Molecular modelers often struggle with one recurring challenge: visual clarity.
Whether you’re preparing figures for a publication, a presentation, or simply trying to interpret complex systems more clearly, the way molecules are rendered can have a huge impact on your understanding. Subtle visual improvements—like enhanced lighting, shadows, or ambient occlusion—can reveal structural insights that are otherwise hidden in plain sight.
If you’re using SAMSON, you already have extensive control over visual styles built right into the platform. Let’s explore the Rendering section of the Preferences panel in SAMSON, where you can customize almost every aspect of molecule visualization.
Why It Matters
Publishing high-quality visuals requires going beyond basic rendering. Different viewing contexts call for different settings: You might want high realism for a presentation or clean simplicity for schematic figures. SAMSON provides many settings that help you reach the visual outcome you need.
Getting There
To open the Preferences panel, go to Interface > Preferences or use:
- Ctrl + K on Windows/Linux
- Cmd + , on macOS
Key Rendering Settings You Should Know
Here’s a brief guide to the most useful settings:
Ambient Occlusion
Simulates realistic light diffusion in deeper regions of molecular structures, enhancing the perception of depth. Use Object-space ambient occlusion for realism or Screen-space for performance.
Shadows
Shadows help understand relative positions between atoms or molecules. Useful when arranging complex assemblies and determining spatial relationships.
Lighting
Controls multiple light sources. Adjust light color, intensity, and specular reflections to simulate anything from matte surfaces to plastic-like molecule surfaces.
Background
Choose from black, white, default, or custom gradient backgrounds. The right background can dramatically alter contrast and improve visibility.
Bloom
Adds a subtle glow to the brightest areas in your scene for a polished look. Ideal for presentation slides or publication figures.
Depth of Field
Simulates camera blur on distant parts of the scene. Helps to focus attention on specific molecular areas (like a ligand in a binding site).
Silhouettes
Outlines object edges to clearly separate molecular regions based on depth. Especially helpful in crowded systems.
Selection
Customize how selections are highlighted—including opacity, color, and outline—so you can better see what’s active or will be selected.
A Few Practical Tips
- Need faster rendering for less powerful machines? Consider disabling shadows and silhouettes.
- Exporting visuals? Set Anti-Aliasing (under Rendering) to avoid jagged edges in high-res screenshots.
- Want a publication-style look? Try white background + silhouettes + ambient occlusion.
These tools allow you to fine-tune rendering for accuracy, beauty, or speed—whichever you need most.
To learn more and explore all rendering options in detail, visit the SAMSON Preferences documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.