Understanding molecular systems is often about more than just numbers—it’s about seeing the structure, interactions, and properties in ways that make patterns and behaviors intuitively clear. That’s where visual models in SAMSON come in.
For molecular modelers, one recurring challenge is effectively analyzing and communicating complex structural data. Whether you’re studying protein folding, analyzing interactions, or preparing publication-ready visuals, having flexible graphical representations of your nanosystem can make all the difference.
What are Visual Models?
In SAMSON, visual models provide graphical representations of atoms, molecules, surfaces, and fields. They don’t change the physics of your model—the structural and interaction data remain unchanged—but they allow you to see your model in a way that supports deeper insight.
Visual models can illustrate different aspects of a nanosystem. Some examples include:
- A secondary structure ribbon diagram for a protein
- A solvent-excluded surface to analyze molecular accessibility
- An isosurface or volumetric display of an electron density or electrostatic field
Using Visual Models in SAMSON
SAMSON provides a set of default visual models that are accessible through several convenient methods:
- Via the context menu of a selected node (atom, residue, etc.)
- From the main menu: Visualization > Add > Visual model
- Using the shortcut:
Ctrl/Cmd + Shift + V
Visual models are context-aware: if you apply them to a selected node, they affect only that node. If nothing is selected, they apply to the whole structure.
Controlling What You See
Some visual models come with customizable parameters. Want thicker ribbons in your protein structure? Or a more transparent surface view? Open the Inspector (via the context menu) and tweak visualization settings on-the-fly.
This level of customization is especially useful when preparing figures or when trying to better highlight specific features of your nanosystem.
Making Analysis Interactive
Visual models in SAMSON are not static. You can interact directly with atoms, residues, or chains based on what’s visually displayed. For example, if your visual model includes a surface, you can click to select underlying residues, depending on your selection filter.
Extending Visual Models
If the default models don’t meet your needs, you’re free to expand. Discover more models via SAMSON Connect, or develop your own using the Extension Generator. SAMSON is modular, making it easy to plug in new types of views as you need them.
Why This Matters
Molecular modeling isn’t just about accuracy—it’s also about clarity. The right view at the right time helps uncover important interactions, pinpoint structural features, and communicate ideas more clearly to peers. Visual models enable this without interfering with the underlying dynamics, structures, or properties of your system.
To learn more, visit the complete documentation for Models in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at samson-connect.net.