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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 ...
The Patterson function is also equivalent to the electron density convolved with its inverse: = (). Furthermore, a Patterson map of N points will have N(N − 1) peaks, excluding the central (origin) peak and any overlap.
Also shown is the radial density, 4πr 2 ρ(r), scaled by a factor of 0.0375. In quantum chemistry, the electron localization function (ELF) is a measure of the likelihood of finding an electron in the neighborhood space of a reference electron located at a given point and with the same spin.
The theory is based on the calculus of variations of a thermodynamic functional, which is a function of the spatially dependent density function of particles, thus the name. The same name is used for quantum DFT, which is the theory to calculate the electronic structure of electrons based on spatially dependent electron density with quantum and ...
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.
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 idealization. The software is designed to be easy-to-learn for novice users, achieved by ensuring that ...
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]