One of the main tools of the structural biologist (computational or experimental) if not, THE main tool, is the molecular viewer he uses. There are various viewers available, but usually each of us, at a certain point at his career, chooses a specific one and specializes in it. It becomes a way of self expression, to the point that using a “non-native” viewer is like talking in a foreign language. (How do I select only the polar atoms within 4.5A of chain B and color them CPK in this awkward viewer ?!?!?! On MY viewer it would take me a second!)
We want to hear what is YOUR molecular viewer of choice. Each viewer is optimized for a different set of tasks. E.g. VMD is designed for molecular dynamics, UCSF Chimera integrates many molecular analysis tools, Rasmol is a quick and dirty command line operated little fellow, not producing the nicest figures though, PyMOL creates good looking figures and is highly scriptable (as we demonstrated before in PyMOL scripts), while Jmol is web oriented and easy to embed in web pages.
There are other software available, please tell us in the comments what’s your favorite viewer advantages and what are the disadvantages of the other “lesser” viewers.