When viewing a molecular system, a list of coordinates or a ball-and-stick representation can get you only so far. Molecular modelers often need to see what matters—secondary structures, surfaces, fields, or density isosurfaces—to understand interactions, identify regions of interest, or prepare materials for presentations and publications. That’s where visual models in SAMSON come in.
In this post, we introduce SAMSON’s Visual Models: what they are, how to apply them, and how they help molecular modelers make sense of complexity.
What are Visual Models?
Visual models provide graphical representations of nanosystems. Instead of relying solely on atoms and bonds, you can choose to display your molecule or material in ways that highlight specific spatial or physical features.
Examples include:
- Secondary structure representations of proteins
- Gaussian surfaces showing electron density
- Volumetric electrostatic fields
- Solvent-excluded surfaces
Why Visual Models Help
Different visual models can help molecular modelers:
- Compare regions of interest: See parts of a molecule involved in hydrogen bonding or highlight active sites.
- Create publication-quality figures: Choose surface or ribbon-style visuals to make your figures clearer for others.
- Select more effectively: In SAMSON, visual models let you directly select atoms, residues, or chains via their surfaces. This bypasses the need to search through lists or use selection tools manually.
How to Apply a Visual Model
There are several ways to apply visual models in SAMSON:
- Right-click the selection and use the context menu toolbar
- Use the menu: Visualization > Add > Visual model
- Shortcut: Ctrl / Cmd + Shift + V
Visual models are context-sensitive and usually get applied to the selected nodes. If nothing is selected, they’re applied to the entire document.
Editable Parameters
For many visual models, you can adjust how they appear directly via the Inspector. Select the visual model in the Document view and click Inspect. This reveals options to tune properties like surface resolution, color schemes, or transparency.
Surface Selection: A Time-Saver
One notably convenient feature is the ability to select residues or chains through surfaces. For example, if you’re using a Solvent Excluded Surface visual model, clicking on a visual surface can directly highlight relevant atoms or residues—no need to find them manually.
Extending Beyond the Defaults
SAMSON provides several visual models by default, but you’re not limited to those. Many more are available via SAMSON Connect, and if you’re technically inclined, you can even develop your own visual models. Refer to the Extension Generator and the SAMSON Documentation Center to get started.
Whether you’re analyzing molecular systems, preparing snapshots for a presentation, or prototyping your own visualizations, visual models offer intuitive, powerful ways to see what’s going on.
To learn more or dive deeper into visualization options, visit the full documentation on models: https://documentation.samson-connect.net/users/latest/models/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.