Have you ever created a molecular visualization that felt underwhelming, despite being scientifically accurate? If your model seems flat or lacks depth, you’re not alone. One of the most common problems in molecular modeling is a lack of depth perception—making it hard to interpret complex structures at a glance.
Ambient occlusion might be the missing piece.
What is ambient occlusion?
Ambient occlusion (AO) is a rendering technique that enhances the perception of depth by simulating how light is occluded, or blocked, in the crevices and folds of molecular structures. This creates soft shadows in areas that light would naturally have difficulty reaching. In molecular visualization, this helps convey spatial relationships and complex topology far more intuitively.
Two types of AO in SAMSON
The SAMSON molecular design platform offers two AO rendering modes, each useful for different needs:
- Screen-space ambient occlusion (SSAO): This is a fast, efficient way to simulate depth. It adjusts dynamically depending on the camera position but is less physically accurate.
- Object-space ambient occlusion (OSAO): Offers more realism by computing occlusion based on the 3D positions of atoms, though it does come with higher computational cost.
Before and after: why it matters
Here’s a side-by-side comparison showing how ambient occlusion can bring clarity to your models:
Without AO:
With screen-space AO enabled:
Even with just SSAO on, the molecular model stops looking like a flat diagram and begins to feel tangible. This can help other researchers (or your future self) quickly understand spatial layouts, aiding analysis and communication.
How to enable ambient occlusion in SAMSON
Enabling AO is straightforward in SAMSON:
- To quickly turn it on/off, go to Visualization > Options.
- For finer control, open the Rendering > Ambient occlusion section in Preferences.
You can adjust intensity, radius, and quality settings to balance visual fidelity with performance. This is especially handy when working on large biomolecular structures where real-time interactivity is important.
When should you use AO?
If you’re preparing visualizations for presentations, publications, or teaching materials, enabling AO can make a surprising difference in how well your molecular models convey complex 3D arrangements. It’s especially helpful when showcasing folds in proteins, pockets in enzymes, or layered molecular assemblies.
Keep in mind that while OSAO provides more realistic results, SSAO is often good enough—and much faster—for most uses.
Bottom line
If your beautiful molecular models don’t look quite as good on screen as they do in your head, ambient occlusion might be the solution. It takes only a few clicks to enable, and the benefits in visual clarity and presentation can be substantial.
Learn more and explore other rendering effects in the official SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at www.samson-connect.net.