When working with molecular models, it’s often challenging to judge depth and spatial relationships at a glance. Molecules can appear flat and unrealistic, especially when rendered without lighting enhancements. This is a common struggle for molecular modelers who want to create clear, visually appealing images for research, presentations, or publications.
One simple yet powerful visual enhancement in SAMSON is ambient occlusion. It’s a rendering technique that simulates the way light behaves in crevices and enclosed spaces, making those areas appear darker. This effect helps to enhance your perception of depth and gives your molecule a more tangible 3D appearance.
How ambient occlusion works
In real life, light doesn’t reach every part of an object equally—some parts are naturally more occluded and appear darker. Ambient occlusion mimics this principle in graphics rendering.
SAMSON supports two types of ambient occlusion:
- Screen-space ambient occlusion (SSAO): Fast and approximate. It works based on what is visible on the screen, which makes it efficient but dependent on the camera view.
- Object-space ambient occlusion (OSAO): More physically realistic and consistent under camera movement, but requires more computation.
Before and after: the visual impact
Let’s look at a real example: the protein 1AF6 represented using the Ribbons visual model.
Without ambient occlusion:
With screen-space ambient occlusion:
The difference is immediate: depth clues are more prominent, and the structural curvature is easier to perceive. This can be especially useful when trying to highlight complex regions in protein folds or when comparing overlapping structures.
Tweaking parameters in SAMSON
You can enable and control ambient occlusion in two places:
- Quick toggle: Go to Visualization > Options to effortlessly switch ambient occlusion on or off or apply presets.
- Detailed control: For fine tuning, open the Preferences panel and navigate to Rendering > Ambient Occlusion.
This interface allows you to switch between screen-space and object-space ambient occlusion, adjust intensity, and control sampling rates. Try increasing the strength for more dramatic shadows or experimenting with AO radius to manage how far the effect reaches.
When to use it
Ambient occlusion can make a big difference when creating visuals for publications, educational materials, or molecular animations. It’s particularly helpful when working with dense structures or when clarity is critical, such as in ligand-binding site visualizations. Keep in mind that enabling ambient occlusion may slightly increase rendering load—especially OSAO—so consider your system’s capabilities.
To learn more about ambient occlusion and other rendering effects in SAMSON, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.