If you’ve ever struggled with the visual complexity of large molecular systems, you’re not alone. Molecular models are packed with detail, and sometimes it’s hard to quickly tell which atoms are buried inside a structure and which are on the surface. One effective way to fix this is to improve depth perception.
This is where Ambient Occlusion comes in. If you’ve ever looked at a visualization and thought it looked ‘flat’, this powerful rendering feature in SAMSON might be exactly what you need. It subtly shades regions based on how enclosed or exposed they are, providing a more intuitive sense of depth — all without changing the molecular structure or colors.
Why Ambient Occlusion Matters
Ambient occlusion mimics the way light is less likely to reach tight crevices or inner cavities of a molecule. By adding darkness to these areas, your brain interprets them as being deeper, making the entire 3D structure easier to understand at a glance.
This is particularly useful when working with complex proteins, large assemblies, or overlapping molecules where spatial relationships are hard to interpret. Whether you’re preparing figures for publication or simply trying to examine a structure, ambient occlusion can save you time and reduce errors.
Two Flavors of Depth
SAMSON provides two types of ambient occlusion:
- Screen-space ambient occlusion: Fast, approximate, and responsive to camera angle. Great for interactive exploration.
- Object-space ambient occlusion: Slower, but more accurate. Ideal for generating high-quality images.
You can toggle screen-space AO with one click from Visualization > Options, or fine-tune parameters via Preferences > Rendering > Ambient occlusion.
How It Looks
Still not sure whether it’s worth enabling? Here’s a comparison using the 1AF6 structure:
No Ambient Occlusion: Surfaces appear clean but lack visual cues for depth. Everything looks equally exposed.
With Screen-Space Ambient Occlusion Enabled: Shadows are subtly added to corners and crevices, immediately highlighting structural depth.
The difference may seem subtle at first, but when you work with molecular data daily, this kind of visual aid can significantly reduce the time it takes to understand spatial configurations — especially in dense environments.
When to Use It
Consider enabling ambient occlusion when:
- You’re analyzing protein folding or cavity locations.
- You’re preparing export images or animation frames for presentations.
- You find visual saturation too high and need better separation between overlapping regions.
Keep in mind that object-space AO is more computationally demanding. For live work, screen-space AO is typically sufficient.
Final Thoughts
Better visuals lead to better insights. Ambient occlusion is a simple feature with a big impact, especially when clarity and precision are key. Take just a few minutes to experiment with SAMSON’s AO presets and discover how much easier it becomes to explore your molecular models.
To learn more about SAMSON’s visualization options, visit the Rendering Effects documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.