If you’ve ever looked at your molecular model and thought, “Something about the image feels flat,” you’re not alone. Depth perception is essential for interpreting the spatial relationships in molecular structures. But sometimes, even beautifully constructed 3D models fall short visually. One subtle but effective trick to solve this is enabling ambient occlusion.
Ambient occlusion is a rendering technique that simulates the way light interacts with geometry, particularly how crevices and cavities receive less light in the real world. In molecular modeling, this means that deeper parts of molecules appear slightly darker, improving depth perception and making complex structures easier to interpret visually.
What Ambient Occlusion Looks Like
Let’s take a look at an example. Here’s the ribbon visual model of the 1AF6 protein without ambient occlusion:
And the same model with screen-space ambient occlusion enabled:
Notice how the second image has more subtle shading that helps you distinguish the folding and orientation of different parts of the protein. This can be especially helpful when preparing visuals for presentations or when navigating large molecular assemblies.
Two Types: Which Should You Use?
In SAMSON, you can choose between:
- Screen-space ambient occlusion (SSAO): Fast and efficient, SSAO provides a reasonably good approximation of depth but may vary with camera distance.
- Object-space ambient occlusion: More realistic but computationally heavier. Ideal for high-quality still images.
Where to Find It
You can toggle ambient occlusion quickly from Visualization > Options. For more control, including switching between SSAO and object-space AO, go to the Rendering > Ambient occlusion section in the Preferences panel.
Why It Matters
For molecular modelers, especially those working with large protein complexes or nucleic acid folds, visual cues are critical. Ambient occlusion doesn’t just make your image look better–it makes it easier to work with. By enhancing contrast in a physically meaningful way, you reduce visual clutter and improve spatial comprehension.
This is particularly important in scenarios such as:
- Spotting binding pockets or internal channels
- Inspecting biomolecular interactions
- Preparing clear visuals for scientific communication
Plus, because SSAO can be toggled instantly, you can turn it on for quick comprehension and off when performance matters more, such as with very large systems.
Try It Yourself
The next time you’re building or visualizing a biomolecular structure, try enabling ambient occlusion and see how it transforms your understanding of its geometry. It’s a small step that makes a big difference.
You can learn more in the official documentation here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.