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About: Visualization is a(n) research topic. Over the lifetime, 52753 publication(s) have been published within this topic receiving 905026 citation(s). more


Journal ArticleDOI: 10.1016/0263-7855(96)00018-5
Abstract: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. 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. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. 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. Full session logging is supported, which produces a VMD command script for later playback. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. 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. 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 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. more

Topics: Rendering (computer graphics) (52%), Molecular graphics (52%), Visualization (51%) more

36,939 Citations

Journal ArticleDOI: 10.1107/S0021889808042726
Abstract: New software, OLEX2, has been developed for the determination, visualization and analysis of molecular crystal structures. The software has a portable mouse-driven workflow-oriented and fully comprehensive graphical user interface for structure solution, refinement and report generation, as well as novel tools for structure analysis. OLEX2 seamlessly links all aspects of the structure solution, refinement and publication process and presents them in a single workflow-driven package, with the ultimate goal of producing an application which will be useful to both chemists and crystallographers. more

Topics: User interface (59%), Graphical user interface (54%), Visualization (52%) more

14,922 Citations

Journal ArticleDOI: 10.1107/S0021889811038970
Koichi Momma1, Fujio Izumi1Institutions (1)
Abstract: VESTA is a three-dimensional visualization system for crystallographic studies and electronic state calculations. It has been upgraded to the latest version, VESTA 3, implementing new features including drawing the external mor­phology of crystals; superimposing multiple structural models, volumetric data and crystal faces; calculation of electron and nuclear densities from structure parameters; calculation of Patterson functions from structure parameters or volumetric data; integration of electron and nuclear densities by Voronoi tessellation; visualization of isosurfaces with multiple levels; determination of the best plane for selected atoms; an extended bond-search algorithm to enable more sophisticated searches in complex molecules and cage-like structures; undo and redo in graphical user interface operations; and significant performance improvements in rendering isosurfaces and calculating slices. more

Topics: Visualization (53%)

10,557 Citations

Open accessJournal ArticleDOI: 10.1006/CBMR.1996.0014
Robert W. Cox1Institutions (1)
Abstract: A package of computer programs for analysis and visualization of three-dimensional human brain functional magnetic resonance imaging (FMRI) results is described. The software can color overlay neural activation maps onto higher resolution anatomical scans. Slices in each cardinal plane can be viewed simultaneously. Manual placement of markers on anatomical landmarks allows transformation of anatomical and functional scans into stereotaxic (Talairach-Tournoux) coordinates. The techniques for automatically generating transformed functional data sets from manually labeled anatomical data sets are described. Facilities are provided for several types of statistical analyses of multiple 3D functional data sets. The programs are written in ANSI C and Motif 1.2 to run on Unix workstations. more

Topics: Visualization (50%)

8,845 Citations

Journal ArticleDOI: 10.1107/S0021889807067908
Abstract: The program Mercury, developed by the Cambridge Crystallographic Data Centre, is designed primarily as a crystal structure visualization tool. A new module of functionality has been produced, called the Materials Module, which allows highly customizable searching of structural databases for intermolecular interaction motifs and packing patterns. This new module also includes the ability to perform packing similarity calculations between structures containing the same compound. In addition to the Materials Module, a range of further enhancements to Mercury has been added in this latest release, including void visualization and links to ConQuest, Mogul and IsoStar. more

Topics: Visualization (50%)

7,236 Citations

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Topic's top 5 most impactful authors

Kwan-Liu Ma

226 papers, 6.3K citations

Thomas Ertl

198 papers, 5.4K citations

Daniel Weiskopf

165 papers, 3.7K citations

Bernd Hamann

75 papers, 1.2K citations

Hans Hagen

73 papers, 1.7K citations

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