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. You can also create high quality graphics.
This is the successor of WebLab Lite from Accelrys. WebLab Lite though is still available from some sites online. There are several advanced features on Discovery Studio Visualizer including the ability to show ligand binding sites in proteins and create a surface around the ligand.
-- Functionality for building small molecules, and protein and nucleic acid structures
Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture. Many consider this best for all platforms... clearly best for the MAC
Cross-Platform: Molecular builder/editor for Windows, Linux, and Mac OS X.--
Free, Open Source: Easy to install and all source code is available under the GNU GPL.
ArgusLab contains: An interactive 3D molecule builder that allows the user to build and manipulate complex structures; and, a rich suite of computational methods, both quantum mechanical and molecular mechanical, for calculating ground and excited states properties. The program is free for academic use
Mage requires the use of Kinemage files. There are presently available a large number of these files for both education and research purposes (see the Kinemage Home Page for more information. ) You can now run Kinemages on your home page using a Java enabled Mage. Because of the large number of Kinemage files available to the public this makes for an interesting teacher tool. See an example using the Mage Applet for the Fullerene Molecule.
JME Molecular Editor is a Java applet which allows to draw / edit molecules and reactions (including generation of substructure queries) and to depict molecules directly within an HTML page. Editor can generate SMILES or MDL mol file of created structures. You can download a copy at the JME Site.
The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98 and ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA and OPLS-AA/L).
This software is FREE to ACADEMIC users. Commercial users must obtain permission for its use.
This Windows software provides an integrated high quality system for building and modelling molecules (Mopac and Iconc are included) and the system drives PC GAMESS and Tinker. The crystallographic software can solve, refine and examine small molecule crystal structures. The pictures produced range from high quality HPGL to photo realistic rendered 3D. Rendered movies are effective and easy to make using RASMOV. Software for Powder pattern simulation and the detection and display of voids is also available.
YASARA is a molecular-graphics, -modeling and -simulation package for Linux and Windows.YASARA is powered by PVL (Portable Vector Language), a new development framework . PVL allows you to visualize even the largest proteins and enables true interactive real-time simulations with highly accurate force fields on standard PCs. The initial level stage can be downloaded free.
Jmol and Jsmol is a free, open source molecule viewer written in Java. It runs as a standalone application and as a web browser applet. Jmol is a collaboratively developed visualization and measurement tool for scientists and educators. New features being added on an ongoing basis. Users are encouraged to modify it to fit their needs and to contribute their changes to the project. JMol is a Chime/Rasmol replacement.
For Jmol applications See 3D Molecules using Jmol and Jsmol Software
For Jmol downloads see here.
Now Jsmol runs on tablets and works better on the Mac.