When working with complex molecular models, visual clarity can make a big difference in understanding structures, communicating results, or preparing publication-grade visuals. However, users often find that models are cluttered, hard to interpret, or lacking depth—especially when default rendering settings don’t match the specific needs of a visualization task.
Thankfully, SAMSON provides a detailed and flexible set of Rendering Preferences that allow users to tailor how molecular scenes are displayed. These options are tucked within the Preferences > Rendering section and cover everything from ambient lighting and shadows to depth of field and stereoscopic views. Let’s explore how a few targeted adjustments can significantly improve your visual output—and your experience.
Focusing the Viewer with Depth of Field
Have you ever tried to highlight a specific protein-ligand interaction only to have surrounding atoms distract from your point of interest? SAMSON’s Depth of Field settings simulate focus blur, similar to what you’d get from a camera lens.
Once enabled via Preferences > Rendering > Depth of field, this feature subtly blurs distant elements, guiding the viewer’s attention to what really matters.
Adding Realism with Ambient Occlusion
Understanding spatial relationships can be challenging in dense molecular models. Ambient occlusion adds soft shading to the parts of structures that are harder for light to reach—like the grooves of a receptor or the tunnels in an enzyme. This gives models a more 3D appearance and helps users better perceive depth.
Under Preferences > Rendering > Ambient occlusion, you can enable either screen-space (faster) or object-space (more accurate) occlusion.
Simple Edits with Shadows and Silhouettes
Having trouble distinguishing overlapping parts of your models? Try enabling Shadows and Silhouettes. Shadows provide immediate spatial context by anchoring structures against one another, while Silhouettes draw clear outlines to make structural boundaries pop.
Choosing Your Atmosphere with Background and Lighting
Sometimes, switching to a neutral or custom gradient background can reduce eye strain and help focus on specific atoms or subunits. Visit Rendering > Background to make these adjustments. You can also go to Rendering > Lighting to control the intensity, color, and angle of two independent light sources. This allows you to simulate different experimental setups or artistic styles.
Clean Views with Anti-Aliasing and Bloom
For publication or presentation visuals, jagged edges and flat colors can be distracting. Anti-aliasing helps by smoothing boundaries, and the Bloom effect adds a subtle glow around bright areas for enhanced contrast.
Adjust these effects under Rendering > Anti-aliasing and Rendering > Bloom.
Final Thought
Learning how to fine-tune these rendering options makes molecular modeling in SAMSON not only more effective, but also more enjoyable. Even small tweaks—like turning on ambient occlusion or adjusting lighting parameters—can have a big impact on how your models are perceived and understood.
To learn more about SAMSON’s rendering preferences and other customization options, visit the official SAMSON Preferences documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at www.samson-connect.net.