Molecular structures can be highly intricate, often composed of thousands of atoms, bonds, and surfaces interweaving in dense formations. For researchers and molecular designers, interpreting such structures visually isn’t just helpful—it’s necessary. But even with advanced rendering tools, certain spatial cues can be lost in a flat view. This is where ambient occlusion becomes valuable.
If you’ve ever struggled to perceive depth in a molecular visualization—especially when displaying proteins or biomolecular assemblies—ambient occlusion can help you make sense of it all by simulating how occluded areas are naturally darker.
What Is Ambient Occlusion?
Ambient occlusion is a shading technique that mimics the soft shadows that occur in crevices or areas where light is blocked. Rather than creating sharp shadows (like those from a directional light source), ambient occlusion adds subtle darkening in tight or hidden spaces, enhancing depth perception.
In SAMSON, there are two types of ambient occlusion:
- Screen-space ambient occlusion (SSAO): A fast approximation technique influenced by the camera’s view. It’s efficient and suitable for real-time work.
- Object-space ambient occlusion (OSAO): A more accurate, albeit slower method that accounts for surrounding geometry regardless of viewpoint. Ideal for producing high-quality renderings.
Why Use Ambient Occlusion?
Imagine looking at a ribbon model of a protein. Without shading to highlight the grooves and intersections between helices, beta sheets, and loops, the visual model can look flat. With ambient occlusion, hidden pockets and overlapping regions appear darker, providing immediate insight into spatial relationships.
Here’s a comparison between a model without ambient occlusion and one with SSAO enabled:
Notice how the second image reveals more about the folding of the protein, even though the structure hasn’t changed.
How to Enable and Customize It in SAMSON
Turning ambient occlusion on in SAMSON is quick and flexible. Here’s how to adjust it to match your needs:
- For a quick enable/disable: go to Visualization > Options.
- For finer control: visit the Preferences panel under Rendering > Ambient Occlusion.
You can access sliders for adjusting intensity and toggle between SSAO and OSAO depending on whether you need speed or accuracy. Not sure which to choose? Try SSAO for dynamic work and OSAO for static publication-quality visuals.
Everyday Use Cases
- Structural biology: Enhance the perception of binding pockets and channels in large protein complexes.
- Drug design: Identify regions of steric hindrance or buried functional groups more easily.
- Educational visuals: Produce clearer visualizations for slides, papers, or interactive teaching tools.
Even if you’re working with familiar molecules, enabling ambient occlusion might reveal structural nuances you hadn’t noticed before.
Try It Out
If you’ve never used ambient occlusion before, just give it a try in one of your existing documents. It’s a small visual change that can have a big impact on how easily you interpret molecular geometry.
To learn more about ambient occlusion and other rendering settings in SAMSON, visit the official SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here and explore the full platform.