A molecular scene can contain all the right structures and still be hard to interpret. At a glance, neighboring regions may seem to merge, it can be difficult to tell what sits in front of what, and jagged edges can distract from the model. These are often problems of visual readability—not problems with the molecule itself.
SAMSON’s real-time rendering effects can help make depth and structure easier to read. Rather than switching on every effect at once, start with the visual problem you want to solve, then adjust a small number of settings.
Start with depth: ambient occlusion
Ambient occlusion darkens regions that are less exposed to light, adding cues that can make a molecular model feel less flat. In SAMSON, screen-space ambient occlusion is a quick approximation and can be sensitive to camera distance. Object-space ambient occlusion is more realistic but slower. Even the screen-space option can be useful when you want a fast improvement in perceived depth.
Try switching on screen-space ambient occlusion from Visualization > Options, then compare the scene before and after. The example below shows the Ribbons visual model of 1AF6 with and without the effect.
Use shadows to clarify relative position
When the question is “Where is this structure in relation to that one?”, shadows can be especially helpful. They add another cue for judging relative positions—for example, a molecule positioned near a graphene sheet. Toggle shadows in Visualization > Options and check whether the spatial relationship becomes easier to understand.
If you use an older graphics card, SAMSON’s documentation suggests disabling shadows or choosing a lower preset. The aim is a clearer view at a level of performance that works for your system.
Separate regions with silhouettes
Silhouettes can help distinguish regions at different depths by adding outlines. They are worth trying when shading alone does not make the shape or separation of a structure clear. For a simple test, create the Ribbons (secondary structure) visual model for 1YRF, enable silhouettes, and set the thickness to 1.
Finish the edges, then check the background
Once the depth is readable, anti-aliasing can make jagged edges less distracting. FXAA is described as an efficient option for many recent graphics cards, while multisampling can also be adjusted. Anti-aliasing uses more GPU rendering and may slow visualization for large systems, so compare the result against the performance you need.
Background choice also affects how clearly the model stands out. In Preferences > Rendering > Background, you can choose SAMSON’s default, black, white, a custom gradient, or an image. Try a different background if the current one makes your structure difficult to distinguish; you can also switch backgrounds from Visualization > Options.
A quick, repeatable check
- Turn on screen-space ambient occlusion and inspect the depth.
- Add shadows if relative positions are still unclear.
- Try silhouettes when regions need stronger separation.
- Adjust anti-aliasing and background, keeping performance in mind.
- Toggle effects off and on to confirm that each one actually improves the view.
This is a workflow for interactive viewport clarity. For final-quality offline rendering, see Rendering. For the full guide to viewport effects and their settings, visit the SAMSON rendering effects documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.