A molecular model can be structurally correct and still be difficult to read on screen. Atoms may blend together, depth can be hard to judge, and selection outlines or visual effects may feel distracting—or slow on an older graphics card. Instead of changing the model, start by tuning how SAMSON presents it.
Open Interface > Preferences, or use Ctrl+K on Windows and Linux or Cmd+, on Mac. Preferences are grouped into categories, and the search box can help you find a setting quickly. If Automatically test is checked, changes take effect immediately, making it easier to compare the view as you adjust it.
Start with depth cues
When a structure looks flat, ambient occlusion is a useful setting to investigate. It simulates the way deeper, less accessible regions receive less light, making them appear darker and helping convey depth. SAMSON offers two types: screen-space ambient occlusion is an efficient approximation but is sensitive to camera distance; object-space ambient occlusion is more realistic but slower. Try the efficient option first, then consider the slower one if you need a more realistic appearance and your system handles it comfortably.
Shadows can also help reveal the relative positions of objects. If spatial relationships are difficult to perceive, try enabling shadows and compare the result. On an older graphics card, the documentation recommends disabling shadows or choosing a lower preset if performance is a concern.
Silhouettes are another option when neighboring regions are hard to distinguish. They help separate regions with different depths and can make structures more clearly delineated. These effects serve different purposes: ambient occlusion adds shading cues, shadows help communicate relative position, and silhouettes define boundaries. Test them one at a time so you can see which improves the view you are working with.
Make the view easier to interpret
The viewport background affects contrast. In Rendering > Background, you can choose the default SAMSON background, black, white, or a custom gradient with separate top and bottom colors. If a structure or its labels are difficult to distinguish, try another background and check whether the important features become easier to see.
Lighting preferences let you adjust the two point lights and global lighting parameters. Each light has a color, intensity, specular intensity, specular power, and position controlled by longitude and latitude. Specular intensity affects the strength of surface reflections: higher values can make surfaces look more plastic, while lower values make them look more matte. If reflections compete with the structure’s details, adjusting this parameter may help. The first light is typically the main light, and the second is typically a back light.
For selection-related visual clutter, check Rendering > Selection. You can set selection color and opacity, and choose whether to show the selection box. The highlighting color indicates the node under the pointer, helping you anticipate what will be selected. The outline color applies to highlighted or selected nodes. If outlines cause lag on an older graphics card, the documentation notes that setting outline opacity to zero can improve graphics performance.
A simple adjustment routine
- Open Preferences and locate the relevant rendering setting; keep Automatically test enabled if you want changes to appear immediately.
- Change one setting at a time, such as ambient occlusion, shadows, or silhouettes.
- Check both readability and responsiveness, especially after enabling effects that may be slower.
- Adjust the background or selection appearance if contrast or highlighting is distracting.
- Keep the combination that makes the molecular features you care about easiest to inspect.
This approach avoids treating visual effects as a one-size-fits-all preset. The clearest view depends on the structure, the camera position, and the available graphics hardware. 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.