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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 ρ ( r ) {\displaystyle \rho ({\textbf {r}})} or n ( r ) {\displaystyle n ...
Series of density maps for GroEL: from left to right, 4 Å, 8 Å, 16 Å, and 32 Å resolution.The details are smeared away as the resolution becomes lower. Resolution in the context of structural biology is the ability to distinguish the presence or absence of atoms or groups of atoms in a biomolecular structure.
The contour level controlled using the mouse wheel for easy manipulation - this provides a simple way for the user to get an idea of the 3D electron density profile without the visual clutter of multiple contour levels. Electron density may be read into the program from ccp4 or cns map formats, though it is more common to calculate an electron ...
This gives the potential at locations on a particular surface, most commonly a surface of electron density corresponding to overall molecular size. [71] Local ionization potential map – Is defined as the sum over orbital electron densities, ρi(r) times absolute orbital energies, ∈i, and divided by the total electron density, ρ(r). The ...
In many cases, crystallographic disorder smears the electron density map. Weakly scattering atoms such as hydrogen are routinely invisible. It is also possible for a single atom to appear multiple times in an electron density map, e.g., if a protein sidechain has multiple (<4) allowed conformations.
In X-ray crystallography, a difference density map or Fo–Fc map shows the spatial distribution of the difference between the measured electron density of the crystal and the electron density explained by the current model. [1] A way to compute this map has been formulated for cryo-EM. [2]
The bond angle for water is 104.5°. Valence shell electron pair repulsion (VSEPR) theory (/ ... As in methane above, there are four regions of electron density ...
Electron density isosurface map around a covalent bond modelled with the Independent Atom Model in the same scale. Nucleus-centred functions impose lower charge density on the bond path. The primary advantage of the Hansen-Coppens formalism is its ability to free the model from spherical restraints and describe the surroundings of a nucleus far ...