Communicating molecular structures effectively isn’t just about showing atoms and bonds — it’s about delivering clarity. For molecular modelers, one persistent challenge is depth perception: distinguishing foreground and background parts in complex 3D structures. If you’ve ever struggled with interpreting or presenting a dense protein or molecule visualization, you already know how important depth cues are.
This is where Ambient Occlusion in SAMSON can make a difference. Ambient occlusion is a rendering technique that simulates how light is blocked by surrounding geometry, making deeper regions appear darker. The result? A visual cue that immediately enhances your perception of structure depth.
Two Options for Different Situations
SAMSON offers two types of ambient occlusion, each suitable for different needs:
- Screen-space Ambient Occlusion (SSAO): Fast and efficient, SSAO is great for real-time adjustments. The effect varies slightly with the camera’s distance but greatly improves depth perception even on large systems.
- Object-space Ambient Occlusion: This provides a more realistic shadowing effect but is computationally more intensive. Use it when quality trumps speed — for example, in final rendering or publication figures.
Here’s a visual comparison using the Ribbon representation of the 1AF6 molecule. First, without any ambient occlusion:
Now, with screen-space ambient occlusion turned on:
Notice how the added shadows give structure to the protein, helping the viewer immediately identify folds and cavities? This small adjustment makes a big impact in both exploratory modeling and clear presentations.
How to Enable It
There are two simple ways to start using ambient occlusion in SAMSON:
- For fast toggling, go to Visualization > Options and switch it on or off instantly.
- For deeper customization, head to Preferences > Rendering > Ambient Occlusion. Here you can tweak the strength, radius, and other parameters to suit your visualization style.
When Should You Use It?
Ambient occlusion is incredibly helpful in situations where:
- You’re building presentations or figures that need to be visually digestible at a glance
- You’re trying to make clear distinctions between nested structures, binding pockets, or molecular surfaces
- Your model is complex and hard to read without added depth
Even for standard structure exploration, enabling SSAO while you work can change how you perceive your model — catching details that are often lost in flatter renderings.
To summarize, ambient occlusion is a small switch with a big payoff. If you’ve been manually adjusting lighting or struggling to “see” shapes properly in your molecular models, take a minute to try this feature in SAMSON. It might just become a default in your workflow.
To learn more about all rendering effects available in SAMSON, 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 download SAMSON at https://www.samson-connect.net