When working on molecular design, seeing is more than believing — it’s sometimes the only way to fully grasp what’s happening inside nanosystems. But for many researchers and students, figuring out how to effectively visualize structural components can be time-consuming or confusing.
This is where Visual Models in SAMSON come into play. Designed to convey structure through a wide range of representations — from secondary structures to isosurfaces — visual models help transform data into insight.
What are Visual Models?
In SAMSON, visual models are applied to represent structural or computed elements with clarity. You can use them to give visual meaning to atoms, molecules, fields, and more. Whether it’s a Gaussian surface or a cartoon rendering of a protein’s secondary structure, visual models help you explore and present your data more effectively.
Common examples include:
- Secondary structure representations of proteins
- Gaussian and solvent-excluded surfaces
- Volumetric representations of electrostatic fields
How to Apply Visual Models
You have several options to apply a visual model in SAMSON:
- Use the context toolbar that appears when nodes are selected
- Navigate to Visualization > Add > Visual model within the main menu
- Keyboard shortcut: Ctrl/Cmd + Shift + V
If you don’t select anything, the visual model is applied to the whole document by default. This makes it quick to apply models globally or only to specific atoms, residues, or molecules.
Why This Matters
Being able to visually dissect complex structures empowers better decision-making and understanding. For instance, highlighting residues directly on a surface representation can bring attention to active sites or key ligands without labor-intensive selection steps.
This representation allows residue selection via surface clicking. The type of surface and the active selection filter determine whether clicking targets atoms, residues, or chains.
Customization for Clarity
Once applied, many visual models support customization. For example, selecting a visual model within the Document view and choosing Inspect opens its parameters in the Inspector panel. Depending on the visual model, you can modify rendering styles, opacities, resolutions, and more.
Can You Add More?
Yes. By default, SAMSON includes a library of visual models, but you can expand capabilities by installing Extensions from SAMSON Connect. Developers can also create custom visual models through the available extension generator and developer documentation.
In Summary
Visual models in SAMSON offer a simple yet powerful way to get clearer insights from complex systems. Understanding how to use and customize them unlocks more effective communication, presentation, and analysis of your nanoscale data.
To explore the full documentation on visual models and related tools, visit: SAMSON Documentation: Models
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.