This has to do with your view option settings. Some of the view options which are more tailored for protein folding and protein design don't work too well if you're interested in the individual atom identities (e.g. for ligand design puzzles).
If you're looking for atom coloring, we recommend you adjust your view options to Color: "Score/Hydro+CPK" and View Protein: "Binding Site" (or "Cartoon Ligand"). But feel free to play around with the view settings to come up with settings that you like best.