When working with complex molecular systems, the visual output can quickly become overwhelming. Proteins, ligands, water molecules, and other components are often jumbled together in multiple representations and colors. As a result, getting a clean, informative image of your model often means spending extra time manually adjusting views, color schemes, and display modes — over and over again.
This is a common pain point for molecular modelers who want to quickly inspect a system, prepare a figure, or simply navigate through a structure. In SAMSON, the solution lies in a feature that is often underused but extremely powerful: Visual Presets.
What are Visual Presets?
Visual presets in SAMSON are a fast way to apply pre-defined combinations of visual representations, color schemes, actions, and more to your molecular system with just a click. You can think of them as workflows—configured in advance—that instantly clean up and style your structure for specific tasks, such as analyzing a receptor-ligand complex or presenting a polymeric molecule.
What Makes Visual Presets Useful?
Instead of toggling visual models for atoms, trying to color chains manually, or hiding water molecules one by one, you can apply a preset that already contains all these choices. For example, the Protein-Ligand visual preset might:
- Hide water and ions
- Display the protein backbone in ribbons
- Render the ligand using Van der Waals spheres
- Use per-chain coloring for clarity
All of this happens as soon as you apply the preset—giving you a clean, focused representation in seconds.
Where to Find Them
You can access presets from the Home > Visual preset or Visualization > Visual preset menu in SAMSON. After selecting a preset, it is applied either to your selection or to the entire structure if nothing is selected.
Customizing or Creating Your Own Presets
If the default presets don’t meet your unique needs, you can create your own using the Visual Preset Editor. With this editor, you define “steps,” each consisting of:
- A node selection (e.g., ligands, receptors)
- Optional actions (e.g., zoom, hide, label)
- Optional visual models (ribbons, licorice, spheres)
- Optional color schemes (chain-based, constant, per-occupancy)
The editor gives you a lot of control while staying easy to use. Adding a new step is just a matter of clicking the “Add step” button and choosing the parameters. You can even build custom selectors using SAMSON’s Node Specification Language if the defaults don’t cover your needs.
Applying, Saving, and Reusing
After editing your visual preset, you can save it for reuse. SAMSON loads all saved visual presets along with the defaults at startup, so your custom styles are always ready to go. This is especially helpful for creating consistent visuals across different projects or publications.
Conclusion
Visual presets in SAMSON help you declutter complex molecular models and apply consistent, high-quality visuals—without losing time on repetitive manual setup. Whether you’re inspecting structures or preparing visuals for presentations, this feature can become a core part of your workflow.
To learn more about visual presets and how to create your own, 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.