When working with complex molecular systems, it can be challenging to keep track of atoms, residues, and structural regions – especially when they’re rendered as a sea of spheres and sticks. If you’ve ever found yourself squinting at your molecular scene, trying to select just the right group of atoms, SAMSON’s visual models might make your work much easier.
This blog post introduces an often overlooked but highly practical feature in SAMSON: visual models that enable intuitive structure selection through surfaces. Whether you’re selecting residues from a protein surface or setting up a field visualization, visual models can streamline your workflow and improve how you interact with your nanosystem data.
Why Visual Models Matter
In SAMSON, a visual model is more than a way to make your molecules look appealing. It provides a graphical mapping of underlying data, assisting both analysis and interaction. For example, a secondary structure visual model highlights helices and sheets for proteins, while a solvent-excluded surface offers insight into the molecular boundary by effectively representing the molecule’s “shape in water”.
But here’s where it gets more interesting: visual models support direct geometry-based interaction. That means you can select atoms, chains, or other structural elements by simply clicking on their visible representations. This makes it much faster to build selections, apply operations, or analyze regions of interest.
How It Works
Once a visual model like a molecular surface is applied, atom selection becomes surface-aware. Instead of clicking through several overlapping atoms or trying to traverse a tree of structural nodes, you can just click — the surface handles the mapping.
Selection through visual models depends on the current selection filter. For example, depending on your filter settings, clicking a protruding loop on a surface might select entire residues rather than individual atoms.
Here’s how to add and work with a visual model:
- Use the Visualization > Add > Visual model menu
- Right-click on a selection and choose a visual model from the context menu
- Or use the shortcut: Ctrl/Cmd + Shift + V
Tweak and Explore
Each visual model can be customized using the Inspector. For example, with a secondary structure visual model applied, you could adjust ribbon width, color settings, and display modes for better clarity or presentation.
Another helpful feature is that default visual models support geometry-based selection of residues through the rendered surface, which can look like this:
This makes visual models particularly effective for tutorials, simulations, and figure preparation when you need both clear visuals and easy access to molecular parts.
Start Exploring
You can browse and install more visual models through SAMSON Connect. These let you go beyond the default toolkit with additional representations such as isosurfaces, vector fields, or custom electron density outlines.
For those interested in extending SAMSON further, the platform provides extensive documentation on how to create your own visual models using SAMSON Extensions. This can be especially helpful if your research involves novel representations of molecular data.
To learn more about how visual models work in SAMSON and how to apply them, 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.