One of the biggest challenges in molecular modeling is accurately perceiving spatial relationships between atoms and structures, especially in complex biomolecules. When depth perception is poor, it’s easy to misinterpret interactions, miss structural features, or create visualizations that are unclear to colleagues and collaborators.
Fortunately, SAMSON offers a rendering effect that directly tackles this issue: ambient occlusion. If you’re creating figures for a paper, building presentations, or simply trying to better understand your system, ambient occlusion can make a big difference in how your models are perceived.
What is Ambient Occlusion?
Ambient occlusion simulates the way light interacts with crevices and occlusions, making deeper or hidden areas appear darker. This provides subtle, realistic shading, helping your eye intuitively perceive depth and proximity.
In SAMSON, you can choose between two types of ambient occlusion:
- Screen-space ambient occlusion (SSAO): Fast and efficient, this method approximates occlusion based on the current camera view. It’s suitable for interactive use and provides immediate improvement in depth perception.
- Object-space ambient occlusion: More accurate and consistent across views, this method is slower but more realistic, making it ideal for high-quality visualizations or final renders.
You can enable or disable ambient occlusion in one click with Visualization > Options, or change parameters for finer control in Preferences > Rendering > Ambient occlusion.
Comparing With and Without Ambient Occlusion
Here’s a Ribbons visual representation of the 1AF6 protein. The first image shows the model without ambient occlusion; everything appears equally lit, making depth harder to judge:
Now here it is with screen-space ambient occlusion enabled. Notice how pockets and overlapping strands become much easier to distinguish:
When Should You Use It?
If you’re:
- Building complex visual scenes with overlapping structures
- Preparing educational materials that need clarity
- Collaborating with non-experts who may not intuitively read 3D representations
- Working with models where fine structural detail matters
…then ambient occlusion is worth turning on. And since SSAO is efficient even on modest hardware, you can likely use it interactively.
How to Enable or Customize Ambient Occlusion
To get started quickly, just go to Visualization > Options and toggle ambient occlusion on or off. For more detailed tuning (such as intensity, radius, or number of samples), use the Preferences panel under Rendering > Ambient occlusion:
Not sure what settings work best? Start with SSAO for interactivity. For final renders or volumetric scenes, test object-space ambient occlusion.
Learn more about ambient occlusion and other rendering options in the SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.