One of the most common challenges molecular modelers face when visualizing complex structures is depth perception. When everything in the scene appears equally lit and flat, it becomes difficult to distinguish overlapping elements or internal cavities, reducing realism and interpretability.
This is where ambient occlusion comes in. In SAMSON, ambient occlusion (AO) is a rendering technique that improves depth perception by simulating how exposed each part of the structure is to ambient light. More occluded areas receive less light and are thus darker, helping to visually separate overlapping regions.
What Is Ambient Occlusion?
Ambient occlusion enhances realism by imitating the shading effect that occurs in crevices and tight spaces due to limited ambient light exposure. In molecular modeling, this means structural grooves, tunnels, or folds naturally appear darker, making it easier to interpret spatial relationships with the naked eye.
Two Types of Ambient Occlusion in SAMSON
- Screen-space ambient occlusion (SSAO): Fast and efficient, this method calculates occlusion based on the image currently being displayed. It’s a good default if you’re working on large systems and need real-time performance.
- Object-space ambient occlusion (OSAO): More computationally intensive, but it provides higher visual accuracy by calculating occlusion based on the actual 3D geometry of objects. Best for high-quality images or animations.
How to Use It
You can quickly enable or disable ambient occlusion via Visualization > Options. For more control, including the type of AO and its parameters, head to the Rendering > Ambient Occlusion section of the Preferences panel.
Before and After: A Quick Comparison
Let’s take a look at a protein visualized without AO:
Now, here is the same structure with screen-space ambient occlusion enabled:
Notice how the shaded cavities and overlaps provide a sharper 3D impression? Subtle shadows in complex structures make visual inspection much faster and help collaborators or students understand what they are looking at—especially in presentations or educational material.
When to Use Ambient Occlusion
- For publication-ready images: Add AO to produce cleaner and more informative figures for research papers.
- In teaching: AO helps students see folds, pockets, and interfaces more clearly in large macromolecules.
- During modeling: Enable AO temporarily while building or inspecting geometric assemblies like protein-ligand complexes to interpret their spatial organization.
While AO adds visual depth, keep in mind that it does demand some GPU resources. If you are visualizing a large system or working on an older graphics card, you may want to stick to screen-space AO or deactivate it when not needed.
To learn more about ambient occlusion and other rendering effects available in SAMSON, visit the documentation page at https://documentation.samson-connect.net/users/latest/rendering-effects/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.