Visual clarity is one of the most common challenges in molecular modeling. When molecules are complex and tightly packed, depth perception often becomes difficult — making interpretation, communication, and publishing harder than it should be.
If you’ve ever struggled to distinguish between overlapping or nested regions of a biomolecule, SAMSON’s ambient occlusion feature might be exactly what you’re looking for.
What is Ambient Occlusion?
Ambient occlusion is a rendering technique that simulates how light interacts with surfaces — specifically, how areas that are tucked away from light (like gaps and folds) appear darker. This adds realistic shading that helps the human eye better perceive depth and spatial relationships.
Why It Matters in Molecular Modeling
In structural biology or nanomedicine, details matter. Seeing where certain residues are located, or identifying pockets in a protein structure, can hinge on subtle visual cues. Ambient occlusion helps enhance those cues without manually adjusting the model’s geometry or camera repeatedly.
Two Types of Ambient Occlusion in SAMSON
- Screen-space ambient occlusion (SSAO): Very efficient and ideal for real-time work. It reacts to camera motion, which makes it responsive in interactive sessions.
- Object-space ambient occlusion (OSAO): More realistic and less dependent on the camera. It’s slower but often better for high-quality exports and presentation images.
How to Enable It
You can turn ambient occlusion on or off through Visualization > Options for a quick toggle. For detailed tweaking, head to:
Interface > Preferences > Rendering > Ambient Occlusion
There, you can select the algorithm (SSAO or OSAO), configure its resolution, strength, and bias.
Seeing the Difference
Take a look at this example using the Ribbons visual model of 1AF6. The first image here shows the model without ambient occlusion:
Now, look at the same structure with SSAO enabled. Notice how the grooves and folds in the protein structure become much clearer:
Tips for Better Results
- Use ambient occlusion alongside depth of field and lighting presets for presentations or publication-quality renders.
- Switch to OSAO when preparing high-quality still images or animations.
- Don’t forget GPU resources: turning on multiple effects simultaneously on large systems might slow down rendering on older hardware.
Even small enhancements in rendering can significantly improve collaboration, teaching, or publication clarity. If you regularly visualize molecular structures, ambient occlusion is a subtle but impactful tool to keep in your visualization toolkit.
To learn more about ambient occlusion and other rendering effects in SAMSON, you can visit the full documentation page here: https://documentation.samson-connect.net/users/latest/rendering-effects/.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.