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MM XRD: Free open-source: Java 3D applet or standalone program: Ovito: MM XRD EM MD: Free open-source: Python [13] [14] PyMOL: MM XRD SMI EM: Open-source [15] Python [16] [self-published source?] According to the author, almost 1/4 of all published images of 3D protein structures in the scientific literature were made via PyMOL. [citation ...
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 ...
Model inadequacies such as incorrect or missing parts and unmodeled disorder are the other main contributors to , making it useful to assess the progress and final result of a crystallographic model refinement. For large molecules, the R-factor usually ranges between 0.6 (when computed for a random model and against an experimental data set ...
This technique is computationally fast, but the 2D results do not provide a good sense of depth of the original data. To improve the sense of 3D, animations are usually rendered of several MIP frames in which the viewpoint is slightly changed from one to the other, thus creating the illusion of rotation .
William Lawrence Bragg proposed a model where the incoming X-rays are scattered specularly (mirror-like) from each plane; from that assumption, X-rays scattered from adjacent planes will combine constructively (constructive interference) when the angle θ between the plane and the X-ray results in a path-length difference that is an integer ...
A powder X-ray diffractometer in motion. X-ray crystallography is the experimental science of determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract in specific directions.
To obtain high-quality data in X-ray CTR measurements, it is desirable that the detected intensity be on the order of at least [citation needed]. To achieve this level of output, the X-ray source must typically be a synchrotron source. More traditional, inexpensive sources such as rotating anode sources provide 2-3 orders of magnitude less X ...
Three-dimensional X-ray diffraction (3DXRD) is a microscopy technique using hard X-rays (with energy in the 30-100 keV range) to investigate the internal structure of polycrystalline materials in three dimensions.