1. Select both atoms in the Chimera main window:
• Hold down "control" on your keyboard while clicking on the first atom.
• Hold down "control" and "shift" on your keyboard while clicking on the second atom.
Both atoms should be highlighted in very faintly in green.
2. From the Chimera menu, select Tools / Structure Analysis / Distances.
3. The Chimera Structure Measurements window should open.
• Click "Create" (red).
• The pair of atoms defining the distance should show up (green).
• A line connecting the two atoms should appear in the Chimera window.
• You can adjust the color and thickness of this line in the Sophia
Structure Measurements window (blue).
4. In the Sophia Trajectory Viewer window, click "bonds". A plot of the bond length vs. time should appear in the Bonds Plot window.