One of the first challenges molecular modelers face when visualizing large and complex structures is how to make spatial relationships clear. Proteins overlap, structures twist around each other, and it’s easy to lose depth perception. A flat-looking model might look aesthetically clean—but it can be confusing when you’re trying to untangle the 3D architecture of a molecule.
That’s where Ambient Occlusion can help. This rendering technique simulates how light interacts with cavities and enclosed spaces, making deeper regions appear darker. In other words, it visually approximates how light reaches (or doesn’t reach) different parts of a model, increasing the depth perception without changing the model itself.
Types of Ambient Occlusion in SAMSON
SAMSON provides two techniques for using ambient occlusion:
- Screen-space ambient occlusion (SSAO): This is a faster technique that estimates depth based on what’s visible on screen. It’s lightweight and very helpful for quick interactive work, although it depends on the camera angle.
- Object-space ambient occlusion (OSAO): This approach computes occlusion based on the geometry of the object itself, giving more accurate results but requiring more computational effort.
Even the simpler screen-space ambient occlusion can make a noticeable difference. Compare the following two images:
Without ambient occlusion:
With screen-space ambient occlusion enabled:
Notice how the second image adds a sense of depth—loops fold into themselves, and different structural layers become easier to distinguish.
How to Enable and Adjust Ambient Occlusion
You can activate ambient occlusion in two ways in SAMSON:
- For immediate toggling: use the Visualization > Options menu.
- For fine-tuning: go to Preferences > Rendering > Ambient Occlusion.
In the Preferences panel, you can:
- Enable/disable SSAO or OSAO.
- Adjust the occlusion strength or blend parameters.
- Choose presets suited for performance or quality, depending on your GPU’s capabilities.
When to Use It
Ambient occlusion is especially useful when:
- Preparing figures for publication or reports.
- Presenting complex structural data in meetings or lectures.
- Inspecting deeply embedded binding sites or cavities where lighting plays a role in visibility.
It adds clarity, subtly enhancing shapes without overwhelming the visual appearance or introducing distracting effects.
Performance Tips
Since ambient occlusion affects lighting calculation, performance may vary based on the model size and graphics card. If you’re working on a very large system, try using only screen-space ambient occlusion with optimized presets to maintain interactivity.
Want to learn more settings and tweaks? Take a look at the complete rendering guide in the SAMSON documentation: Rendering Effects Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at samson-connect.net.