For any molecular modeler dealing with complex structures, visualization isn’t just a convenience — it’s essential. Whether preparing publication images, presentations, or simply exploring molecular systems, manually adjusting representations, colors, visibility, and selections can quickly become repetitive and time-consuming.
Visual Presets in SAMSON offer a practical solution. They let you quickly apply multiple visual representations and color schemes at once, and—more importantly—they’re entirely customizable. If you’re tired of repeatedly setting up the same views for ligands, protein backbones, or active sites, Visual Presets can help you automate and streamline that process in just a few clicks.
Create Exactly the Views You Need
Every Visual Preset in SAMSON is a sequence of steps. Each step includes:
- A selection of nodes (e.g., receptor, ligand, water molecules)
- Optional actions (e.g., hide, zoom, label atoms)
- Optional visual model (e.g., ribbons, Van der Waals, licorice)
- Optional color scheme (e.g., per chain, constant color)
This modular structure means you can tailor your visualizations precisely to your needs. Want ligands highlighted in bright green and shown in licorice style, but protein backbones in cartoons colored by chain? That can be a single preset.
How to Build Your Own Preset
You can start with an existing preset and modify it—ideal if you need just slight tweaks—or build from scratch:
- Go to Home > Visual preset > Create… or Visualization > Visual preset > Create…
- Click the
to add a new preset or step. - Define a selection (e.g., “Ligands”). If needed, use the More… option to open the Find window and use the Node Specification Language (NSL) for advanced filtering.
- Add actions (Hide, Zoom, etc.) and visual models.
- Pick a color scheme. You can double-click to customize palettes or define constant coloring per group.
You can move steps up or down to control the order in which they apply. Once set, save your custom preset—next time you need that exact look, it’s just one click away.
Customize Once, Use Forever
Your custom presets are saved and loaded every time SAMSON launches. They become part of your workflow, giving you visual consistency and saving time across projects.
Want to remove an action or step? Just hover over it and click the X. It’s that simple.
Why It Helps
The ability to switch between high-contrast visuals for presentations, publication-style renderings, or detailed explorations — all with one click — makes Visual Presets an underrated but highly useful feature in SAMSON. For those juggling ligand-protein interactions, water networks, hydrophobic clusters, and more, Visual Presets can become your visual cheat sheet.
To learn more about how to fully leverage this feature and learn advanced customization options, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/visual-presets/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.