PyMOL
- A free and flexible molecular graphics and modelling package which can be also used to generate animated sequences.
- http://pymol.sourceforge.net/

Brabosphere
- Open source program for the 3D visualisation of molecular systems and their properties. It also acts as a frontend for the QM program package BRABO. Runs on various Unix platforms, Windows, and MacOS X.
- http://www.brabosphere.be

CueMol
- Free molecular structure visualization and rendering program for Windows.
- http://cuemol.sourceforge.jp/en/

Swiss-PdbViewer
- A free program for viewing and analyzing several proteins at the same time. Some energy minimzation and homology modeling features are also included.
- http://www.expasy.org/spdbv/

Nanotube Modeler
- A program for generating and visualizing the xyz-coordinates for nanotubes, nanocones, nanosheets, and fullerenes. For Windows; free demo version available.
- http://jcrystal.com/products/wincnt/

Santorini and Patmos, Molecular Viewer and Screensaver
- Read XYZ or PDB files of atoms and display them in a 3-dimensional view on Windows PCs.
- http://homepage.ntlworld.com/oeffner/development.htm

PyMolWiki
- User-contributed wiki to supplement the PyMOL documentation.
- http://www.pymolwiki.org/

UCSF Chimera
- Highly extensible, interactive molecular graphics program. It is the successor to UCSF Midas and MidasPlus. Free of charge for academic, government, non-profit, and personal use.
- http://www.cgl.ucsf.edu/chimera/

Facio
- 3D-Molecular Modeling Software, available at no charge for the Windows platform. Has functions for visualization of biomolecules and results from GAMESS QM calculations, and for aligning and modifying structures.
- http://www1.bbiq.jp/zzzfelis/Facio.html

MOLMOL
- A free program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with emphasis on structures determined by NMR. Runs on UNIX and Windows NT/95. The site offers an online tutorial.
- http://hugin.ethz.ch/wuthrich/software/molmol/index.html

Protein Explorer
- A web-based viewer for the 3D structures of proteins, DNA and RNA. Requires Netscape and the Chime plugin, which is only available for Windows9x.
- http://www.umass.edu/microbio/chime/pe/protexpl/

MOLDEN
- Pre- and post-processing program for molecular and electronic structure, with Z-matrix editor, electron density visualization, and molecule animations. Available for Unix and VMS; free for academic use.
- http://www.cmbi.ru.nl/~schaft/molden/molden.html

ChemCraft
- Windows-based program for visualization of molecular structures, vibrational modes, molecular orbitals, energy gradient and other properties from log files produced by the GAMESS and Gaussian packages.
- http://www.chemcraftprog.com

SweetMollyGrace
- A suite of freeware tools for automating work of rendering and animating molecules. Generates high quality images of molecules from PDB, XYZ, or molfiles using raytracing tools (Povray and Raster3D).
- http://rodomontano.altervista.org/engSweetMG.php

gOpenMol
- A free program for the analysis of molecular dynamics trajectories and the display of molecular orbitals, electron densities and electrostatic potentials. Supports many file formats like the GaussianXX, Jaguar, CHARMM, and AMBER.
- http://www.csc.fi/gopenmol/

PovChem
- A chemical visualization and illustration program. Reads PDB files and exports POV-Ray files for producing high-resolution ray-traced images. Available for Windows, Linux, Mac, and SGI.
- http://www.chemicalgraphics.com/PovChem/

Viewmol
- An open-source graphical front end for computational chemistry programs such as Gaussian, Gamess, and Mopac. Available for Linux, FreeBSD, Mac OS X, and other Unices.
- http://viewmol.sourceforge.net/

JIMP - The Interactive Molecule Program
- Program for Linux and Windows for viewing and manipulating 3D structures of molecules and orbitals. Renders publication quality images and performs Fenske-Hall SCF calculations.
- http://www.chem.tamu.edu/jimp/

Jmol
- Open source molecule viewer written in Java. It runs as a standalone application and as a web browser applet.
- http://jmol.sourceforge.net/

Molda
- A molecular model building program for displaying data from MM2, MOPAC, Gaussian94, charmm and amber4 outputs. Supported on most windows, mac and unix platforms.
- http://www.molda.org/

Molcular Model Kits
- Plastic molecular structure models for research and education in science, intended especially for biochemistry.
- http://www.hgs-model.com/

RasMol
- Molecular visualization freeware for proteins, DNA, and macromolecules. Freely available for Windows, Macintosh, and UNIX.
- http://www.umass.edu/microbio/rasmol/

Biodesigner and iMol
- A molecular viewer for Windows9x systems with sequence editor and protein builder. Free for academic use. Additionaly the iMol molecule viewer is available for Mac OS X systems.
- http://www.pirx.com/

ProteinScope
- ProteinScope is a free program to view and create animations of Protein Data Bank PDB files.
- http://www.proteinscope.com

Ymol
- A free molecular visualization and animation program for the X window system. Creates images and movies, using either the built in renderer or povray. Still alpha.
- http://www.teoroo.mkem.uu.se/daniels/ymol.html

Historical Molecular Graphics
- Digitized versions of 16mm movies of molecular structures produced in the early days of interactive molecular graphics.
- http://www.umass.edu/molvis/francoeur/movgallery/moviegallery.html

Labquip
- Plastic molecular models for constructing polypeptides and DNA molecules.
- http://www.labquip.clara.net/index.html

Molymod Molecular Models
- Plastic molecular models for use in chemistry, biochemistry, molecular biology (DNA double helix), semiconductors and crystal lattice structures.
- http://www.molecular-model.com/

VMD
- A free program for visualization and analysis of biological systems such as proteins, nucleic acids, and lipid bilayer assemblies.
- http://www.ks.uiuc.edu/Research/vmd/

OpenRasMol
- Provided for the convenience of users and software developers of open source versions of RasMol.
- http://www.openrasmol.org/

Grasp
- A visualization and analysis program useful for the display and manipulation of the surfaces of molecules and their electrostatic properties. Commercial software.
- http://honiglab.cpmc.columbia.edu/grasp/

DTMM
- Desktop Molecular Modeller: A simple program for constructing and viewing small molecules and proteins in 3D with some energy calculation/minimization capabilities. Run on any PC with Windows 9X/NT. Commercial software.
- http://www.polyhedron.co.uk/dtmm/dtmm.html

OpenScience
- A directory of links to free molecule viewers and editors.
- http://www.openscience.org/links.php?section=56