For many molecular modelers, clarity in visualization is more than aesthetic—it’s essential for understanding structure, function, and interaction. Whether you’re interpreting protein folding or preparing visual outputs for a publication, good molecular graphics save time and reduce risk of misinterpretation.
In SAMSON, visual models are dedicated nodes designed specifically for these visualization needs. But how and when should you use them, and what’s under the hood?
What Are Visual Models?
A visual model in SAMSON defines how structures and properties are visually represented. Unlike structural models that define atoms and bonds, visual models are concerned with making that structure visible in a meaningful way. Examples include secondary structure ribbons for proteins, Gaussian and isosurfaces of electron densities, and volumetric displays of scalar or vector fields like electrostatics.
Why Use Visual Models?
One recurring challenge is selecting what gets displayed and how. You might want to highlight hydrogen bonds in one case and focus on solvent-excluded surfaces in another. SAMSON allows molecule-specific graphics and context-dependent highlighting.
Visual models can be applied:
- Via the context toolbar based on selected elements
- Through the Visualization > Add > Visual Model menu
- With the shortcut: Ctrl/Cmd + Shift + V
Adjusting Parameters in the Inspector
Want to change colors, transparency, or surface algorithms? The Inspector panel in SAMSON allows fine-tuning of visual model attributes. First, select the visual model in the document tree, right-click, and choose Inspect.
Highlight & Select with Surfaces
Another key benefit is surface-based interaction. Depending on the current selection filter, surfaces allow users to click and highlight specific atoms, residues, or chains. For example, clicking on a Solvent Excluded Surface (SES) to isolate or analyze a residue is quick and intuitive.
Extending Visual Models
Have a custom way to represent data or want a personal visual pipeline? You can create your own visual models using the SAMSON Extension Generator. Start with the developer documentation and tailor your visualization layer as needed.
Where to Go From Here?
- Browse available visual models and extensions at SAMSON Connect
- Explore presets and color schemes in the Visualizing section
- Fine-tune selections using selection filters
Visual models are more than decorative—they’re central to efficient molecular design workflows. They help make the invisible, visible—and often, understandable.
To learn more about visual models and how they relate to other model types in SAMSON, visit the full documentation page on models in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.