For molecular modelers, the ability to see the system they work on is a key part of understanding, interpreting, and communicating results. Whether you’re looking at atomic arrangements, protein folding, or electrostatic maps, meaningful visualizations go beyond aesthetics—they are functional tools in research and discovery.
SAMSON, the integrative platform for molecular modeling and simulation, introduces a modular approach to this through its concept of Visual Models. This blog post explains how visual models work in SAMSON, why they matter, and how you can customize or even build your own.
What Are Visual Models?
In SAMSON, visual models are representations that give life to structural models: they let you see molecular structures and properties as they are structured in your document. You can think of them as layers on top of your data, making it graphically accessible.
Examples include:
- Cartoon or ribbon diagrams for proteins
- Gaussian and solvent-excluded surfaces
- Volumetric maps of electron or electrostatic fields
Here’s a look at some of the default options included in SAMSON:
Who Is This Useful For?
If you’re a structural biologist, chemoinformatician, or computational chemist, visual models can help you:
- Quickly check structural integrity (e.g., bond connectivity)
- Highlight and select key regions of interest (e.g., active sites)
- Prepare clear, publication-ready figures
How Do You Apply Visual Models?
You can apply visual models to selected parts of your molecular system or globally to the entire document. Here are some ways to do that:
- Use the context toolbar when a node is selected
- Navigate to Visualization > Add > Visual model menu
- Use the shortcut:
Ctrl/Cmd+Shift+V
Customizing Your View
Once a visual model is added, you can fine-tune how it appears. Want a protein ribbon to be thicker? Prefer a translucent surface rendered with gradient lighting? Head to the Inspector tab after selecting the visual model in the Document View and click Inspect. You’ll unlock a range of parameters depending on the visual model type.
Interactive Highlighting
One particularly helpful feature: many visual models support interaction. Depending on your current selection filter, you can click directly on a surface or a cartoon to select atoms, residues, or whole chains. This makes visual models more than just eye candy—they become interactive tools.
Want to Build Your Own?
If you’re developing new visualization ideas, SAMSON lets you go further. You can create your own visual model types using the Extension Generator. This opens the door to customizing how your fields, properties, or novel data types are visualized.
To learn more about how visual models work in SAMSON and how you can use or develop them, visit the official documentation: https://documentation.samson-connect.net/users/latest/models/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.