Visualizing complex molecular systems can be time-consuming, especially when you’re frequently applying recurring color schemes and representations. If you’ve ever found yourself repeatedly adjusting visualization settings in SAMSON to match your preferences, you’re not alone. Thankfully, there’s a better way to streamline this process: custom visual presets.
A visual preset in SAMSON is a bundle of display settings—visual models, colors, labels, zoom levels, and more—that you can apply in just one click. While SAMSON ships with a handy set of default presets, creating your own can save time and help you maintain consistent visuals for presentations, publications, or collaborative work.
Why Create Your Own Presets?
Every molecular modeler has different needs. A computational chemist might want to highlight hydrogen bond donors in ligands, while a structural biologist may focus on ribbon representations and active sites. Creating custom visual presets allows you to:
- Apply your preferred visualization style instantly
- Standardize visuals across multiple systems
- Reduce repetitive actions when working on similar structures
How to Start
To create a new visual preset, go to Home > Visual preset > Create… or Visualization > Visual preset > Create….
You can either modify an existing preset or create one from scratch. If you’re starting from scratch, use the plus button (
) to add a new step to your preset.
What Goes into a Step?
Each step in a visual preset includes four elements:
- Selection: Define which structural nodes the step applies to (e.g., ligands, receptors, water, or custom selections using the Node Specification Language).
- Actions: You can zoom to a selection, hide atoms, or add labels.
- Visual Model: Choose from models like Van der Waals, licorice, ribbons, and more.
- Color Scheme: Apply consistent coloring criteria like “per chain,” “per element,” or constant color.
More Flexibility with Custom Selections
If the default selections don’t capture what you need, scroll down the list and click More…. This opens the Find window, where you can build your own selection conditions using SAMSON’s Node Specification Language.
Polishing Your Preset
After defining several steps, you can:
- Reorder them with Move up or Move down
- Delete unnecessary steps
- Modify color palettes by double-clicking on them
Once done, either press Apply to test it or Save visual preset to reuse it in future SAMSON sessions.
TIP: Share or Reuse
If you believe your preset would help others, you can also contact the SAMSON team via the Send feedback button in the interface to suggest adding it to the default presets.
Creating visual presets is a small investment of time that can significantly enhance your workflow, reduce repetition, and help you deliver consistent, publication-ready visuals. You’ll thank yourself the next time you open a large biomolecular system and are able to visualize it beautifully in one click.
Want to dive deeper? Check out the full documentation page on visual presets in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download them at https://www.samson-connect.net.