When working with complex macromolecular structures, it can be challenging to distinguish overlapping elements or perceive spatial depth accurately. Whether you’re preparing a figure for publication or exploring a structure visually, the depth may seem flattened, making interpretation harder than it needs to be.
In SAMSON, a molecular design platform, this common issue has a streamlined solution: Ambient Occlusion.
What is Ambient Occlusion?
Ambient occlusion is a technique used in 3D rendering to enhance realism by simulating the way light behaves in enclosed or obscured regions. In molecular modeling, this translates into a better perception of cavities, folds, and spatial relationships between atoms or residues.
In SAMSON, you have access to two types of ambient occlusion:
- Screen-space ambient occlusion (SSAO): A fast approximation based on image-space rendering. It’s efficient but dependent on the camera viewpoint.
- Object-space ambient occlusion: More realistic lighting, accounting for the 3D geometry of molecules directly, though computationally heavier.
Visual Comparison
Consider the Ribbons visual model of protein 1AF6 with and without SSAO. The version without ambient occlusion looks relatively flat:
Now compare it with SSAO enabled. Subtle shadows give a stronger sense of depth and internal structure:
Why It Matters
This might seem like a small difference at first glance, but for molecular modelers, it greatly improves:
- Navigation: Faster interpretation of spatial relationships during exploration.
- Visualization: Helpful communication tool for figures and presentations.
- Design: Easier to identify binding pockets or cavity depths.
How to Enable It in SAMSON
To enable or customize ambient occlusion in your workspace:
- Go to Visualization > Options to quickly toggle SSAO on or off.
- For fine-tuning, go to Interface > Preferences > Rendering > Ambient occlusion.
Is It Always Better?
Not necessarily. SSAO slightly burdens the GPU, so for very large systems or older hardware, you might consider toggling it off. That said, for everyday work and high-quality rendering, the benefits typically outweigh the cost.
Final Thoughts
Ambient occlusion is a small change that results in a big impact for spatial perception. If your molecules look flat or hard to read, it might be time to enable this feature and explore different presets.
To learn about additional rendering effects and see how to combine ambient occlusion with other tools like anti-aliasing or depth of field, visit the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.