If you’ve ever struggled to make your molecular models look more three-dimensional, you’re not alone. Many molecular modelers face the same issue: molecules that should pop visually instead appear flat and lifeless. The culprit? Often, it’s the lack of ambient occlusion, a subtle but powerful rendering effect that dramatically improves depth perception.
Ambient occlusion (AO) simulates how light is occluded or blocked in crevices and recesses of a structure. This helps recreate the shadowing that occurs naturally in physical objects, making the geometry easier to read and more visually engaging—even in static scenes. It’s especially useful in complex biomolecules where understanding spatial relationships matters.
Types of Ambient Occlusion
SAMSON offers two types of ambient occlusion:
- Screen-space ambient occlusion (SSAO): More efficient, fast, and often good enough for real-time rendering. However, it’s sensitive to the camera’s distance.
- Object-space ambient occlusion (OSAO): More accurate and realistic, but it takes longer to compute.
While OSAO delivers better quality, SSAO is often the go-to for interactive workflows where speed matters.
Turning It On
You can activate and customize AO easily through:
- Visualization > Options for quick toggling and preset switching.
- The Rendering > Ambient occlusion section in the Preferences panel for more detailed control.
See the Difference
Let’s take a look at a real example: the Ribbons visual model of 1AF6. With ambient occlusion disabled, the image lacks depth and appears washed out:
Now, here’s the same model with screen-space ambient occlusion enabled. Notice how the deeper regions of the molecule appear darker, enhancing three-dimensionality and making it easier to interpret:
When to Use AO
Ambient occlusion is particularly helpful when:
- You’re creating figures for publications or presentations.
- You need to highlight structural features like pockets, grooves, or folds.
- You’re preparing educational materials that must be visually clear.
Even in real-time visual analysis, enabling SSAO can help you better understand the morphology of your molecular system without rotating endlessly to uncover depth.
For slower workflows (e.g., rendering animations or high-quality stills), switching to object-space AO can provide even greater realism.
Small Change, Big Payoff
It’s easy to overlook ambient occlusion, especially when working quickly. But enabling it takes just a second and can deliver significant benefits to your visualization’s clarity. It won’t solve all your rendering challenges—lighting, shadows, and surface representation also play crucial roles—but it’s one of the simplest ways to add visual depth with immediate impact.
Learn more about AO and other rendering tools in the full documentation: SAMSON Rendering Effects.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.