When a molecular scene looks flat: three rendering changes that restore depth

A molecular scene can contain all the right structural information and still be difficult to read. Overlapping regions may seem to merge, it can be hard to tell which object sits in front of another, and fine edges can look jagged. Before changing the molecular model or hiding parts of it, try adjusting the viewport’s depth cues.

In SAMSON, ambient occlusion, shadows, and silhouettes each help with a different part of this problem. They can be switched on or off from Visualization > Options; their parameters are available in the Rendering section of Preferences. Think of them as complementary tools rather than a collection of effects to enable automatically.

Start with ambient occlusion

Ambient occlusion darkens regions that are less exposed to light. In a molecular view, that extra shading can make grooves, contacts, and closely packed parts easier to distinguish. It is a useful first adjustment when the scene feels too uniformly lit or lacks a clear sense of depth.

SAMSON provides screen-space and object-space ambient occlusion. Screen-space ambient occlusion is an efficient approximation, though its appearance can depend on the camera distance. Object-space ambient occlusion is more realistic but slower. For a quick viewport improvement, try screen-space ambient occlusion first, then inspect the result while moving or zooming the camera.

Molecular ribbons without ambient occlusion — Without ambient occlusion, depth differences may be less apparent.

Molecular ribbons with screen-space ambient occlusion — Screen-space ambient occlusion adds shading that can help reveal depth.

Use shadows to read relative positions

Shading within a molecule helps reveal its shape, but it may not be enough to show how separate objects are positioned relative to one another. Shadows can make that relationship easier to judge—for example, when a molecule is shown near a surface. If the scene still feels spatially ambiguous after adjusting ambient occlusion, try enabling shadows.

Compare the two views below: the shadow gives a clearer visual cue about the molecule’s position relative to the graphene sheet behind it. If performance is a concern, especially on an older graphics card, the documentation recommends disabling shadows or choosing a lower preset.

Molecule near a graphene sheet without shadows — Without shadows, the objects’ relative positions can be harder to perceive.

Molecule near a graphene sheet with shadows — Shadows add another cue for judging the relationship between objects.

Add silhouettes when regions still run together

Silhouettes emphasize the outlines of objects and can help separate regions at different depths. They are especially worth testing when the molecular shape is difficult to follow against nearby structure. In the example below, the Ribbons visual model of 1YRF is shown with silhouettes enabled and the thickness set to 1.

The 1YRF Ribbons visual model with silhouettes — Silhouettes make boundaries easier to follow in a complex view.

A simple adjustment order

Enable ambient occlusion if the scene lacks depth within the molecular structure.
Add shadows if you need to judge the positions of separate objects or a molecule relative to a surface.
Try silhouettes if boundaries between regions remain hard to follow.
Reassess the view after each change. Turning on every effect at once makes it harder to tell which one improved readability.

These effects change the real-time viewport appearance. For a final high-quality offline image, use SAMSON’s rendering workflow instead; for broader choices of visual models and visibility, consult the visualization guide. Explore the full Rendering effects documentation for settings and additional examples.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at www.samson-connect.net.