A molecular scene can contain all the right structural information and still be hard to read. Ribbons overlap, distant parts blend into the background, and it may be difficult to tell which object sits in front of another. The problem is often not the model itself, but the visual cues used to interpret depth.
In SAMSON, a useful starting point is to add depth cues gradually. Ambient occlusion can bring out recessed regions, while shadows help distinguish relative positions. Silhouettes can make regions at different depths easier to separate. These effects are designed for the real-time viewport, so you can assess the result as you work.
Start with ambient occlusion
Ambient occlusion darkens regions that are less exposed to light. In a molecular scene, this can make folds and overlaps easier to perceive without changing the structure or visual model. Compare the same view with the effect off and on:
For a quick test, toggle screen-space ambient occlusion from Visualization > Options. Its settings are in Preferences > Rendering > Ambient occlusion. Screen-space ambient occlusion is efficient, but its appearance is sensitive to camera distance. If the shading changes noticeably as you zoom, that is a characteristic of this method, not necessarily a change in the molecule.
SAMSON also supports object-space ambient occlusion. It is more realistic, but slower. For interactive work, try the screen-space option first; consider the slower method when its appearance better suits the view you need.
Use shadows to clarify positions
Ambient occlusion helps describe local depth, but it may not be enough when you need to understand how separate objects are positioned relative to one another. Shadows can make those spatial relationships easier to read. In the example below, the protein is shown in relation to the graphene sheet behind it.
Toggle shadows in Visualization > Options, or adjust them in Preferences > Rendering > Shadows. If your graphics card is older, the documentation recommends disabling shadows or choosing a lower preset. This is a useful tradeoff: a clear interactive view is more helpful than an effect that makes the viewport slow to use.
Add outlines when regions still merge
Silhouettes can help separate regions with different depths. They are particularly worth testing when the molecular form is difficult to distinguish against itself or the background. Enable them from Visualization > Options, then adjust their settings under Preferences > Rendering > Silhouettes. The documentation’s example uses the Ribbons visual model for molecule 1YRF with silhouette thickness set to 1.
A practical order is to enable one effect at a time: first ambient occlusion for surface depth, then shadows for relationships between objects, and finally silhouettes if boundaries still need definition. Recheck the scene after changing the camera distance, since screen-space ambient occlusion is camera-sensitive. If an effect makes the view less readable, turn it back off; more effects do not automatically mean a clearer scientific image.
These controls affect the real-time viewport. For final-quality offline rendering, use the separate Rendering using Cycles guide. For the complete overview of viewport effects and their settings, see the SAMSON rendering effects documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.