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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]
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 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.
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 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.
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 ...
Mechanism of how density of states influence V-A spectra of tunnel junction. Scanning tunneling spectroscopy is an experimental technique which uses a scanning tunneling microscope (STM) to probe the local density of electronic states (LDOS) and the band gap of surfaces and materials on surfaces at the atomic scale. [1]