One of the key challenges faced by molecular modelers is effectively conveying spatial depth and structure in complex molecular scenes. Whether you’re presenting your work in a publication or simply trying to better understand a molecular structure, visual clarity can make a significant difference.
If your molecules look flat, unclear, or pieces blend together visually, ambient occlusion might be the rendering effect you’re missing. In SAMSON, ambient occlusion adds subtle shadows to regions that are less exposed to light — making grooves, channels, and internal pockets more visible. It’s an easy way to make your molecules stand out and appear more three-dimensional.
What Is Ambient Occlusion?
Ambient occlusion simulates how light behaves in concave and occluded parts of a scene. In molecular terms, this helps you distinguish which parts of a molecule are buried inside the structure versus those that are on the surface. SAMSON supports two types:
- Screen-space ambient occlusion (SSAO): A fast and efficient method that still enhances depth perception effectively. It works well for interactive work.
- Object-space ambient occlusion: A more realistic but slower method that produces excellent results for still images or final renderings.
How to Use It in SAMSON
To quickly enable or disable ambient occlusion, go to Visualization > Options. For more detailed control, open the Preferences panel and navigate to Rendering > Ambient Occlusion.
Within this panel, you can:
- Toggle SSAO or object-space ambient occlusion.
- Adjust the intensity and sampling levels to balance quality and performance.
Before and After: Why It Matters
Let’s take a vivid example. The image below shows the ribbons visual model of the molecule 1AF6 without ambient occlusion. Structures can appear visually disconnected, and subtle grooves or curves may be hard to interpret:
Now compare it to the same model with SSAO enabled. Note how the secondary structures appear more defined, and the entire scene has more visual depth:
When Should You Use It?
Consider enabling ambient occlusion when you:
- Are analyzing spatial relationships in proteins, nucleic acids, or complexes.
- Are capturing high-quality snapshots for presentations or publications.
- Need to differentiate between buried and exposed regions of a molecule.
For very large systems, screen-space ambient occlusion is preferable, as it’s much faster than the object-space method. You might choose the more accurate version when preparing figures with fine visual detail.
Final Tip
Try toggling ambient occlusion along with other rendering effects like lighting or fog to find combinations that clarify your molecular scene the most. It’s about enhancing comprehension, not just aesthetics.
To explore more rendering techniques in SAMSON, visit the complete 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.