Seeing Molecules: A Straightforward Guide to Visual Models in SAMSON

For molecular modelers, visual clarity can make or break a project. Whether you’re inspecting protein structures, analyzing electrostatic surfaces, or preparing materials for publication, you often need to translate invisible concepts into intuitive images. That’s where visual models become essential in SAMSON, the molecular design platform.

Visual models allow you to display information such as molecular geometry, electron densities, scalar fields, and more, in various representations. These models are more than just cosmetic; they are tools for analysis, communication, and even interaction during modeling and simulations.

What Are Visual Models?

Visual models in SAMSON provide graphical representations of molecular systems. This includes representations like secondary structures of proteins, Gaussian surfaces, electron density isosurfaces, and even volumetric views of physical fields such as electrostatics. They allow molecules and their environments to be seen in intuitive and interactive ways.

Some default visual models

Why They Matter

One of the recurring frustrations among researchers is spending too much time generating publication-quality visuals or struggling to interpret data using limited views. Visual models help solve this by:

  • Making it easier to inspect structural regions or anomalies.
  • Highlighting properties such as electrostatics, residue types, or solvent accessibility.
  • Improving the clarity of presentations and publications.

How to Apply Visual Models

There are multiple ways to add a visual model in SAMSON:

  • Use the context toolbar when something is selected.
  • Go to Visualization > Add > Visual model.
  • Or use the shortcut: Ctrl+Shift+V (Windows/Linux) or Cmd+Shift+V (macOS).

If nothing is selected, the visual model applies to the entire molecular document.

Customizing Your Views

After adding a visual model, you can customize its appearance directly through the Inspector. To do this:

  1. Select your visual model in the Document view.
  2. Right-click and choose Inspect.
  3. Adjust parameters like surface transparency, isovalue thresholds, color schemes, or representation styles depending on the model.

Visual model parameters in the Inspector

Interactive Selection and Highlighting

Some visual models also let you interact with the molecular system directly. For example, using the Solvent Excluded Surface representation, you can highlight and select specific atoms, residues, or chains by hovering. This feature connects immediately to how you filter selections in the interface, improving modeling efficiency.

Highlighting residues on the Solvent Excluded Surface

Extending Visual Models

SAMSON provides a default set of visual models, but you are also free to install new ones from SAMSON Connect or create your own via SAMSON Extensions if you are a developer. This offers room for fine-tuned custom displays tailored to your specific research area or datasets.

Conclusion

If you’ve ever wrestled with making molecular data visually compelling—or just visible—visual models in SAMSON provide convenient, customizable tools to make molecular structure and property analysis easier and more insightful. Once you’re familiar with their use, applying them becomes a fast, helpful part of your everyday modeling routine.

To learn more, visit the full documentation here: SAMSON Visual Models Documentation.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.

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