If you work with molecular visualizations, chances are you’ve sometimes found it hard to understand the structure of crowded regions or complex folds. Molecules can often look flat or difficult to interpret—especially in ribbon or surface models where depth is essential. That’s where ambient occlusion in SAMSON comes in.
Ambient occlusion is a technique from computer graphics that improves the perception of depth by simulating how exposed each point in a scene is to ambient light. In simpler terms: regions that are more ‘hidden’ appear darker. This creates a subtle shading effect that helps the 3D structure stand out more clearly.
Two Types of Ambient Occlusion in SAMSON
SAMSON supports two flavors of ambient occlusion:
- Screen-space Ambient Occlusion (SSAO): A fast approximation that calculates darkness based on the camera view. It’s computationally cheap and can usually run in real time.
- Object-space Ambient Occlusion (OSAO): More accurate, but slower, since it analyzes the actual geometry of the object rather than relying on screen pixels.
Even SSAO on its own can make a significant difference, especially when preparing visuals for publications or presentations.
Switching It On
To enable or customize ambient occlusion in SAMSON:
- Go to Visualization > Options to quickly enable or disable the effect.
- For more control, open Preferences > Rendering > Ambient Occlusion. Here, you can fine-tune the intensity, radius, and other parameters.
Before and After
Here is an example of the 1AF6 molecule rendered in the Ribbons visual model:
Without ambient occlusion:
With screen-space ambient occlusion enabled:
With ambient occlusion enabled, creases and folds in the structure become more apparent. This is especially useful when working with large biomolecules where depth cues are crucial for understanding structural relationships.
Performance Considerations
Enabling ambient occlusion introduces minimal overhead when using SSAO, but OSAO might slow things down for very large systems. You can easily switch between presets that balance speed and quality, depending on the size of your system or the clarity required for visualization.
A Useful Tip
If you’re preparing figures or screenshots for publication, try combining SSAO with anti-aliasing and shadows. The combined effect results in much cleaner, clearer, and more understandable molecular images without post-processing.
Understanding molecular shape doesn’t have to mean staring at ambiguous blob-like renderings. Ambient occlusion gives your models a sense of volume and structure that your brain intuitively understands. Less visual noise, more clarity. Easy as a checkbox.
To learn more about the rendering options in SAMSON, 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 download SAMSON at https://www.samson-connect.net.