A molecular scene can contain all the right structural information and still be hard to read. Atoms overlap, depth is unclear, or selection highlights compete with the model. Turning on every visual effect may seem like the solution—but some effects cost rendering performance, and others can make a view harder to interpret. A better approach is to adjust the settings in a deliberate order, checking what each change adds.
In SAMSON, the relevant controls are grouped under Preferences > Rendering. Open Preferences from Interface > Preferences, or use Ctrl+K on Windows and Linux, or Cmd+, on Mac. If Automatically test is checked, preference changes immediately affect the interface and rendering, making it easier to compare settings as you work.
Start with cues that reveal depth
Ambient occlusion darkens regions that are less exposed to light, helping show how parts of a molecule sit relative to one another. SAMSON offers 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. Try the efficient option first when you want a quick improvement, and assess the result from the camera distances you actually use.
Shadows can also help communicate relative positions. If the scene is difficult to read, try enabling them and compare. On an older graphics card, the documentation suggests disabling shadows or choosing a lower preset if performance is a concern.
Silhouettes are another way to separate regions at different depths. They can make structural boundaries easier to distinguish, particularly in a crowded view. As with other effects, judge the result on the specific model: a setting that clarifies one scene may be less useful in another.
Make edges and selection readable
Jagged edges can distract from the structure. In Rendering > Anti-aliasing, Fast Approximate Anti-Aliasing (FXAA) is described as typically efficient and available on most recent graphics cards. It is a useful option to test when edges look rough, though the result depends on your graphics hardware.
Selection styling matters too: you need to see what is selected without losing sight of the model. Under Rendering > Selection, you can adjust the selection color and opacity, show or hide the selection box, and control highlighting and outline colors. The highlighting color indicates the node under the pointer, helping you anticipate what will be selected. If outlines are contributing to lag on an older graphics card, setting outline opacity to zero may improve graphics performance.
Use the background to support the structure
A background is not just decoration: it affects how easily you distinguish the model from the viewport. Under Rendering > Background, the available choices are the default SAMSON background, black, white, or a custom gradient between user-defined top and bottom colors. If a structure blends into the background, try a contrasting option before changing the model’s appearance. A simple background can also be helpful when preparing a clear view for discussion or a capture.
A simple tuning routine
- Choose a background that separates the molecule from the viewport.
- Test ambient occlusion to improve depth cues, keeping camera-distance sensitivity and performance in mind.
- Add shadows or silhouettes only if they make spatial relationships easier to read.
- Try anti-aliasing if edges are distracting.
- Adjust selection colors and outlines so interaction remains visible without obscuring the structure.
- Revisit performance after each change, especially on older graphics hardware.
Changing one setting at a time makes it easier to tell whether an effect actually helps. For more detail on these controls and the other preference categories, see the SAMSON Preferences reference.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.