This section contains lists of free software and web applications that are designed to display large biomolecules. Links to additional information on each tool are provided, including program documentation (manual, tutorials, etc.)

Our main tool for high-quality molecular graphics images and animations is PyMOL. PyMOL has excellent capabilities in creating high-quality images from 3-D structures and it has well developed functions for manipulating structures and some basic functions to analyze their chemical properties. The possibilities to write scripts and plugins as well as to incorporate PyMOL in custom software are vast and superior to most other programs.

Standalone Applications

open in new windowBALL View
BALLView is molecular viewer and modeling tool. It combines visualization capabilities with powerful modeling functionality including implementations of force field methods and continuum electrostatics models.
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open in new windowChimera
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.
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open in new windowDeepView Swiss-PDB Viewer
DeepView Swiss PDB Viewer user-friendly molecular visualization program. It includes in addition various building and modeling tools.
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open in new windowDino
DINO is a real time 3-D visualization program for structural biology data.
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open in new windowDiscovery Studio Visualizer
DS (Discovery Studio) Visualizer is a cut-down version of a commercial DS viewer/editor-program sold by Accelrys, which is free and very user-friendly.
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Friend
Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA.
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open in new windowiMol

iMol is a molecular visualization application for Mac OS X operating system.

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open in new windowJmol
Jmol is an open source molecular viewer written in Java. It can be used as applet which displays the molecule within a web browser or as standalone application.
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open in new windowMGLTools MGLTools is a software for visualization and analysis of molecular structures. It incude three main application: ADT, a graphical front-end for setting up and running AutoDock; PMV, molecular viewer and Vision, a visual-programming environment Read More Info
open in new windowPyMOL
PyMOL is open-source molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations.
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open in new windowVMD
VMD (Visual Molecular Dynamics) is a free molecular visualization program for displaying, animating, and analyzing large bimolecular systems using 3-D graphics and built-in scripting.
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Web Applications

open in new windowCn3D
Cn3D is an open-source code visualization tool for biomolecular structures, sequences, and sequence alignments. Cn3D is typically run from a web browser as a helper application for NCBI's Entrez system.
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Friend
Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA.
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open in new windowJmol
Jmol is an open source molecular viewer written in Java. It can be used as applet which displays the molecule within a web browser or as standalone application.
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Web Services

FirstGlance in Jmol FirstGlance in Jmol offers one-click views of any molecule (PDB file) including secondary structure, ribbons, amino to carboxy (or 5' to 3') rainbow, Composition, Hydrophobic/Polar, Charge and much more .
open in new windowPOLYVIEW-3D

Web-based tool for macromolecular structure visualization. The server enables combining versatile structural and functional annotations with simple web-based interface for creating publication quality structure rendering, as well as animated images.

open in new windowPOLYVIEW-MM Web-based platform for animation and analysis of ensembles of molecular models (e.g. molecular dynamic trajectories, multiple conformations from structure prediction or docking calculations)