Understanding complex biomolecular structures often involves navigating dense 3D environments filled with atoms, ribbons, and other intricate representations. But even with the most accurate geometry, sometimes something just “feels off” — flat visuals that make it difficult to distinguish between foreground and background elements.
This is a common pain point for molecular modelers and researchers: depth perception. If your proteins and ligands seem to float uniformly in space, lacking spatial cues beyond perspective, then it’s time to explore a powerful (yet easy-to-use) feature in SAMSON: Ambient Occlusion.
What is Ambient Occlusion?
Ambient occlusion simulates how exposed each point in a scene is to ambient lighting. In biological terms, it darkens the crevices and areas between tightly packed residues — places where light would naturally have a harder time reaching.
It’s a subtle but effective rendering technique that adds realism and depth, helping you instantly recognize structural organization and spatial positioning. SAMSON offers two types you can switch between:
- Screen-space ambient occlusion (SSAO): A fast, efficient method for quickly boosting depth, especially suitable for interactive work.
- Object-space ambient occlusion: More realistic, but computationally heavier — suitable for final visualizations or presentations.
Seeing the Difference
Consider the Ribbons representation of PDB structure 1AF6. Without ambient occlusion, the structure looks flat and its depth is ambiguous:
Now, turn on screen-space ambient occlusion with one click from Visualization > Options, and the perception immediately improves:
The difference might not be dramatic at first glance, but as you rotate and inspect crowded molecular environments, this added contrast plays a significant role in helping your eyes parse the geometry.
How to Activate and Customize
To turn ambient occlusion on or adjust its parameters:
- Go to Visualization > Options — for quick toggling or switching presets
- For full control, use Interface > Preferences > Rendering > Ambient Occlusion
Want a subtle shading in the background while preserving rendering speed? Stick with SSAO.
If producing a high-quality still frame is your goal, toggle on object-space ambient occlusion for added realism.
When and Why To Use It
Ambient occlusion is particularly useful when:
- You’re analyzing active sites with deep crevices
- You need to understand the relative positioning of domains or subunits
- You’re preparing screenshots or animations for papers or presentations
- You want your visuals to have more structure, even when using simple color schemes
It’s a small switch with a big effect. 🧪🔦
To dive deeper into rendering effects in SAMSON, including ambient occlusion and other parameters, you can consult the full documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.