PyMOL

PyMol is a complex tool designed for scientific professionals that need to know the molecular structure of different substances.

The application is very complete, open source, and not suitable for beginners.

The program allows for a multitude of activities, including: joining and pulling apart molecules, arbitrarily selecting atoms, rendering high quality images, etc.

To work with PyMol you may use the GUI and command line together. From the menu of the application, you have access to a multitude of configuration options: zoom, labeling, coloring, and so on.

One of the most interesting features of this utility is the ability to create movies from the movement of charged molecular structures in the program.

If you perform a task often, PyMol supports scripts to avoid having to repeat the same steps over and over.

PyMol's rendering functionality uses 'built-in ray' technology that provides shade and a sense of depth in virtually eery scene. The output format of PyMOL IS PNG.