Molecular Graphics

• BioEditor
  A tool for creating and viewing dynamic, formatted structure annotations; for Windows
   
• canDo Shockwave 3D PDB Viewer
  Free, easy to use tool for viewing molecular structures through a Web page--streams data directly from PDB on Windows and Mac (OSX or PPC); developed in Ireland
• Chemscape Chime
  From MDL Information Systems. This program allows visualisation of structures with Windows, Macintosh (with Netscape 4.x only), and (as version 0.9z) SGI/Irix. For further information about Chime see the UMass Chime Resources Page
• Chimera
  Interactive molecular modeling system, free to academic/non-profit; displays multiple sequence alignments and associated structures, atom-type and H-bond identification, molecular dynamics trajectories (AMBER format), and offers ligand-screening interface (DOCK), filter by number/position of H-bonds, and extensibility to create custom modules - for Windows, Linux, Mac OS X, IRIX, and Tru64 Unix
• 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
• iMol
  Open GL graphics program displays small, large, and multiple molecules; measures distances and angles, superimposes structures, calculates RMSD between atom coordinates, structurally aligns chains, and displays dynamics trajectories. For Mac OS X incl. 10.2
• Java3D Molecular Visualisastion System
  Free Java/Java3D progam and source code for Windows or Unix
• Mage and Kinemages
  Interactive molecular display for research and educational uses. Free, open source for Windows and Mac (OSX or PPC), Unix, and Linux. A Java version does 3-D Web display without plug-ins.
• MOLMOL
  A program for displaying, analyzing, and manipulating the 3-D structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR; for Mac OSX, Windows, Unix, Linux
• MolScript
  A program for displaying structures in both detailed and schematic formats and writing images in various formats for Unix
• MolView and MolView Lite
  Free molecular visualization programs for the Mac PPC
• PDB2MGIF
  Free, user-friendly server that converts PDB files to animated gif files that can be used in Web pages and presentations. Simple step-by-step instructions can be found here. Works on Mac OSX, Windows, Unix, Linux
• PocketMol
  Program to view and manipulate PDB files on a PocketPC

• ProteinScope
  Free viewer to display and manipulate PDB files and create animations and slides of proteins for Windows
• PyMOL
  A free and open-source molecular graphics system for visualization, animation, editing, and publication-quality imagery. PyMOL is scriptable and can be extended using the Python language. Supports Windows, Mac OSX, Unix, and Linux
• Qmol
  A lightweight OpenGL based molecular viewer for Windows
• RasMol
  A free viewing system for PDB coordinate files that runs on Mac PPC, Windows, Unix, and Linux systems. Open source versions are also available.
• Raster3D
  A set of tools for generating high quality raster images of proteins or other molecules. Freeware for Mac OSX, Windows, Unix, and Linux
• RasTop (v. 2.0)
  A free user-friendly graphical interface to RasMol molecular visualization software (v. 2.7.2.1), available for Windows and Linux
• Ribbons
  A program for molecular illustration and error analysis, for for Mac OSX, Windows, Unix, and Linux
• RmscopII
  A Tcl/Tk script responsible to redirect PDB files or RasMol scripts to multiple RasMol sessions; can be used as a Web browser helper application or as a standalone program for Mac (OSX or PPC), Windows, or Unix
   
• Swiss PDB viewer available from Australia | Bolivia | Canada | China | Korea | Switzerland | Taiwan | USA
  A 3D graphics and molecular modeling program for the simultaneous analysis of multiple models and for model-building into electron density maps. The software is available for Mac (OSX or PPC), Windows, Linux, or SGI
   
• Uppsala Electron Density Server
  Generated density maps
• VMD
  VMD (Visual Molecular Dynamics) runs on many platforms including MacOS X, and several versions of Unix and Windows. VMD provides visualization, analysis, and Tcl/Python scripting features, and has recently added sequence browsing and volumetric rendering features. VMD is distributed free of charge.
• WebMol
  A Java PDB Viewer. WebMol was designed to display and analyze structural information contained in the Protein Data Bank (PDB). It can be run as an applet or as a stand-alone application for Mac OSX, Windows, Unix, and Linux
• World Index of Molecular Visualization Resources
  A Visitor-Maintained Indices (VMI)^TM Site by Eric Martz and Trevor D. Kramer. Contains many links to visualization tools, tutorials, and other resources.