For many molecular modelers, one significant challenge isn’t running simulations or optimizing structures—it’s presenting their results in a way that is easy to understand. Whether you’re working in research, education, or communication, visual clarity can save time, reduce misinterpretation, and make your work stand out. That’s where visual models in SAMSON can make a difference.
Visual models in SAMSON aren’t just cosmetic. They allow users to graphically represent structures, fields, and features of nanosystems, helping people see what they’re analyzing, manipulating, or designing. These models provide intuitive feedback and are extremely useful when dealing with complex systems like proteins, nucleic acids, or nanoparticles.
What are visual models?
Visual models provide graphical representations of nanosystems. These may include common depictions such as:
- Secondary structure models of proteins (ribbon, cartoon)
- Gaussian surfaces (e.g., molecular orbitals)
- Isosurfaces of scalar fields like electron density
- Volumetric representations (e.g., electrostatic fields)
By using these, modelers can instantly spot features or errors that would be missed with structural data alone.
How do you apply visual models?
Applying visual models in SAMSON is straightforward. Visual models can be added in several ways:
- From the context toolbar menu of a selection
- Through the menu:
Visualization > Add > Visual model - Using the shortcut: Ctrl/Cmd + Shift + V
If nothing is selected, the visual model is applied to the entire document, which can be perfect for general overviews. Otherwise, selected parts can be enhanced with specialized representations. This is especially useful for highlighting domains, binding pockets, or secondary structures.
Customizing visual parameters
Some visual models offer adjustable parameters. For example, the secondary structure visual model lets you fine-tune how it’s displayed using the Inspector. To do this:
- Select the visual model node in the Document view
- Right-click and choose Inspect to access settings
With these options, it’s easy to focus attention on key features or prepare your model for presentation or publication.
Highlighting and selecting with visuals
One particularly helpful feature is that SAMSON’s default visual models allow for direct interaction. For example, on a solvent-excluded surface, clicking highlights atoms, residues, or chains depending on your current selection filter.
This can make editing and isolating parts of your system far more intuitive than using tree-based node navigation alone.
Want to go further?
Visual models provided with SAMSON cover many standard needs, but if your work calls for something more specific, you can develop your own. Check the developer documentation on creating SAMSON Extensions to get started.
To learn more about visual models and other types of models in SAMSON, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.