Visual clarity is crucial when studying molecular structures. Whether you’re presenting a molecular mechanism or investigating the details of a ligand-binding site, your visual output must aid — not hinder — understanding. Fortunately, SAMSON offers an extensive set of rendering preferences that can help molecular modelers create clear, informative, and aesthetically pleasing views of molecular systems.
From lighting and shadows to fog and silhouettes, SAMSON’s rendering settings give you full control over how your molecules appear on screen. If you’ve ever struggled with depth perception in a complex structure, or tried to produce publication-ready visuals from a 3D model, this guide is for you.
Ambient Occlusion: Making Depth Visible
Ambient occlusion adds realistic shading based on how exposed each point of the molecule is to light, helping viewers better understand structural depth.
- Screen-space ambient occlusion: Fast, good for most interactive uses.
- Object-space ambient occlusion: Higher quality, better suited for static renderings.
Shadows and Lighting: Structure Through Contrast
Shadowing enhances the spatial relationship between atoms and improves the perception of proximity. You can adjust:
- Light direction using longitude and latitude
- Specular intensity and power to control surface reflections
- Ambient light to define the base illumination
Silhouettes and Fog: Highlight What Matters
Silhouettes provide outlined contours of molecules, which are especially helpful in scenes with limited contrast. Fog introduces progressive fading of distant parts, focusing the viewer’s attention on the foreground.
Focus and Realism
If you’re aiming for realism or emphasis, try out:
- Depth of field – Blur distant regions when zoomed in, mimicking camera lenses.
- Bloom – A subtle glow around bright areas to simulate imaging artifacts.
- Pinhole view – Emphasizes the center of the scene, useful for presentations.
Labeling, Selection, and Structural Details
Customize labels and selection effects to match your workflow. Choose label fonts and how atom distances and angles appear. Adjust selection color, opacity, and highlighting outlines — a small tweak that can drastically improve clarity when working in dense structures.
Projections and Stereo Views
Switch on orthographic projection to avoid distortion if you’re analyzing large biological assemblies. Planning to use 3D glasses? Enable stereo rendering to experience depth in a literal way.
Each of these preferences can seem minor when viewed in isolation. But together, they play a critical role in making your molecular modeling more effective, whether you’re analyzing, teaching, or publishing.
You can access all these settings via Interface > Preferences or by pressing Ctrl + K on Windows/Linux or Cmd + , on Mac.
Learn more in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON from https://www.samson-connect.net.