One of the subtle but most impactful challenges in molecular modeling is conveying depth and spatial relationships in complex structures. When presenting or analyzing molecular scenes, especially dense ones involving proteins or assemblies, it can be hard to read the 3D shape properly just with color and size. This is where ambient occlusion can help.
Ambient occlusion is a rendering technique designed to improve the perception of depth in molecular visualizations by darkening crevices and areas less exposed to light. The effect makes it easier to distinguish features like binding pockets, folds in secondary structures, and areas of packing, all of which would otherwise blend into one another.
What is Ambient Occlusion?
Ambient occlusion simulates the natural shading that occurs when light is partially blocked by surface geometry. For molecular modelers, this translates to a faint shadowing in pockets and tighter regions, which gives a softer yet clearer view of spatial hierarchies within a model.
SAMSON supports two types of ambient occlusion:
- Screen-space ambient occlusion (SSAO): A fast approximation that depends on the camera view. It gives a very helpful, immediate enhancement but can be less accurate when rotating or zooming.
- Object-space ambient occlusion: A more accurate, but slower rendering that calculates shadows based on geometry, independent of the camera.
Activating and Customizing Ambient Occlusion in SAMSON
Enabling screen-space ambient occlusion in SAMSON is just a click away, via Visualization > Options. For more precise control, head over to the Rendering > Ambient Occlusion section of the Preferences panel.
You can fine-tune parameters like intensity and radius to match your model’s complexity and your hardware’s capabilities. For presentations, stronger settings can emphasize structural detail. For interactive work, lighter settings speed things up while still giving useful depth cues.
Seeing the Difference
Here’s a visual comparison of a protein structure rendered with and without ambient occlusion:
Without ambient occlusion:
With screen-space ambient occlusion enabled:
Notice how the protein’s grooves and folds become clearer once ambient occlusion is turned on. Though subtle, it helps guide the eye and adds instant realism, especially when visualizing secondary structures or preparing images for communication purposes.
Tip: For publication-quality renders, consider using object-space ambient occlusion if speed is not a constraint.
Why This Matters
When dealing with molecular simulations and structural biology data, we often focus on accuracy. But perception is just as important — especially when sharing findings with research teams, writing papers, or recording educational content. Ambient occlusion helps ensure your audience sees what matters, without distraction or confusion.
Want to explore more rendering techniques to enhance your scene clarity beyond ambient occlusion? You can learn about other effects such as bloom, depth of field, fog, and lighting tweaks by visiting the full SAMSON documentation page on Rendering Effects.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.