Visual clarity is a recurring challenge in molecular modeling. When working with complex structures—particularly in 3D—being able to intuitively grasp spatial relationships between atoms and molecules can significantly improve understanding and communication. Whether you’re preparing publications, creating teaching materials, or just navigating crowded atomic environments, visual depth matters.
Fortunately, SAMSON’s Preferences panel provides a robust suite of rendering settings designed to help you address this exact issue—without needing external tools or rendering engines. In this blog post, we’ll explore how depth-related visual features such as ambient occlusion, fog, shadows, silhouettes, and depth of field can be adjusted to enhance the readability of your molecular scenes.
💡 Why Depth Perception Matters
When molecules begin to overlap in a 3D scene or stretch over a large spatial region, distinguishing between foreground and background becomes difficult. This can obscure structural insights or lead to misinterpretations. Enabling effects such as fog or ambient occlusion can make a dramatic difference in making spatial relationships clearer at a glance.
📘 Go-to Settings in SAMSON
1. Ambient Occlusion
This simulates how exposed each point in a scene is to ambient lighting. It darkens recessed or less exposed areas, improving depth perception. Choose between screen-space ambient occlusion (faster) and object-space ambient occlusion (more realistic).
2. Depth of Field
Just like real cameras, this setting allows distant structures to blur, thereby making focused regions stand out more clearly. Makes a huge difference when zooming in on a ligand or active site.
3. Fog
Fog is a subtle but highly effective way to reduce visual clutter. It progressively blends distant objects into the background based on camera position. Parameters like near distance, far distance, and strength offer precise control.
4. Shadows
Shadow effects help you perceive how far apart objects lie in space. This can be particularly useful in protein-ligand complexes where relative depth matters.
5. Silhouettes
Silhouettes apply thin outlines to objects based on their geometry and view angle. Use this to clearly separate overlapping parts of structures, especially in crowded models.
🛠️ Where to Find These
All these options are available in the Preferences panel under Rendering. Access it via Interface > Preferences in the menu or press Ctrl+K (Windows/Linux) or Cmd+, (Mac).
✅ Final Thoughts
These tweaks require no scripting, no heavy rendering, and zero external software. They’re fast to activate and can dramatically improve your modeling experience. Try enabling ambient occlusion and shadows, then zoom into your molecule with depth of field on—you’ll notice the difference immediately.
To learn more about rendering preferences and other visualization tools in SAMSON, visit the official documentation page at https://documentation.samson-connect.net/users/latest/preferences/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.