A molecular scene can contain all the right structures and still be hard to read. When molecules overlap, it may be difficult to tell which parts are closer, where one region ends, or how a structure sits relative to a surface. The answer is not always to change the molecular representation. Often, a few real-time rendering effects can make the existing view easier to interpret.
In SAMSON, ambient occlusion, shadows, and silhouettes each add a different kind of depth cue. They are useful for different reasons, so it helps to treat them as separate tools rather than turning on every effect at once.
Start with ambient occlusion for depth
Ambient occlusion darkens regions that are less accessible to light. In a molecular view, this can make grooves, contacts, and areas between nearby parts appear more spatially defined. It is often a good first adjustment when a structure looks visually flat.
SAMSON provides screen-space and object-space ambient occlusion. Screen-space ambient occlusion is efficient, though its appearance is sensitive to camera distance. Object-space ambient occlusion is more realistic but slower. You can switch screen-space ambient occlusion on or off from Visualization > Options, or adjust ambient occlusion settings under Preferences > Rendering > Ambient occlusion.
Add shadows to clarify relative positions
Ambient shading helps reveal form; shadows help you judge where objects sit in relation to one another. This matters when a molecule is positioned near a surface or another structure. Without shadows, the gap or overlap between the objects may be difficult to read. Enabling shadows can make their relative positions clearer.
Try comparing the same view with shadows off and on before adjusting other settings. The shadows control is available in Visualization > Options; more detailed settings are in Preferences > Rendering > Shadows. If you are using an older graphics card, the documentation recommends disabling shadows or choosing a lower preset.
Use silhouettes to separate regions
When neighboring parts of a structure blend together, silhouettes can help distinguish regions at different depths. They add outlines that make boundaries easier to follow, particularly in a ribbon representation. You can toggle silhouettes through Visualization > Options and adjust their settings under Preferences > Rendering > Silhouettes.
A useful way to evaluate silhouettes is to start with the thickness set to 1, as in the documented 1YRF example. Check whether the outlines clarify boundaries without distracting from the molecular structure.
A simple way to tune the view
- Choose a representative camera angle. Effects can look different as the view changes, so assess them on the scene you need to understand.
- Toggle one effect at a time. Compare ambient occlusion, shadows, and silhouettes separately to see which cue addresses the problem.
- Keep the useful effects. If an effect makes the structure harder to read, switch it off or adjust its settings rather than adding more effects.
- Check performance. Rendering settings can affect responsiveness. Anti-aliasing, for example, uses more GPU rendering and may slow visualization for large systems.
These effects are for improving the interactive viewport. For final-quality offline rendering, use the SAMSON rendering guide. For the full explanation of real-time rendering effects, learn more in the documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.