Are Your Molecular Visualizations Doing Enough? Understanding Visual Models in SAMSON

Visualizing molecular systems isn’t just about making things look good. It’s about clarity, insight, and helping you make the right decisions for your research. If you’ve used tools where atoms and bonds are shown as 3D sticks and spheres by default, you might feel limited. SAMSON offers a more structured, customizable approach through visual models, providing more flexible representations to convey different molecular features.

So what exactly is a visual model in SAMSON? Put simply, it’s a graphical representation of a nanosystem. But beneath that simplicity lies a system designed to adapt to your scientific needs — whether you want to highlight secondary protein structures, display surfaces, or visualize vector fields like electrostatics.

Why Visual Models Matter

Let’s say you’re analyzing a protein–ligand complex. You may want to view the solvent excluded surface to understand how exposure might affect ligand binding, or switch to ribbons or cartoon models to interpret the overall folding more clearly. Every visual model in SAMSON can help highlight a different physical or chemical property of your system.

Here’s what sets SAMSON’s visual models apart:

  • You can apply visual models to specific parts of your system (atoms, chains, residues) or to the whole structure.
  • Each model has parameters you can inspect and adjust — offering almost complete control over how your system is perceived.
  • SAMSON provides several visual models by default, and additional ones can be added via SAMSON Connect.

Working With Visual Models

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

  • Use the context toolbar of a selection
  • Go to Visualization > Add > Visual model
  • Use the shortcut Ctrl/Cmd + Shift + V

Once added, you can fine-tune parameters using the Inspector to change color schemes, level of detail, transparency, and many other properties. This level of customization is often overlooked, but extremely valuable when preparing figures or presentations.

Secondary structure visual model parameters in the Inspector

Contextual Interaction

One powerful feature is how seamlessly visual models in SAMSON integrate with selection tools. For example, you can directly click on a surface to select atoms, residues, or chains depending on the current selection filter.

Highlighting residues on the Solvent Excluded Surface

This is especially useful in large biomolecular systems where traditional selection might be slow or unintuitive. If you’ve ever tried clicking through atom-by-atom on large systems, you know how much time this can save.

Extending with Your Own Visual Models

If you’re looking for something more domain-specific or custom, SAMSON allows you to develop your own visual models as SAMSON Extensions. This can be done through the Extension Generator, and further resources are available in their Developer Guide.

To summarize, visual models in SAMSON serve far more than an aesthetic purpose. They are tools to shape how molecular structures are interpreted by the eye—and by the mind. Whether you’re analyzing charge distributions, structural motifs, or preparing publication-ready images, updating how you use visual models can improve both speed and clarity in your workflow.

To dive deeper into this topic, visit the original SAMSON documentation page.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.

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