When you’re working on a molecular model, getting the science right is step one. But communicating it effectively—especially visually—is just as important. A common challenge molecular modelers face is that 3D structures often appear flat and hard to interpret due to lack of depth perception in visualizations. This is especially noticeable when preparing figures or animations for publications and presentations.
Ambient occlusion is a rendering technique that helps solve this by simulating how light behaves in real environments. It’s not just about making molecules look nice—it’s about clarity, comprehension, and producing visual models that convey structural relationships clearly.
What Is Ambient Occlusion?
Ambient occlusion improves the perception of depth by darkening areas that are less exposed to ambient light—essentially, it simulates shadows in crevices and corners. In SAMSON, two types of ambient occlusion are available:
- Screen-space Ambient Occlusion (SSAO): A fast, camera-dependent approximation. It’s useful for real-time interaction and gives immediate visual depth.
- Object-space Ambient Occlusion (OSAO): More realistic and stable, but slower. Ideal for high-quality render exports and final animations.
A Visual Comparison
Let’s take a look at what this means in practice. Below are two images of the protein 1AF6 using the Ribbons visual model:
Without ambient occlusion:
With screen-space ambient occlusion enabled:
The difference is clear. Enabling ambient occlusion significantly improves depth perception, making structural folds and cavities much easier to interpret at a glance.
Getting Started
In SAMSON, ambient occlusion settings are easy to access:
- For quick toggling, use Visualization > Options.
- For finer control, go to the Rendering > Ambient occlusion section in the Preferences panel.
Try experimenting with both SSAO and OSAO depending on your needs. Use SSAO for real-time model exploration, and switch to OSAO for static images where maximum depth clarity is critical.
Why It Matters
Ambient occlusion is not just eye candy—it improves your ability to interpret models, communicate results, and reduce viewer confusion. Whether you’re creating teaching visuals, journal graphics, or just trying to better understand your system, this rendering effect adds invaluable clarity.
To learn more about rendering effects in SAMSON, including ambient occlusion, visit the full documentation page: https://documentation.samson-connect.net/users/latest/rendering-effects/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.