The visualization panel

The Protein Optimizer shows the selected residue as Ball and Stick. Additional visualization styles can be checked to visualize interactions between the selected residue and its surroundings. Show nearby atoms shows atoms in steric contact with the residue's side chain. Hydrogen bonds from the residue are marked with dashed blue lines, and potential hydrogen bonds - hydrogen bonds which would be formed if the protonation was changed - are marked with dashed yellow lines.

Show clashes shows the parts of a residue that clash with the surrounding structure. Clashes are only shown for atoms that have been modeled, either with the Find and Model Structure tool, or using the modify residue panel. Clashes are marked as transparent red regions around the affected atoms.