One of the most common challenges molecular modelers face is making molecular structures easy to interpret visually. When complex molecular systems are densely packed or intricately folded, it’s often hard to distinguish between overlapping parts or to perceive depth clearly.
If you’re struggling to make your molecular visualizations intuitive and easier to navigate—or to prepare visuals for presentations—there’s a simple effect in SAMSON that can help: Ambient Occlusion.
What Is Ambient Occlusion?
Ambient occlusion (AO) simulates how light interacts with space in a 3D environment. Specifically, it darkens areas that are less exposed to ambient light—like crevices, pockets, or parts of the structure hidden behind others. The result is a subtle shading effect that gives depth cues, improving the perception of 3D structure in molecular models.
In SAMSON, you can choose between two AO methods:
- Screen-space ambient occlusion (SSAO): Fast and efficient; depends on camera distance.
- Object-space ambient occlusion: More realistic but computationally heavier.
Why It Matters for Molecular Modeling
Visualizing molecules in 3D is essential to understand their structure-function relationships, interactions, and spatial arrangements. But without ambient occlusion, the models can appear flat—even unrealistic—making it hard to differentiate between foreground and background elements.
With ambient occlusion enabled, you immediately notice an improvement in depth perception. This can reduce cognitive load during analysis and make your figures more effective, whether for publication, teaching, or documentation.
Before and After: A Visual Example
Below is the Ribbons visual model of the 1AF6 molecule:
Without ambient occlusion:
With screen-space ambient occlusion enabled:
Notice how the enabled AO darkens regions that are tucked away or shielded from ambient light. This helps separate structural layers and makes the molecule feel more 3D.
How to Enable It in SAMSON
You can enable screen-space ambient occlusion quickly through:
- Visualization > Options — One-click access to switch it on/off.
For more precise control (e.g., strength, radius):
- Open Preferences from the main menu.
- Go to Rendering > Ambient Occlusion.
You can adjust parameters like sampling rate and strength to fit your system and GPU. If you’re visualizing large complexes or dynamics, balancing quality and performance may be necessary.
Tip:
Even if your system can’t handle object-space ambient occlusion efficiently, screen-space AO provides a significant improvement with minimal performance cost.
Ambient occlusion might seem like a minor visual tweak, but for molecular modelers, it’s a powerful tool to bring out the structure in complex systems—quickly, effectively, and without post-processing.
To explore more rendering options like bloom, depth of field, fog, or shadows, visit the full documentation here: https://documentation.samson-connect.net/users/latest/rendering-effects/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.