Jmol

Jmol is a Java-based molecular viewer.
The home page is http://jmol.sourceforge.net.
It can be downloaded from there.
You run the program by simply clicking on jmol.jar.
It is mostly fully intuitive.

Change background colour
Archive–Console
write in the console:
background white

Change the colour of an atom
color @9 orange

Use default colours for all atoms (with two different colour schemes)
color atoms cpk
set defaultColors Jmol
set defaultColors Rasmol

Add or remove cartoon for protein structure
cartoon on/off
ribbons on/off
Render in POV-ray:
Click on Icon or Archive–Export–POV-ray
Ensure that the povray program is installed (and give the absolute path):
brew install povray

Create or delete bonds
write in the console:
connect 3.0  (_CU) (_N) create   # creates bonds between Cu and N shorter than 3.0 Å
connect 4.0 (_FE) (_FE) delete # deletes bonds between Fe and Fe shorter than 4 Å
connect @2 @9 single  # Make a single bond between atoms 2 and 9