Molecular scraps-youtube

www.rbvi.ucsf.edu/chimera

Molecular graphics and analyses were performed with the UCSF Chimera package. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311).

UCSF Chimera--a visualization system for exploratory research and analysis. 

I have been using Chimera for about 10 years.
It is Python extensible and very powerful alone but can be used collaboratively and as a port for other molecular dynamics software.