Visualizing complex molecular systems can be surprisingly time-consuming. If you’re a molecular modeler, you probably know the drill: load your structure, apply styles, color atoms, hide waters, zoom to region of interest, repeat. What if you could automate these repetitive steps into a single click that applies all your favorite styles?
This is where visual presets in SAMSON come in. They’re a great time-saver for anyone regularly preparing molecular scenes for analysis, teaching, or publication. Even better, SAMSON lets you create your own visual presets—tailored exactly to your workflow.
What is a Visual Preset?
A visual preset is a compact, configurable recipe for how your molecular systems should look. It defines what is shown, how it’s shown, and what colors are applied—all in one place. Visual presets can contain multiple steps, where each step applies a specific combination of:
- Selection (e.g. ligands, receptors, heavy atoms)
- Actions (e.g. hide, label, zoom)
- Visual model (e.g. ribbons, Van der Waals, licorice)
- Color scheme (e.g. per chain, constant color)
Customizing Your Workflow
With the Visual Preset Editor, you can create a new visual preset from scratch or start from an existing one and tweak it your way. Here’s the process:
- Go to Home > Visual preset > Create…
- Click the
button to start a new preset - Click Add step and pick what you want the step to apply to (e.g. Ligands)
- Optionally add actions like Hide or Zoom on selection
- Choose a visual model like Van der Waals or Licorice
- Color it based on whatever attribute you prefer (element, chain, occupancy, etc.)
- Repeat for more steps if needed, then hit Apply or Save visual preset
Here’s how the editor interface looks:
Want even more control? Click More… when selecting nodes to compose custom selections using the powerful Node Specification Language. And if you’re unhappy with the color palette, double-click it to choose your own hues or revert to defaults. The editor gives you full flexibility.
Why Use Custom Presets?
Custom visual presets help you work more efficiently and reduce cognitive friction. For example, instead of adjusting visualization settings each time you load a protein-ligand complex, you can save a preset with:
- Receptor in ribbons colored by chain
- Ligands in licorice, colored by atom
- Water hidden
- Zoom on the ligand automatically
Next time, all you need is one click. This is particularly useful when working with multiple structures in a series or creating consistent imagery for presentations or publications.
Sharing and Feedback
If you’ve built a particularly useful visual preset and think others could benefit, SAMSON even gives you a way to share it! Click on Send feedback to suggest your preset for inclusion in future SAMSON releases.
Save time and keep your visualizations consistent — your future self will thank you.
Learn more in the full Visual Preset documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.