Molecular viewers
Resources
World Index of Molecular Visualization Resources
http://www.molvisindex.org
Molecular Visualization Resources, all free and open source, collected by Eric Martz.
http://www.MolviZ.Org
Introduction to molecular viewers at the RCSB.
http://www.rcsb.org/robohelp_f/#molecular_viewers/introduction_to_molecular_viewers.htm
Interactive viewers
Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry.
http://jmol.sourceforge.net/
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.
http://kinemage.biochem.duke.edu/software/king.php
WebMol Java PDB Viewer, WebMol was designed to display and analyze structural information
contained in the Brookhaven Protein Data Bank (PDB).
http://www.cmpharm.ucsf.edu/~walther/webmol.html
RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle.
http://www.rasmol.org
Swiss-PdbViewer 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.
http://www.expasy.ch/spdbv/
FirstGlance in Jmol is the easiest way to look at the 3D structures of proteins, DNA, RNA, and their complexes.
http://molvis.sdsc.edu/fgij/index.htm
Visualization software
MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules,
http://hugin.ethz.ch/wuthrich/software/molmol/index.html
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.
http://www.ks.uiuc.edu/Research/vmd/
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.
http://www.cgl.ucsf.edu/chimera/
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.
http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml
The Molecular Biology Toolkit (MBT) is a Java-based protein visualization and analysis toolkit. The toolkit provides classes for efficiently loading, managing and manipulating protein structure and sequence data. The MBT also provides a rich set of graphical 3D and 2D visualization components which can be easily "plugged together" to produce applications having sophisticated graphical user interfaces.
http://mbt.sdsc.edu/
PyMOL is a USER-SPONSORED molecular visualization system on an OPEN-SOURCE foundation.
http://pymol.sourceforge.net/
VEGA ZZ is the evolution of the well known VEGA OpenGL package and includes several new features and enhancements making your research jobs very easy. VEGA was originally developed to create a bridge between most of the molecular software packages only, but in the years, enhancing its features, it's evolved to a complete molecular modelling suite. This software is FREE for non-profit academic uses.
http://users.unimi.it/~ddl/vega/index2.htm
MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.
http://www.avatar.se/molscript/
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.
http://www.dino3d.org
The MICE application provides high quality, interactive visualization of molecular scenes.
http://mice.sdsc.edu/
iMol is a free molecular visualization application for Mac OS X operating system. The program is an indispensable tool for chemists and molecular biologists.
http://www.pirx.com/iMol/
Molview is a Macintosh application that can read several types of coordinate files and display ribbon, CPK, stick, ball&stick, and surface figures. The interface is completely interactive (i.e. no comand line input). There are countless options that control the display colors and characteristics.
http://www.danforthcenter.org/smith/MolView/molview.html
The "Java Molecular Viewer" (JMV) is a molecule viewer program written in Java and Java3D developed by the NIH ( the US National Institute Of Health ). It is designed to be an easy-to-use, platform neutral molecular visualization tool which can be used standalone or integrated into a larger program.
http://www.frontiernet.net/~imaging/molecular_modeling.html
MGLTools is a software developed at the Molecular Graphics Laboratory (MGL) of The Scripps Research Institute for visualization and analysis of molecular structures. AutoDock is an automated docking software designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. PMV is a powerful molecular viewer that has a number of customizable features and comes with many pluggable commands ranging from displaying molecular surfaces to advanced volume rendering. Vision is a visual-programming environment in which a user can interactively build networks describing novel combinations of computational methods, and yielding new visualizations of their data without actually writing code.
http://mgltools.scripps.edu/
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
http://www.ks.uiuc.edu/Research/vmd/
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.
http://accelrys.com/products/discovery-studio/visualization/discovery-studio-visualizer.html
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.
http://www.expasy.ch/spdbv/
Jamberoo (former JMolEditor) is a program for displaying, analyzing, editing, converting, and animating molecular systems.
http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html
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.
http://www.geneinfinity.org/rastop/
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.
http://www.openrasmol.org/
Explore any 3D macromolecular structure model, mostly for teaching purpose.
http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/index.htm
Protein structure visualization server can be used to generate schematic representations of secondary structures and relative solvent accessibilities, allowing one to highlight selected residues, e.g. polymorphic or involved in protein-protein interactions.
http://polyview.cchmc.org/
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.
http://bioeditor.sdsc.edu/
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.
http://skuld.bmsc.washington.edu/raster3d/raster3d.html
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).
http://www.bioinformatics.org/molekel/wiki/
The ribbons software package by Mike Carson is designed to display molecular models as rendered images.
http://www.cbse.uab.edu/ribbons/
Molecule viewer useful for visualising crystals, molecules or proteins.
http://development.oeffner.net/
Molegro Molecular Viewer is a free cross-platform application for visualization of molecules
http://www.molegro.com/mmv-product.php
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.
http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:GRASP2
Special rendering, movies
MovieMaker is a web server that allows short (~10 sec), downloadable movies to be generated of protein dynamics.
http://wishart.biology.ualberta.ca/moviemaker/
SweetMollyGrace is a suite of freeware and shareware tools for automating work of rendering and animating molecules.
http://rodomontano.altervista.org/engSweetMG.php
A viewer for automated active-site predictions for polypeptides
http://bioinformatics.cm-uj.krakow.pl/reveal/
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.
http://qutemol.sourceforge.net/
This server generates animated images as well as publication quality static slides of protein 3D structures using the PDB formatted data.
http://polyview.cchmc.org/polyview3d.html