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The EM Data Bank or Electron Microscopy Data Bank (EMDB) collects 3D EM maps and associated experimental data determined using electron microscopy of biological specimens.. It was established in 2002 at the MSD/PDBe group of the European Bioinformatics Institute (EBI), where the European site of the EMDataBank.org consortium is located.
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.
In order to obtain an interpretable electron density map, both amplitude and phase must be known (an electron density map allows a crystallographer to build a starting model of the molecule). The phase cannot be directly recorded during a diffraction experiment: this is known as the phase problem .
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 ...
Conventionally, they are displayed as isosurfaces with positive density—electron density where there's nothing in the model, usually corresponding to some constituent of the crystal that hasn't been modelled, for example a ligand or a crystallisation adjutant-- in green, and negative density—parts of the model not backed up by electron density, indicating either that an atom has been ...
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 ...
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 ...
Charge carrier density, also known as carrier concentration, denotes the number of charge carriers per volume. In SI units, it is measured in m −3. As with any density, in principle it can depend on position. However, usually carrier concentration is given as a single number, and represents the average carrier density over the whole material.