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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 ...
Crucial for 3DXRD is the idea to mimic a three-dimensional detector by positioning a number of two-dimensional detectors at different distances from the centre of rotation of the sample, and exposing these either simultaneously (many detectors are semi-transparent to hard X-rays) or at different times.
These scattering methods generally use monochromatic X-rays, which are restricted to a single wavelength with minor deviations. A broad spectrum of X-rays (that is, a blend of X-rays with different wavelengths) can also be used to carry out X-ray diffraction, a technique known as the Laue method.
The size of the translation step is commonly aligned with the X-ray beam's horizontal size. In a perfect scenario for any pencil-beam scanning tomographic method, the measured angles should match the number of translation steps multiplied by π/2, adhering to the Nyquist sampling theorem. However, this number can often be reduced in practice be ...
Graph-tool, a free Python module for manipulation and statistical analysis of graphs. NetworkX, an open source Python library for studying complex graphs. Tulip (software) is a free software in the domain of information visualisation capable of manipulating huge graphs (with more than 1.000.000 elements).
The method has also revealed the structure and function of many biological molecules, including vitamins, drugs, proteins and nucleic acids such as DNA. X-ray crystallography is still the primary method for characterizing the atomic structure of materials and in differentiating materials that appear similar in other experiments.
The Levenberg-Marquardt method finds a local optimum. Due to the curve having many interference fringes, it finds incorrect layer thicknesses unless the initial guess is extraordinarily good. The derivative-free simplex method also finds a local optimum. In order to find global optimum, global optimization algorithms such as simulated annealing ...
Interpretation of PAE values allows scientists to understand the level of confidence in the predicted structure of a protein: Lower PAE values between residue pairs from different domains indicate that the model predicts well-defined relative positions and orientations for those domains.