One common challenge in molecular modeling is distinguishing molecular features in dense or complex structures. When visualizing intricate biomolecular environments, depth perception becomes crucial to avoid misinterpretation — especially when analyzing binding interfaces, cavities, or packed atom regions.
That’s where Ambient Occlusion in SAMSON comes in. This rendering option simulates how light behaves in occluded (less exposed) spaces, giving you a better sense of shape and depth — helping your eyes parse the 3D structure more effectively.
What Is Ambient Occlusion?
Ambient occlusion is a shading technique that darkens enclosed or obstructed areas, mimicking the way light struggles to reach certain regions. In SAMSON, this can make it much easier to understand spatial arrangements by giving a more realistic sense of where structures protrude or recede.
When enabled, deeper crevices in the molecule look slightly darker, and protrusions appear naturally more lit. This depth cue is particularly useful for static imagery, publication figures, or presentations where clarity matters.
Two Types of Ambient Occlusion in SAMSON
- Screen-space ambient occlusion (SSAO): Fast and approximate. This option is based on what’s visible on the screen and is camera-dependent. It’s great for real-time exploration, with minimal performance cost.
- Object-space ambient occlusion (OSAO): More accurate, and based on object geometry, not screen. This creates consistent depth shading regardless of camera angle, but can be slower — ideal when creating high-quality visuals.
Even the faster, screen-space version can make a huge difference in clarity:
How to Enable Ambient Occlusion
To modify this setting:
- Open the Preferences panel by navigating to Interface > Preferences or pressing Ctrl + K (or Cmd + , on Mac).
- Go to the Rendering > Ambient Occlusion section.
- Select the desired type of occlusion and fine-tune any available parameters.
When to Use It
- During molecular inspection: Enhance your structure exploration by enabling SSAO and better detecting overlaps or embedded groups.
- For high-quality exports: Switch to OSAO when preparing visuals for papers or posters — it’s slower but generates cleaner, publication-quality images.
- In presentations: Help audiences follow your explanations more easily by enabling occlusion-based depth shading that adds natural contrast and depth.
There’s no one-size-fits-all: try both options and see what fits your workflow best. Remember that ambient occlusion is just one of many rendering tools in SAMSON that can improve not just how things look, but how effectively you can work with them visually.
To explore the full range of rendering and visual customization settings in SAMSON, head to the official Preferences documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.