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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 ...
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.
Reconstructing the 3D shape of the grains is nontrivial and three approaches are available to do so, respectively based on simple back-projection, forward projection, algebraic reconstruction technique and Monte Carlo method-based reconstruction. [10]
This is the method used in the original discovery of X-ray diffraction. Laue scattering provides much structural information with only a short exposure to the X-ray beam, and is therefore used in structural studies of very rapid events (time resolved crystallography). However, it is not as well-suited as monochromatic scattering for determining ...
X-ray diffraction computed tomography is an experimental technique that combines X-ray diffraction with the computed tomography data acquisition approach. X-ray diffraction (XRD) computed tomography (CT) was first introduced in 1987 by Harding et al. [1] using a laboratory diffractometer and a monochromatic X-ray pencil beam.
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).
SciPy (pronounced / ˈ s aɪ p aɪ / "sigh pie" [2]) is a free and open-source Python library used for scientific computing and technical computing. [3]SciPy contains modules for optimization, linear algebra, integration, interpolation, special functions, FFT, signal and image processing, ODE solvers and other tasks common in science and engineering.
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.