Spacefill view
The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called 'spacefill' view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, etc.
In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.
Ball-and-stick molecular model
This view shows chymotrypsin in the familiar representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.
Now we can see all the atoms in the protein, but again, it's difficult to get a feel for how it is organised. It's very difficult to follow the chain of amino acids that makes up the protein, for example.
Amino acid trace
Here's a much more simplified view that of amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!
What we really need to do next is to have a basic introduction to protein structure. This link will take you to a page that introduces you to the basic concepts.
