PyMOL

PyMOL is a comprehensive and powerful application that allows you to design and then visualize molecular structures.

It enables the 3D visualization of all kinds of proteins and molecules, together with their related trajectories and surfaces. Since this tool is a very complex one, advanced functions like ray tracing or animating the 3D structures are also supported.

Although based on an open source project, a generally-available version of PyMOL that includes additional advantages is offered for a price for non-educational purposes. This version, called “Incentive PyMOL”, includes an installer for Windows (the original open-source PyMOL is a Python-based project which can't be installed just as easy on Windows systems), incentive documentation, user support and handy tutorials, or even built-in tools like a molecular morphing tool. There are also extensive video exporting capabilities that let you create MOV or MPEG video files containing various molecular animations.

PyMOL impresses mostly thanks to its numerous functions and features. It's amazingly powerful and comprehensive but unfortunately it's also not exactly suitable for beginners. Its interface requires spending some time to learn the ropes first.

In conclusion, PyMOL is great especially for experts and professionals that need a powerful and reliable solution to view, render, animate and export 3D molecular structures.