One of the common frustrations in molecular modeling is the difficulty of understanding the 3D structure of large biomolecules on a 2D screen. Structures can appear flat or confusing, and subtle spatial relationships might get lost, especially when visualizing complex protein folds or molecular assemblies. If you’ve ever had trouble distinguishing which parts of your structure are in front or behind, you’re not alone.
Ambient occlusion is a rendering effect designed to enhance visual depth, by simulating the way light behaves in real-world environments. In short, it makes recessed regions darker because they receive less light—just like in real life. This subtle shading helps convey 3D structure more effectively, allowing clearer perception of folds, cavities, and spatial arrangements.
In SAMSON, ambient occlusion comes in two main flavors:
- Screen-space ambient occlusion (SSAO): Fast and efficient, this method approximates occlusion based on what is visible on the screen. Ideal for interactive modeling, it offers a good balance between visual clarity and performance.
- Object-space ambient occlusion: More realistic and physically accurate, this method actually considers the geometry of objects in 3D space. It requires more computational power but produces more detailed shadows and depth.
You can quickly toggle SSAO in Visualization > Options, or adjust more advanced parameters in the Preferences > Rendering > Ambient Occlusion panel, such as intensity, radius, and bias.
Let’s look at a concrete example. Below is a visualization of the 1AF6 protein using the Ribbons model. First, the rendering without ambient occlusion:
And this is the same model with SSAO enabled:
The difference is subtle but meaningful. Shadows appear in crevices and between overlapping ribbons. The protein feels more three-dimensional, more tangible. This improvement can help not just with aesthetics, but also with practical understanding of molecular structures—whether you’re analyzing a binding site or preparing publication-quality visuals.
For users with powerful systems or for rendering high-resolution images, switching to object-space ambient occlusion can produce photorealistic results. But even SSAO—enabled with one click—makes a big difference in daily modeling work.
To adjust ambient occlusion settings:
- Go to Interface > Preferences > Rendering > Ambient Occlusion.
- Tune intensity, radius, and other parameters for desired depth effect.
- Use the Automatically test checkbox to preview changes instantly.
Ambient occlusion is one of several rendering effects in SAMSON designed to improve usability for molecular modelers. Whether you’re exploring structures interactively or producing visuals for a presentation or article, it is worth enabling.
To learn more about rendering effects in SAMSON, visit the original documentation page: https://documentation.samson-connect.net/users/latest/rendering-effects/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download and install SAMSON at https://www.samson-connect.net