Making Molecular Visualization More Intuitive with SAMSON’s Visual Models

Molecular modelers often spend significant time adjusting how molecular structures are visualized to interpret and present their data clearly. Whether working with protein secondary structures, electrostatic fields, or electron densities, having intuitive control over visual representation is essential. Yet, many modeling platforms make this either too rigid or too technical for everyday use.

Fortunately, SAMSON offers a flexible framework through visual models that makes visualization of nanosystems both adaptable and user-friendly. This blog post breaks down how visual models work in SAMSON—and how they can significantly streamline your visualization tasks.

What Are Visual Models?

Visual models in SAMSON are not structural data. Instead, they act like overlays that convert raw nanosystem data into graphical forms suitable for analysis or presentation. You can think of them as specialized rendering layers that enhance your ability to see what’s going on inside your system.

Examples of visual models include:

  • Secondary structure displays for proteins
  • Gaussian and solvent-excluded surfaces
  • Isosurfaces for electron density values
  • Volumetric mappings of scalar or vector fields (e.g., electrostatics)

How to Apply Visual Models

There are multiple ways to apply visual models, depending on your preference. You can:

  • Use the context toolbar after selecting atoms or molecules
  • Select Visualization > Add > Visual model from the main menu
  • Use the keyboard shortcut Ctrl/Cmd + Shift + V

Once applied, visual models can be adjusted in the Inspector. This allows you to tweak parameters like transparency, color schemes, resolution, and more.

Choosing the Right Visualization

By default, SAMSON provides several visual models. These can be expanded further via SAMSON Connect, which gives you access to additional downloadable Extensions.

Some default visual models

If you’re unsure which model to use, a good starting point is the secondary structure visual model for proteins. This gives immediate insight into alpha-helices and beta-sheets in your structure. Electrostatic or scalar fields are suitable for analyzing molecular interactions, density distributions, or localization of charged regions.

Selection Refinement and Highlighting

One helpful feature enabled by visual models is intelligent selection filtering. For example, depending on the type of visual model in use, you can highlight or select entire residues, chains, or atoms directly via surfaces. This simplifies navigation and editing, especially in large systems.

Highlighting residues on the Solvent Excluded Surface

Custom Visual Models

If you need something specialized, SAMSON provides tools to develop your own visual models. This allows domain-specific representations or research-specific visuals tailored to your data. More details are available in the SAMSON Extension Generator section of the developer documentation.

Summary

Instead of working around limited visualization tools, SAMSON’s visual models give you the flexibility to explore nanosystems in a graphical, meaningful way. Whether you’re preparing a publication figure or verifying atomic-level interactions, visual models help bridge the gap between data and understanding.

To learn more about visual models, visit the official SAMSON documentation page on models.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from www.samson-connect.net.

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