When visualizing complex molecular systems in 3D, capturing depth and spatial relationships clearly is often a challenge. Have you ever looked at your protein or material structure and felt it looked flat or lacked realistic depth perception? If so, you’re not alone.
One of the most effective ways to enhance depth perception in molecular visualization is through the use of ambient occlusion. This rendering effect helps simulate subtle shadows in crevices and cavities where light would naturally be more occluded. The result? Your molecules look more three-dimensional, easier to interpret, and visually compelling.
What is Ambient Occlusion?
Ambient occlusion (AO) adds depth cues by simulating how exposed each point in a 3D scene is to ambient lighting. Regions that are more enclosed (like crevices in molecular surfaces) receive less light and appear darker, mimicking how light behaves in the real world.
SAMSON handles two types of ambient occlusion:
- Screen-space ambient occlusion (SSAO): A fast approximation that adapts based on camera position. Efficient and ideal for quick rendering.
- Object-space ambient occlusion (OSAO): More accurate but slower. Provides realistic shading regardless of camera angle.
How to enable Ambient Occlusion in SAMSON
You can toggle AO quickly via Visualization > Options or dive into its detailed settings in Preferences > Rendering > Ambient Occlusion.
For instance, enabling screen-space AO with default settings can dramatically improve the appearance of your models, highlighting subtle structural contours without altering any geometry.
Visual Comparison
Below is an example of the Ribbons model of the 1AF6 molecule shown without and with screen-space ambient occlusion:
Without ambient occlusion:
With screen-space ambient occlusion:
Notice how the occlusion of deeper regions adds a soft shadow that brings structural hierarchy to life? Structures appear easier to interpret, especially in dense protein or polymer systems where distinguishing backbone folds or internal pockets is crucial.
When to use AO (and when not to)
Use ambient occlusion when you’re preparing visualizations for presentations, publications, or teaching materials. It adds visual clarity without modifying the underlying data. However, since SSAO is camera-dependent and OSAO is computationally heavy, it may be better to disable it while manipulating very large systems in real-time to maintain performance.
Tips for Best Results
- Use AO in combination with shadows and custom lighting setups for maximum visual clarity.
- Switch between AO presets in Visualization > Options for quick comparisons.
- Try both SSAO and OSAO depending on whether speed or realism is your priority.
If you are unsure whether AO alone is sufficient, try taking screenshots with and without it—you’ll almost certainly appreciate the visual difference.
To learn more about how ambient occlusion and other rendering effects can help refine your molecular visualizations, visit the full documentation page here: 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