A molecular scene can contain all the right structural information and still be difficult to read. Overlapping components may seem to occupy the same space, a protein can blend into a surface behind it, or the edges of a model can disappear against the background. These are common viewport problems—not necessarily problems with the molecule itself.
In SAMSON, a few real-time rendering effects can add useful depth cues. Rather than turning everything on at once, it helps to know what each effect contributes and choose the smallest combination that answers the visual question you have.
Start with ambient occlusion
Ambient occlusion darkens regions that are less exposed to light, helping the eye read indentations and nearby structural features as depth. It is often a good first adjustment when a molecular model looks flat or crowded.
SAMSON offers screen-space and object-space ambient occlusion. Screen-space ambient occlusion is efficient, 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; if the result changes noticeably as you move the camera, keep that camera sensitivity in mind.
You can toggle screen-space ambient occlusion from Visualization > Options. For more control, find its parameters under Rendering > Ambient occlusion in Preferences.
Use shadows to clarify relative position
Ambient occlusion helps define local depth, but it may not be enough to show how separate objects sit relative to one another. Shadows provide another cue. They can make it easier to distinguish a molecule from a sheet or other structure behind it.
Compare the scene with shadows off and on, especially when two objects overlap in the view. If the shadow makes the scene easier to interpret, keep it; if it adds visual clutter or slows a large scene, try a lower preset or disable it. Older graphics cards may benefit from a lower preset.
Shadows can be toggled in Visualization > Options, with additional settings under Rendering > Shadows in Preferences.
Add silhouettes when boundaries are hard to follow
Silhouettes can help separate regions at different depths by making their outlines easier to see. They are especially useful when a ribbon model’s shape is difficult to trace through overlapping parts. Enable them from Visualization > Options, then adjust their settings in Rendering > Silhouettes. A thickness of 1 is the example used for the 1YRF ribbon model in the documentation.
A practical order for tuning the view
- Identify the problem. Is the scene flat, are object positions unclear, or are boundaries difficult to trace?
- Choose one matching cue. Try ambient occlusion for local depth, shadows for relationships between objects, or silhouettes for clearer outlines.
- Check the result from your working camera angle. In particular, screen-space ambient occlusion can be sensitive to camera distance.
- Consider performance. If a large system becomes slower, reduce or disable effects that are not helping your current task.
- Adjust the background if needed. A contrasting background can make the scene easier to read; SAMSON offers default, black, white, custom-gradient, and image backgrounds in its Rendering preferences.
The aim is not to make the viewport look more dramatic. It is to make the structural relationships you need to inspect easier to see. For final-quality offline rendering, use the separate rendering workflow; these effects are for interactive viewport appearance.
For more details and additional effects, including anti-aliasing, lighting, fog, and depth of field, see the SAMSON rendering effects documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.