One of the recurring challenges in molecular modeling is how to visually explore and present complex nanosystems. Whether you’re designing a macromolecular assembly, analyzing electron density data, or preparing figures for a presentation, you’ve probably wished for better control over how your molecular models appear. Fortunately, SAMSON offers an elegant solution: Visual Models.
In SAMSON, visual models are used to generate customized graphical representations of nanosystems. These range from showing protein structures with secondary structure ribbons to detailed isosurfaces of electron densities. If you’ve ever manually tried to produce publication-quality images or struggled to highlight specific atoms and residues, you’ll want to know everything about this feature.
What are Visual Models?
Visual models in SAMSON don’t alter your data—they help you see your data. Think of them as overlays applied to your molecular structure. You can choose different visual models depending on what aspects of the system you want to highlight.
For instance:
- Secondary structures: Highlight alpha helices or beta sheets in proteins.
- Electrostatic fields: Visualize scalar or vector field distributions over space.
- Surfaces: Display solvent-excluded surfaces or Gaussian isosurfaces for better shape understanding.
How to Apply Visual Models
You can apply visual models in several ways:
- Right-click on selected nodes in the document and apply visual models through the context menu.
- Use the main menu:
Visualization > Add > Visual model - Keyboard shortcut: Ctrl/Cmd + Shift + V
If nothing is selected, the visual model is applied to the entire document by default.
Customizing Your Visualization
Visual models in SAMSON aren’t static—they’re customizable. You can change visualization parameters directly in the Inspector. To do that:
- Select your visual model in the Document view
- Right-click and choose Inspect
With these settings, you can adjust representations like ribbon thickness, color schemes, or isosurface levels to match your desired emphasis—be it clarity, aesthetics, or insight.
Simplifying Selection and Highlighting
Complex molecular systems can be hard to navigate. Visual models in SAMSON make this easier. When a visual model is active, you can directly pick atoms, residues, or chains from the graphical representation based on your current selection filter.
This is particularly helpful on surfaces like the Solvent Excluded Surface (SES), which allows for fast and intuitive selection.
Want More Options?
SAMSON comes with default visual models, but you can always expand your toolkit. Head over to SAMSON Connect to download additional visual models, or check out the Extension Generator if you want to develop your own representations.
This modularity lets you adapt SAMSON to your specific research or presentation needs, whether you’re focusing on clarity for educational purposes or detail for simulation insight.
To learn more about visual models and their applications, visit the full SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at https://www.samson-connect.net.