOL is widely used. PyMOL is one of the few mostly open-source model visualization tools available for use in structural biology. The Py part of the software's name refers to the program having been written in the programming language ...
PREDITOR (PREDIction of TORsion angles) is a freely available web-server for the prediction of protein torsion angles from chemical shifts. [1] For many years it has been known that protein chemical shifts are sensitive to protein secondary structure, which in turn, is sensitive to backbone torsion angles.
In chemistry an eclipsed conformation is a conformation in which two substituents X and Y on adjacent atoms A, B are in closest proximity, implying that the torsion angle X–A–B–Y is 0°. [1] Such a conformation can exist in any open chain, single chemical bond connecting two sp 3-hybridised atoms, and it is normally a conformational ...