One common challenge in molecular modeling is distinguishing structural depth in complex representations. When working with multi-layered biomolecular assemblies or detailed ligand-protein interactions, the visual flatness of the scene can make it hard to interpret spatial relationships.
Luckily, SAMSON offers a way to address this: ambient occlusion—a simple but effective rendering option that dramatically enhances the perception of spatial structure in molecular scenes.
Why Depth Perception Matters
Visual cues in 3D molecular models help researchers validate docking results, communicate findings to collaborators, and prepare publication-ready graphics. Without depth cues, key interaction sites might get visually lost or misinterpreted.
Introducing Ambient Occlusion
Ambient occlusion (AO) simulates how light behaves in reality—darkening crevices and shaded regions where light is naturally less likely to reach. In SAMSON, this results in a more natural and interpretable rendering of molecular surfaces and assemblies.
Two AO Modes in SAMSON
- Screen-space ambient occlusion (SSAO): Fast and resource-efficient. It provides a good sense of depth by approximating occlusion from 2D screen-space information. However, it can vary depending on the camera distance.
- Object-space ambient occlusion (OSAO): More realistic and stable, but also more computationally expensive. Ideal for high-quality static renderings such as figures for presentations or publications.
How to Enable Ambient Occlusion in SAMSON
To access AO settings, open the Preferences panel by navigating to Interface > Preferences from the menu or press Ctrl + K on Windows/Linux or Cmd + , on macOS.
Then, go to Rendering > Ambient occlusion. You’ll see the following panel:
From here, you can:
- Enable or disable AO
- Choose between screen-space and object-space AO
- Fine-tune intensity and radius parameters
When to Use Each Mode
Use SSAO when you’re working interactively and need fast feedback, such as during model building or ligand fitting. It’s light on system resources and updates in real-time as you manipulate molecules.
Use OSAO when preparing high-resolution images, especially if the final output will be used in publications, slides, or promotional materials. The added visual fidelity can make molecules appear more three-dimensional and polished.
Tips for Better Visualization
- Combine ambient occlusion with bloom or depth of field for cinematic effect.
- Adjust light direction in the Rendering > Lighting panel for more control over shading.
- Blend with transparent backgrounds in PNG format under Interface > Captures when exporting images.
Ambient occlusion is a subtle but powerful tool that helps reveal relationships between atoms, residues, and domains just by improving graphical fidelity. Even a simple toggle can significantly enhance how your models are perceived—by you and others.
For more information on ambient occlusion and other rendering settings, visit the full documentation at SAMSON Preferences Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.