Avogadro offers a semantic chemical builder and platform for visualization and analysis. The 1.0 release series of Avogadro is the main focus of the results discussed here. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. It offers flexible, high quality rendering, and a powerful plugin architecture.
Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.read more read lessĪbstract: The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input.
One of the design concepts of Phaser was that it be capable of a high degree of automation. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F+ and F−, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences ΔF.
The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. Abstract: Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods.
0 kommentar(er)
