For many molecular modelers, the challenge isn’t generating data — it’s understanding it. Whether you’re looking at protein structures, electron densities, or electrostatic fields, visual clarity can make the difference between insight and information overload.
This is where Visual Models in SAMSON can help. These models provide flexible and effective graphical representations of molecular systems. The ability to customize how you see your data makes analysis more intuitive and presentations more communicative.
What Is a Visual Model?
Visual models in SAMSON are graphical layers that render structural or computed data in various formats. They’re like visualization overlays: from ribbons representing secondary protein structure to colored surfaces indicating an electrostatic potential field.
Each visual model can be applied to specific parts of your system — atoms, residues, chains — or the entire document. Combined with SAMSON’s selection filters, this lets you precisely control what is shown and how.
Why Does It Matter?
Imagine you’re studying a protein with several domains and binding sites. Visualizing the secondary structure (e.g., α-helices and β-sheets) helps you notice structural motifs. Adding a surface that displays electrostatic potential helps predict molecular interactions.
The visual model becomes a tool for understanding, not just display.
Examples of Visual Models
Some default visual models available in SAMSON include:
- Secondary structure ribbons (great for proteins)
- Gaussian and solvent-excluded surfaces
- Isosurfaces of electron density or electrostatic fields
- Volumetric representations
How to Apply a Visual Model
There are several ways to apply a visual model in SAMSON:
- Use the context toolbar after selecting atoms or structures
- Navigate to Visualization > Add > Visual Model
- Use the shortcut:
Ctrl/Cmd+Shift+V
If nothing is selected, visual models apply to the entire document by default, which is handy for quick overviews.
Fine-Tuning What You See
You can adjust many visual models through the Inspector. Just select a visual model in the Document view and click Inspect. Parameters like thickness, color, resolution, or transparency can often be customized.
This means you can highlight hydrophobic patches, emphasize charged areas, or create visuals tailored for collaboration or publication.
Mixing and Stacking
You can stack multiple visual models for richer representations. For instance, overlaying a molecular surface with a field map helps visualize where docking interactions might occur. It’s all about creating clarity with complexity — not hiding it.
Want to Go Further?
If you’re developing your own SAMSON Extensions, you can even create custom visual models for new types of data or alternative visualizations.
To learn more about visual models in SAMSON and how they integrate into modeling workflows, check out the full documentation page: https://documentation.samson-connect.net/users/latest/models/
SAMSON and all SAMSON Extensions are free for non-commercial use. To get started, visit https://www.samson-connect.net.