One of the most common frustrations in molecular modeling is constantly reconstructing the same types of visualizations: highlighting ligands, showing ribbons for proteins, zooming in on active sites, choosing color schemes, and setting up camera perspectives. When models become complex, even small changes can become time-consuming. If you’ve found yourself repeating these steps, SAMSON has a feature that can help: custom visual presets. Here’s how you can build and reuse them.
Visual presets in SAMSON are a way to bundle together a series of visualization steps—such as node selections, applied actions, visual models, and color schemes—into a single click. Once created, they can be applied to any structure quickly, helping you streamline your workflow and maintain visual consistency across sessions and projects.
Why this matters
Imagine you’re working on a protein-ligand system and want to always show the receptor in ribbons colored by chain, the ligand in licorice with atom-based coloring, and hide water molecules. Without visual presets, you would need to manually apply all these steps for every new structure you open. With a custom preset, you set it up once—and reuse it indefinitely.
Creating Your Own Visual Preset
To start crafting a visual preset, navigate to Home > Visual preset > Create… or Visualization > Visual preset > Create….
Now click the 
Add step button to begin defining your visualization workflow.
Each step in a visual preset includes four customizable parts:
- Selection of nodes (e.g., protein, ligand, water)
- Optional actions (e.g., zoom to selection, hide nodes, etc.)
- Visual model type (e.g., ribbons, van der Waals)
- Color scheme (e.g., per element or constant color)
The interface gives you default selections (like “Ligands” or “Receptor”), but you can also define custom ones using the Node Specification Language.
For each step, you can then choose what actions to apply (hide atoms, add labels, zoom), which representation to use (ribbons, stick, surface), and how to color nodes based on structural attributes.
If you choose a constant color scheme, you can double-click the color palette and select from predefined or custom palettes. If needed, the default palette can always be restored.
When you’re satisfied with your preset, click Save visual preset. The next time you launch SAMSON, it will be there with your default ones—ready to use.
Reusing and Modifying Presets
You can duplicate an existing visual preset and modify it if you want to make small changes. Want to make a version that highlights hydrogen bonds or labels specific atoms? Clone your base preset and add an extra step.
Steps can be reordered with the Move up / Move down buttons or deleted entirely. This gives you full control over how your visualization is assembled.
And yes—you can apply different styles to different parts of a complex system (e.g., apply a surface representation to the receptor but a stick representation to cofactors) all within the same visual preset.
Get Consistency in Just One Click
Once you’ve set up your favorite visualization styles, you can keep applying them to new systems without having to manually reconstruct each step. It’s especially useful when generating publication figures or preparing multiple protein-ligand systems for comparison.
Learn more about how to create and apply visual presets in the full SAMSON Visual Presets documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.