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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 ...
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 ...
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]
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 ...
The program ShelXle [2] is a graphical user interface for the structure refinement program SHELXL. [3] ShelXle combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo-Fc) maps.
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 ...
Projects the electron wave functions and density onto a real-space grid to calculate the Hartree and exchange-correlation potentials and their matrix elements. Besides the standard Rayleigh-Ritz eigenstate method , it allows the use of localized linear combinations of the occupied orbitals (valence-bond or Wannier-like functions), making the ...
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.