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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.
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 ...
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 iterative model building, it is common to encounter phase bias or model bias: because phase estimations come from the model, each round of calculated map tends to show density wherever the model has density, regardless of whether there truly is a density. This problem can be mitigated by maximum-likelihood weighting and checking using omit maps.
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.
A difference map built with m and D is known as a mFo – DFc map. [3] The use of ML weighting reduces model bias (due to using the model's phase) in the 2 Fo–Fc map, which is the main estimate of the true density. However, it does not fully eliminate such bias. [4]
The arrangement of the electrons in the sample is described quantum mechanically by an "electron density". The electron density is a function of both position and energy, and is formally described as the local density of electron states, abbreviated as local density of states (LDOS), which is a function of energy.
If an electron from a shell with a higher energy level jumps to fill the hole, the energy difference can be emitted as a fluorescent photon (figure 1 (b)). In the Auger phenomenon, when the electron jumps from the higher energy level, its energy instead causes an adjacent or nearby electron to be ejected, forming an Auger electron (figure 1 (c ...