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Molecular Visualization
Resources
World Index of Molecular Visualization Resources
Molecular Visualization Resources, all free and open source, collected by Eric Martz.
Interactive Servers
FirstGlance in Jmol is the easiest way to look at the 3D structures of proteins, DNA, RNA, and their complexes.
The aim of this service is to provide an easy way to generate pictures and movies of protein structures, with the concern of integrating the most frequently used concepts of the molecular graphics fields via the software Dino. High definition pictures and movies are produced via the use of the Megapov engine founded on the Persistance of Vision Ray tracer - POV-Ray engine.
This server generates animated images as well as publication quality static slides of protein 3D structures using the PDB formatted data.
Service for the analysis and visualization of the ensembles of molecular models.
Interactive Viewers
Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry.
DeepView is an application that provides a user friendly interface allowing to analyze several proteins at the same time. Swiss-PdbViewer can be used as a helper application for browsers.
Cn3D is NCBI's 3D structure viewer. As a helper application for your Web browser, it allows you to interactively view 3D structures, sequences, and sequence alignments. Cn3D simultaneously displays structure, sequence, and alignment, with annotation and alignment editing features, for use with 3-D structures from NCBI's Entrez; available for Windows, Macintosh, and Unix.
KiNG (Kinemage, Next Generation) is an interactive system for three-dimensional vector graphics. It supports a set of graphics primitives that make it suitable for many types of graphs, plots, and other illustrations; although its first use was to display macromolecular structures for biophysical research.
RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle.
Vizualization Software
PyMOL is a USER-SPONSORED molecular visualization system on an OPEN-SOURCE foundation.
BALLView is a standalone molecular modeling and visualization application.
UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.
MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.
DINO is a realtime 3D visualization program for structural biology data. It runs under X-Windows and uses OpenGL. Supported architectures are Linux-i586 and Mac OSX.
DeepView - Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.
Commercial-grade graphics visualization is available for free to all academic, government and commercial researchers through Discovery Studio (DS) Visualizer. With DS Visualizer, you can visualize and share molecular information in a clear and consistent way, and in a wide variety of industry-standard formats.
MGLTools is a software developed at the Molecular Graphics Laboratory (MGL) of The Scripps Research Institute for visualization and analysis of molecular structures.
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code.
RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle. This site is provided for the convenience of users of RasMol and developers of open source versions of RasMol.
RasTop brings a friendly graphical user interface to the program RasMol. The result is a unique multi-windows, multi-molecular visualization program where atom manipulations are quick and simple, and do not require any typing on a command line, for Windows only.
BioEditor is a standalone Windows program. BioEditor contains features that enable the user to enter text, graphics, sequence, dynamic structural images and references. Many features link directly to resources on the World Wide Web.
Molekel is an opensource (GPL) multiplatform molecular visualization program being developed by the Visualization and Data Analysis group at the Swiss National Supercomputing Centre (CSCS).
QuteMol is an open source (GPL), interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilites through OpenGL shaders to offers an array of innovative visual effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins.
Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs process atomic coordinates from PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc.
Jamberoo (former JMolEditor) is a program for displaying, analyzing, editing, converting, and animating molecular systems.
Molecule viewer useful for visualising crystals, molecules or proteins.
The RCSB Viewers suite of frameworks provides the capability of creating 3-d viewing applications. The libraries are Java based, and rely on JOGL (Java OpenGL) to do the 3d rendering. This resource is for developpers only.
GRASP2 is an updated version of the GRASP program used for macromolecular structure and surface visualization. It is written for the Windows operating system and contains a large number of new features and scientific tools.
iMol is a free molecular visualization application for Mac OS X operating system. The program is an indispensable tool for chemists and molecular biologists.
Special Rendering & Movies
MovieMaker is a web server that allows short (~10 sec), downloadable movies to be generated of protein dynamics.
SweetMollyGrace is a suite of freeware and shareware tools for automating work of rendering and animating molecules.
A viewer for automated active-site predictions for polypeptides
The Web Bench
The Web Bench
is the essential companion to the biologist, bringing informational resources and a collection of tools & calculators to facilitate work at the bench and analysis of biological data.
Check out the full online bench here
Check out the full online bench here
Sequence Analysis with GenBeans
Try GenBeans: Best free software for DNA sequence editing!
FEEDBACK
Your comments & your suggestionsare appreciated. Please, notify us for resources and tools that you would like to see on this bench!
