![]() In addition to atomic co-ordinates and connectivities, the Protein Data Bank stores structure factors and phases, although these latter data are not placed in any uniform format. species from which the molecule has been obtained, resolution of diffraction data, literature citations and specifications of secondary structure). Text included in each data entry gives pertinent information for the structure at hand (e.g. ![]() The Bank stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies. The Protein Data Bank is a computer-based archival file for macromolecular structures. VMD is written in C++, using an object-oriented design the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. Full session logging is supported, which produces a VMD command script for later playback. ![]() VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. Molecules are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids.
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