A molecular scene can contain all the right structural detail and still be hard to read. Ribbons overlap, nearby and distant parts blend together, and it can be difficult to judge how a molecule sits relative to another object. Before changing the model or hiding parts of it, try adjusting the viewport’s depth cues.
In SAMSON, rendering effects such as ambient occlusion, shadows, and silhouettes can make spatial relationships easier to see in real time. The useful approach is to add them deliberately: start with the effect that addresses the problem you see, then check whether the result is clearer without becoming visually distracting.
Start with ambient occlusion
Ambient occlusion darkens regions that are less exposed to light, which can help reveal depth in a molecular structure. It is a good first option when folds or closely packed regions look visually flat. Compare the same view with the effect off and on:
SAMSON provides screen-space and object-space ambient occlusion. Screen-space ambient occlusion is an efficient approximation, though its appearance is sensitive to the camera distance. Object-space ambient occlusion is more realistic but slower. If the effect seems too strong or changes as you move the camera, revisit its settings rather than assuming the structure itself is at fault.
Use shadows to judge relative position
Ambient occlusion helps describe depth within a form; shadows can help show how separate objects relate to one another. This is useful when a molecule is positioned near a surface or another structure. In the example below, shadows make the relationship between 1YRF and the graphene sheet easier to perceive.
If shadows affect performance, especially on an older graphics card, try a lower preset or turn them off. The goal is a more legible view, not using every effect at once.
Add silhouettes when regions merge
Silhouettes can help separate regions at different depths by outlining their forms. They are particularly useful when viewing a ribbon representation with overlapping parts. In SAMSON, you can switch silhouettes on or off from Visualization > Options, and adjust their settings in Preferences > Rendering > Silhouettes. A thickness of 1 is used in the documentation’s 1YRF ribbon example.
Keep edge quality separate from depth
Anti-aliasing smooths jagged edges; it does not create depth information. It can be a helpful finishing adjustment once the scene is readable. FXAA is typically efficient, and combining it with a multisampling factor of 2 is the documented “Higher quality” example. Higher-quality settings require more GPU rendering and may slow visualization for large systems. If performance becomes an issue, reduce anti-aliasing before concluding that the scene needs a different visual model.
A quick order of operations
- Find the problem: Is the structure itself flat-looking, are separate objects hard to position, or are overlapping regions difficult to separate?
- Choose one cue: Try ambient occlusion for depth shading, shadows for relative positions, or silhouettes for separating regions.
- Compare the same view: Toggle the effect in Visualization > Options and check whether it improves readability.
- Check performance and camera behavior: Adjust the relevant settings in the Rendering section of Preferences, and keep in mind that screen-space ambient occlusion depends on camera distance.
- Polish edges last: Add anti-aliasing if jagged boundaries are distracting, while considering the GPU cost.
These effects change how the viewport communicates the scene; they do not change the molecular model. For interactive appearance controls and their settings, see the SAMSON rendering effects documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at samson-connect.net.