Understanding the three-dimensional structure of molecules is critical in molecular modeling and design. However, even with powerful visualization tools, complex molecular models can sometimes feel surprisingly flat on screen. This visual ambiguity hinders structural interpretation, especially in densely packed biomolecular systems.
Enter ambient occlusion, a rendering effect available in SAMSON that helps bring clarity to molecular depth. By simulating how ambient light is naturally blocked in the crevices and inner parts of molecular structures, ambient occlusion makes it easier to distinguish concave regions and understand spatial arrangements at a glance.
What is Ambient Occlusion?
Ambient occlusion (AO) mimics the way light subtly darkens areas that are less exposed, such as the interior of protein folds or pockets in molecular surfaces. Rather than casting harsh shadows, AO darkens regions affected by geometry itself — enhancing depth perception without overwhelming the molecular view.
Two Types of AO in SAMSON
- Screen-space ambient occlusion (SSAO): Fast and efficient, this method adjusts based on the camera’s viewpoint, delivering immediate, dynamic depth cues.
- Object-space ambient occlusion (OSAO): More accurate but computationally heavier, this method provides a refined approximation of light access across surfaces regardless of camera position.
Why It Matters for Molecular Modelers
Visualizing molecular shapes and interactions often requires distinguishing between overlapping chains, side chains, or ligand binding pockets. When ambient occlusion is disabled, molecules can appear like a flat amalgam of atoms and bonds. With AO enabled, the same molecule reveals structural details more clearly – a huge benefit when analyzing enzyme active sites, docking poses, or crowded molecular environments.
How to Enable Ambient Occlusion in SAMSON
Enabling AO in SAMSON takes just one click in the Visualization > Options menu. For deeper customization, navigate to the Rendering > Ambient occlusion section in the Preferences panel. There, you can select between SSAO and OSAO and fine-tune parameters like radius and intensity to match your visualization needs.
See the difference yourself:
Without ambient occlusion (notice how everything blends together):
With screen-space ambient occlusion enabled (depth subtly revealed):
Even though SSAO is an approximation, it significantly improves model readability–and rarely introduces performance issues on modern GPUs. If you’re preparing graphics for publications or presentations, enabling ambient occlusion alone can make your images stand out with minimal effort.
Tips
- If real-time rendering speed matters, start with SSAO.
- For high-quality exports, consider switching to OSAO before saving images.
- Use ambient occlusion in combination with other effects like shadows or depth of field for even richer visual clarity.
To learn more about rendering effects in SAMSON, visit the 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 SAMSON here.