One common challenge for molecular modelers is going from raw data — a list of atoms, their positions, or interaction energies — to a clear and compelling representation of a molecular structure or phenomenon. Whether you’re trying to understand a protein folding pathway, visualize a molecular surface, or explore electron densities, a good visual model can go a long way toward making data easier to interpret — and share.
In SAMSON, this is exactly what Visual models are designed to do. They are graphical representations that make molecular systems comprehensible at a glance. The platform provides a flexible set of built-in visual models and offers additional options through its SAMSON Connect marketplace.
What Are Visual Models?
A visual model in SAMSON might be used to render a backbone ribbon of a protein, an isosurface of an electron density, or a molecular surface highlighting hydrophobic regions. These models are not just for aesthetics; they help identify biochemical patterns, spot active sites, or validate simulation results.
How to Apply Them
Applying a visual model in SAMSON is straightforward. These models can be applied to a selected set of nodes (e.g. atoms, residues, chains) or to the entire molecular system if nothing is selected. Here are three primary ways to add one:
- Use the context toolbar that appears when you select part of a molecule
- Navigate through Visualization > Add > Visual model
- Use the shortcut: Ctrl/Cmd + Shift + V
Once a visual model has been applied, you can even customize its parameters. To do that, go to the Document view, select the visual model, right-click it, and then choose Inspect.
This gives you a panel where you can adjust surface resolution, threshold levels (for electron densities), color modes, and more, depending on the visual model you’re using.
Why It Matters
Let’s say you’re modeling a solvent-excluded surface and want to interactively highlight the residues that lie on it. With the appropriate visual model in SAMSON, you can highlight and even select these features directly by clicking on the surface — a much more intuitive experience than examining atom lists.
This is especially helpful in collaborative settings or presentations, where being able to visually communicate protein-ligand interactions or molecular folding pathways can make discussions far more productive.
Want to Go Further?
For developers, SAMSON also provides the opportunity to create custom visual models using the Extension Generator. Whether you need a new way of displaying hydrogen bonding networks or a specialized electrostatic field representation, SAMSON’s architecture allows you to design what you need.
To learn more, see the full documentation on SAMSON visual models.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.