A molecular scene can contain all the right atoms and bonds and still be difficult to read. Without clear depth cues, it may be hard to tell which parts are nearer, how structures sit relative to one another, or where a ligand lies in a pocket. The model has not changed—but the view may be making its spatial relationships harder to see.
In SAMSON, two useful rendering controls for this problem are ambient occlusion and shadows. They can help clarify depth without changing the molecular structure. You can find both under Preferences > Rendering. Open Preferences from Interface > Preferences, or use Ctrl+K on Windows and Linux or Cmd+, on Mac. If Automatically test is enabled, preference changes immediately affect the interface and rendering, making it easier to compare the result as you adjust settings.
Start with ambient occlusion
Ambient occlusion makes deeper or less accessible regions darker, which can help the eye read the shape of a molecule. SAMSON offers two types:
- Screen-space ambient occlusion is an efficient approximation, but its appearance is sensitive to the distance from the camera.
- Object-space ambient occlusion is more realistic, but slower.
A practical way to evaluate the effect is to use the same view while you compare settings. Look at regions where atoms or structural elements overlap, and check whether the added shading makes their arrangement easier to interpret. Then zoom in and out: because screen-space ambient occlusion depends on camera distance, a setting that reads well in a close-up may look different in a wider view. If the shading distracts from the structure, reduce or disable it rather than treating stronger contrast as automatically better.
Add shadows when relative positions are unclear
Shadows can provide another cue about relative positions. They are particularly useful when a view feels visually flat and it is difficult to distinguish how parts of the scene relate in space. The controls are in Preferences > Rendering > Shadows.
Rendering effects can have a performance cost, especially on older graphics cards. If the scene becomes less responsive, try disabling shadows or choosing the lower preset. The aim is not to turn on every effect; it is to keep the structural relationships legible while maintaining a comfortable working view.
Make the background support the structure
Depth cues are easier to assess when the background does not compete with the model. In Preferences > Rendering > Background, you can choose the default SAMSON background, black, white, or a custom gradient made from user-defined top and bottom colors.
Try a different background if the molecule’s colors or outlines blend into the current one. For a custom gradient, consider whether the change in color across the viewport makes the scene clearer or introduces extra visual distraction. Compare the same molecular view before and after changing it.
A quick troubleshooting sequence
- Choose a representative view of the structural feature that is hard to read.
- Adjust ambient occlusion and check the view at more than one zoom level.
- Test shadows if relative positions still feel ambiguous; reduce or disable them if performance suffers.
- Try a different background if the structure lacks contrast.
- Keep the effect settings that make the spatial relationships clearer without obscuring the molecular details.
These controls change how the scene is presented, not the underlying molecular model. That makes them useful to revisit as you move between close-up inspection, broader context, and visual preparation.
For the full list of preference categories and settings, see the SAMSON Preferences documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.