One of the most common challenges in molecular modeling and visualization is understanding the spatial relationships within complex structures. When looking at dense molecular systems, it can be hard to tell which atoms are deep inside a pocket and which are on the surface. This is where ambient occlusion becomes a useful ally.
Ambient occlusion (AO) is a rendering technique that improves depth perception by simulating how light is blocked in different parts of a 3D scene. In molecular models, this translates to highlighting exposed regions and subtly darkening cavities, which makes it easier to read and analyze spatial features—particularly useful when you’re presenting your models to others or exploring new molecules yourself.
Visualizing subtle differences
SAMSON provides two types of ambient occlusion:
- Screen-space ambient occlusion (SSAO) – This is fast and gives an immediate sense of depth, though it depends on the camera’s position.
- Object-space ambient occlusion (OSAO) – Offers more accurate lighting simulations, especially when detailed realism is needed, but is more computationally expensive.
You can quickly switch SSAO on and off from Visualization > Options for on-the-fly adjustments. For deeper customization, head to the Rendering > Ambient Occlusion section in the Preferences panel. Here, you can tweak specific parameters such as intensity, radius, and type of AO.
Before and after: Why it matters
The difference between an image with and without ambient occlusion speaks for itself. Below, you can see the same molecular ribbon model (PDB: 1AF6):
Without ambient occlusion:
With screen-space ambient occlusion enabled:
The second image instantly provides a clearer sense of structure. Crevices are more apparent, folds are easier to identify, and the overall realism of the visualization is improved without being distracting.
Best use cases
Ambient occlusion is particularly helpful when:
- Inspecting binding pockets or active sites where depth perception is key
- Rendering presentation-ready images or publication figures
- Building animations to illustrate conformational changes or docking processes
Even if you’re just exploring a model, keeping ambient occlusion enabled can make navigation more intuitive, especially when rotating or zooming inside dense assemblies.
Things to keep in mind
While SSAO is generally fast, enabling ambient occlusion—like other post-processing rendering effects—may have a noticeable impact on performance for very large structures or systems displayed on older hardware. If performance becomes an issue, try switching from OSAO to SSAO or temporarily disabling the effect until you need to generate high-quality images.
To explore AO settings in detail, visit the full documentation at SAMSON Rendering Effects — Ambient Occlusion.
To learn more about the available visualization options in SAMSON, visit the full rendering effects documentation page: https://documentation.samson-connect.net/users/latest/rendering-effects/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.