Molecular modelers often spend a significant amount of time trying to fine-tune how molecular structures are displayed. Whether it’s for better analysis, clearer presentations, or publication-ready visuals, there’s a constant need to control how nanosystems are represented graphically.
In SAMSON, this is made easier through Visual Models—dedicated tools that provide customized visual representations of nanosystems. These models help you see exactly what you need, from protein secondary structures to electrostatic fields, without losing sight of the underlying data. If figuring out how to rapidly visualize parts of your structure for presentations or analysis has ever been a bottleneck, understanding visual models in SAMSON might save you more time than you think.
What Are Visual Models?
Visual models in SAMSON define how a part of the nanosystem is displayed, without altering the underlying data. For example, you might use a surface representation to highlight solvent accessibility or apply a cartoon model to view a protein’s secondary structure.
Here are just a few examples of what visual models can represent:
- Secondary structure representations of proteins
- Gaussian surfaces or isosurfaces of electron densities
- Volumetric fields (e.g., electrostatic potential)
- Solvent-excluded surfaces for interactive analysis
How to Apply a Visual Model
There are several ways to add a visual model to a selection in SAMSON:
- Right-click on a selection and use the context toolbar menu
- Choose Visualization > Add > Visual model from the menu
- Use the shortcut: Ctrl/Cmd + Shift + V
If no specific nodes are selected, the visual model is applied to the entire document. This makes it easy to switch between different visualization styles on the fly.
Tweak and Fine-Tune in the Inspector
Applying a visual model is just the beginning. With the Inspector panel, you can adjust the visualization parameters of each model—for instance, changing opacity, coloring schemes, or quality for exported images. Simply select the visual model in the Document view and click Inspect from the context menu.
Interactive Highlighting
One useful feature of SAMSON’s visual models is the ability to interactively highlight and select atoms, residues, or chains directly from graphical surfaces. For example, when using a Solvent-Excluded Surface, you can click to identify and select specific residues, improving analysis and interaction precision—especially useful in large proteins or complexes.
Want to Customize Further?
You’re not limited to built-in options. SAMSON users can develop their own visual models using the Extension Generator. If your project requires a unique way of representing molecular data—custom surfaces, dynamic visualizations, etc.—SAMSON lets you go beyond default presets.
Whether you’re preparing a quick presentation or carrying out a detailed structural analysis, visual models in SAMSON offer a flexible and straightforward way to make sense of your molecular systems visually.
To learn more and see additional examples: 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.