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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]
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 phases obtained this way can be used to generate electron density maps. [114] Anomalous X-ray scattering (MAD or SAD phasing) – the X-ray wavelength may be scanned past an absorption edge [a] of an atom, which changes the scattering in a known way. By recording full sets of reflections at three different wavelengths (far below, far above ...
Coot can also display electron density, which is the result of structure determination experiments such as X-ray crystallography and EM reconstruction. The density is contoured using a 3D-mesh. 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 ...
Furthermore, a Patterson map of N points will have N(N − 1) peaks, excluding the central (origin) peak and any overlap. The peaks' positions in the Patterson function are the interatomic distance vectors and the peak heights are proportional to the product of the number of electrons in the atoms concerned.
The Multipole Density Formalism (also referred to as Hansen-Coppens Formalism) is an X-ray crystallography method of electron density modelling proposed by Niels K. Hansen and Philip Coppens in 1978.
The CCP4 file format is file generated by the Collaborative Computational Project Number 4 in 1979. The file format for electron density has become industry standard in X-ray crystallography and Cryo-electron microscopy where the result of the technique is a three-dimensional grid of voxels each with a value corresponding to density of electrons (see wave function) The CCP4 format is supported ...
These X-rays are emitted in all directions (isotropically), and so they may not all escape the sample. The likelihood of an X-ray escaping the specimen, and thus being available to detect and measure, depends on the energy of the X-ray and the composition, amount, and density of material it has to pass through to reach the detector.