If you’re spending a lot of time toggling between complex molecular data and trying to understand the structure’s shape, behavior, or properties, you’re not alone. One of the most common challenges in molecular modeling is bridging the gap between raw data and visual understanding. This is especially important when preparing models for research, teaching, or collaboration.
Fortunately, SAMSON provides a powerful solution to this challenge with its visual models — a practical and flexible way to represent nanosystems graphically. Whether you’re analyzing a protein’s secondary structure, visualizing an isosurface of electron density, or presenting your results, visual models can save you time and improve clarity.
What are Visual Models?
Visual models in SAMSON don’t change the data; they change how you see it. They offer graphical representations of structural nodes, allowing you to work with intuitive visuals based on the model you’re investigating. For example, instead of seeing just atoms and bonds, you can explore:
- Secondary structures of proteins (e.g., helices and sheets)
- Volumetric representations of scalar fields
- Electrostatic and electron density representations
- Gaussian surfaces or solvent-excluded surfaces (SES)
How to Apply Visual Models
Visual models can be quickly applied in several ways, depending on your workflow:
- Using the context toolbar menu on a selected node
- Through the path Visualization > Add > Visual model
- With a keyboard shortcut:
Ctrl/Cmd + Shift+V
If nothing is selected, the visual model is applied to the entire document by default. You can fine-tune parameters through the Inspector once you’ve selected the corresponding visual model in the document view.
From Visualization to Interaction
Good visualization also helps with model interaction. SAMSON allows atomic or residue-level selection by clicking directly on the surface visualization, depending on your current selection filter. This can be useful for editing structures, running simulations, or communicating your work.
Extending Your Toolkit
SAMSON comes with default visual models, but you can expand your options via SAMSON Connect or by developing custom ones using the Extension Generator.
Wrapping Up
Visual models don’t just make your document prettier—they enhance understanding, speed up workflows, and make communication clearer. Whether you’re working solo or with a team, being able to see what you’re modeling is a key advantage.
To learn more about visual models and other model types in SAMSON, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/models/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.