Creating clear, consistent visuals of molecular systems can be a tedious task, whether for scientific communication, teaching, or just keeping track of complex simulations. The common workaround involves repeatedly adjusting representations, color schemes, visibility settings, zoom levels, and more — every time you load a new structure. These steps may seem small, but they pile up fast, especially when you’re working with multiple systems or iterations.
That’s where visual presets in SAMSON come in. Visual presets allow you to save and reuse detailed visualization configurations, all applied in a couple of clicks. It’s a useful way to maintain clarity and consistency while massively reducing repetitive work.
What is a visual preset?
A visual preset is a predefined collection of steps that decide what to show, how to show it, and how it’s colored.
Each step in a preset includes:
- A selection of nodes (e.g., ligands, receptors, metal ions)
- Optional actions (e.g., zoom, hide, label)
- An optional visual model (e.g., ribbons, van der Waals, licorice)
- An optional color scheme (e.g., per chain, constant color)
Applying a visual preset
You can access presets from the Home or Visualization menus. Simply choose one, and it’s applied to the entire document or a specific selection if you’ve made one. The preset will automatically group related visual elements into a new folder in your document.
Create your own preset
One of the most helpful features is the ability to create and save personalized presets. This is especially important when working with similar systems over time. You can:
- Build from scratch, starting from the Create option in the menu
- Modify an existing preset by adding/removing steps or changing models and colors
Each visual preset can contain as many steps as needed, and the interface makes it easy to:
- Select specific nodes (including creating your own definitions using the Node Specification Language)
- Add visualization models like ribbons, surfaces, or sticks
- Color by element, by chain, or use any custom color palette
- Apply multiple actions to a selection, such as zoom or label
Adding a new step is as simple as clicking the plus button, and rearranging the order of steps is just a matter of clicking “Move up” or “Move down.” You can even double-click to change color palettes on the fly or revert to defaults when needed.
Why it matters
If you’ve ever found yourself adjusting multiple settings just to recreate a previous visualization, visual presets can help. They’re especially useful for:
- Quickly preparing publication-quality visuals
- Ensuring consistency across multiple molecules or projects
- Teaching, by applying visually clear representations across different student files
Additionally, saved presets load each time you launch SAMSON. So once you’ve created your visual style, it’s always there when you need it.
Want to integrate your own visual presets into SAMSON’s default set? You can even contact the developers through the “Send feedback” option.
To learn more, visit the original documentation page on visual presets.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.