When working with complex molecular structures, one common challenge is understanding the spatial relationships between different parts of a model. Proteins, ligands, and assemblies can quickly turn into a dense visual web where depth becomes hard to interpret. A powerful yet simple way to address this issue in SAMSON is by enabling ambient occlusion.
Ambient occlusion mimics how light is blocked in deep crevices and occluded areas of a molecular model. It enhances shadows in regions where less light would naturally reach, making complex 3D structures easier to comprehend—especially when you’re preparing figures or animations for presentations or publications.
Two Types of Ambient Occlusion
SAMSON provides two flavors of ambient occlusion:
- Screen-space ambient occlusion (SSAO) — a fast, approximate method that works well for real-time visualization. It’s dependent on the camera’s angle and distance but has a minimal performance cost.
- Object-space ambient occlusion — more accurate and realistic, but computationally heavier. Recommended for static renders and high-quality exports.
Why Use Ambient Occlusion?
Take a look at the comparison below. Without any ambient occlusion, molecular ribbons appear flat and lose spatial definition:
Now, enable screen-space ambient occlusion, and the same model reveals depth and subtle structural relationships. This improvement is especially useful in crowded molecular views or when distinguishing overlapping domains:
How to Enable and Customize
You can quickly toggle ambient occlusion on or off via Visualization > Options. For more control, go to Preferences > Rendering > Ambient Occlusion where you can adjust sampling rates, strength, and choose between screen-space and object-space modes.
This feature becomes even more helpful when combined with other rendering effects like lighting and shadows to create publication-ready visuals or immersive animations. Because ambient occlusion works in tandem with lighting models, it’s a key tool to enrich realism without overwhelming computational resources—especially in SSAO mode.
Potential Use Cases
- Clarify the spatial configuration of protein-binding sites
- Improve depth perception in large macromolecular assemblies
- Generate clearer frames for structural biology tutorials or papers
To learn more about rendering options available in SAMSON—including anti-aliasing, lighting, depth of field, and more—visit the full documentation page: Rendering Effects Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.