Volume-rendering on a 3D hyperwall: A molecular visualization platform for research, education and outreach (original) (raw)
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Journal of molecular graphics, 1995
QMView is designed to facilitate the visualization and interpretation of quantum mechanical data. Capabilities include display of chemical structure, animation of quantum mechanically determined vibrational modes, and depiction of electronic properties and three-dimensional molecular orbitals. QMView has a user-friendly interface that allows users to interactively manipulate many features of the molecular structure and/or property, including positioning and structure representation, via mouse-activated dialog boxes. Although the interface allows input from results of any of the popularly used quantum mechanical software, we have focused on GAMESS, a widely distributed quantum chemistry code. QMView has been designed with the special feature of working in distributed mode with GAMESS, the latter running on a supercomputer, the former running on a Silicon Graphics platform. Ancillary programs provide a method of obtaining output of graphic images in various media, including hardcopy, ...
GPU-powered tools boost molecular visualization
Briefings in Bioinformatics, 2011
Recent advances in experimental structure determination provide a wealth of structural data on huge macromolecular assemblies such as the ribosome or viral capsids, available in public databases. Further structural models arise from reconstructions using symmetry orders or fitting crystal structures into low-resolution maps obtained by electron-microscopy or small angle X-ray scattering experiments.Visual inspection of these huge structures remains an important way of unravelling some of their secrets. However, such visualization cannot conveniently be carried out using conventional rendering approaches, either due to performance limitations or due to lack of realism. Recent developments, in particular drawing benefit from the capabilities of Graphics Processing Units (GPUs), herald the next generation of molecular visualization solutions addressing these issues. In this article, we present advances in computer science and visualization that help biologists visualize, understand and manipulate large and complex molecular systems, introducing concepts that remain little-known in the bioinformatics field. Furthermore, we compile currently available software and methods enhancing the shape perception of such macromolecular assemblies, for example based on surface simplification or lighting ameliorations.
Visualization of Biomolecular Structures: State of the Art
Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The report concludes with an outlook on promising and important research topics to enable further success in advancing the knowledge about interaction of molecular structures.
Visualization of Biomolecular Structures: State of the Art Revisited
Computer Graphics Forum, 2016
Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The survey concludes with an outlook on promising and important research topics to foster further success in the development of tools that help to reveal molecular secrets.
The Molecule Cloud - compact visualization of large collections of molecules
Journal of cheminformatics, 2012
Analysis and visualization of large collections of molecules is one of the most frequent challenges cheminformatics experts in pharmaceutical industry are facing. Various sophisticated methods are available to perform this task, including clustering, dimensionality reduction or scaffold frequency analysis. In any case, however, viewing and analyzing large tables with molecular structures is necessary. We present a new visualization technique, providing basic information about the composition of molecular data sets at a single glance. A method is presented here allowing visual representation of the most common structural features of chemical databases in a form of a cloud diagram. The frequency of molecules containing particular substructure is indicated by the size of respective structural image. The method is useful to quickly perceive the most prominent structural features present in the data set. This approach was inspired by popular word cloud diagrams that are used to visualize...
WAALSURF: Molecular graphics on a personal computer
Computers & graphics, 1987
The advent of increasingly powerful graphics boards for personal computers will soon allow quite advanced molecular graphics applications on inexpensive personal computer configurations. This paper describes an interactive molecular data display program, called WAALSURF, implemented on two different personal computers, IBM's PC-AT equipped with a Professional Graphics Adapter and Commodore's Amiga. These programs allow the inspection of data bases containing data of molecules with some thousand atoms each. The molecular data can be used to generate a range of representations from skeleton, ball-and-stick to space filled Van der Waals surfaces. To foster 3D perception coloring, perspective and lighting depth cues are included, with stereo images as an option. A versatile user interface is provided, allowing the operator to manipulate objects as well as display parameters. Under interactive control the user may rotate molecules in static or animation mode, label sections, strip outer layers and dock molecules while changing the color and the number of atoms displayed. A logging facility is provided to resume a new session where the previous one left off.
Molecular Graphics: Bridging Structural Biologists and Computer Scientists
Structure
Visualization of molecular structures is one of the most common tasks carried out by structural biologists, yet the technical details and advances required to e ciently display molecular structures are often hidden from the end user. During decades molecular viewer software such as Chimera, COOT, PyMOL, or VMD provided the most common solutions to quickly visualize structures. Nowadays, new and e cient ways to depict molecular objects are changing how structural biologists interact with their data. Such novelties are often driven by advances made by computer scientists, but an important gap remains between this community and the final users such as structural and computational biologists. In this perspective article, we clarify how developments from computer graphics and data visualization have led to novel ways of understanding protein structure. We present future developments from computer science that will be beneficial for structural biology. By pointing to canonical papers and explaining technical progress underlying new graphical developments in simple terms, we hope to promote communication between the diāµerent communities to shape future developments in molecular graphics.