Have you ever spent hours building a beautiful molecular model, only to find that the final visualization feels… flat? You’re not alone. Molecular structures are inherently three-dimensional, but without the right rendering techniques, their depth can get lost on screen.
One of the most effective ways to solve this problem is through ambient occlusion. Built into the SAMSON platform, ambient occlusion simulates how light behaves in crevices and folds of a structure—mimicking the way deeper parts of objects are less exposed to light and therefore darker. This subtle shading cue dramatically improves depth perception and brings your molecular models to life.
Understanding Ambient Occlusion in SAMSON
SAMSON provides two types of ambient occlusion:
- Screen-space ambient occlusion (SSAO): A fast approximation that works well for real-time visualization but may vary with camera distance.
- Object-space ambient occlusion: A more realistic, albeit slower, rendering technique that remains consistent regardless of camera placement.
You can enable SSAO directly via Visualization > Options for immediate results. For more fine-grained control, visit Preferences > Rendering > Ambient Occlusion.
What a Difference It Makes
Let’s look at an example. Below is the Ribbons visual model of the 1AF6 molecule…
Without ambient occlusion:
With screen-space ambient occlusion enabled:
That’s a significant improvement in visual clarity. Notice how subtle shading changes make the structure easier to interpret. You can more easily distinguish overlapping regions, surface curvature, and secondary structure elements.
When Should You Use It?
Ambient occlusion is particularly helpful when:
- Creating publication-quality images
- Recording molecular animations
- Demonstrating models in teaching settings
- Working with complex assemblies where spatial relationships matter
Even when working in real-time, enabling screen-space ambient occlusion adds valuable visual cues that make your models more readable—without a major performance cost on most modern systems.
How to Adjust Ambient Occlusion Settings
If you’d like more control over the effect’s intensity and quality, go to:
Preferences > Rendering > Ambient Occlusion
You can tweak screen-space parameters or switch to object-space for higher accuracy. Play with these settings to find the right balance between visual quality and performance for your setup.
Wrap-up
Ambient occlusion is a subtle but powerful tool that can dramatically enhance your understanding of complex molecular structures. Whether you’re designing drugs or teaching biochemistry, turning on this feature lets you present molecular data in a way that’s not just more beautiful—but more informative.
Learn more in the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.