Your reader can click on links in the text, for example to

You can also set up toggle boxes:

This is an example of a Jmol presentation (click on the "About" menu above for more info on Jmol).

The protein is the winged-helix DNA-binding protein Hrfx1, bound to its X-box binding site

This is a classic example of direct read-out via the .

One can see some of the major groove and can actually show some for H-bonding and electrostatic interactions.

Show me the protein .

Show me the protein a different way.

Show me the hydrophobic core, yet another way:

Often, it is easier to turn specific interactions on and off using "checkboxes"