Setting up visualizations for complex molecular systems often takes time—especially when you want consistent style, clarity, and precision across multiple structures or sessions. Whether you’re preparing a publication figure, exploring protein-ligand interactions, or showing a dynamic process to students, you’ve likely repeated the same visualization steps over and over.
If you’re using SAMSON, there’s a faster way: Custom Visual Presets. These allow you to apply a combination of representations, colors, and actions to selections in just one click, streamlining your workflow and saving countless repetitive steps.
What is a Visual Preset?
A Visual Preset in SAMSON consists of a sequence of steps. Each step includes:
- A selection of nodes (parts of the molecular system)
- Optional actions (e.g., hide or zoom)
- An optional visual model (e.g., ribbons or Van der Waals)
- An optional color scheme
You can apply presets to selected nodes or entire documents, and SAMSON even creates a folder organizing the applied models and selections automatically.
Why You Should Create Your Own
Creating your own visual preset helps you:
- Ensure consistent visuals across projects and presentations
- Quickly switch between different visualization styles based on the audience (researchers, students, reviewers)
- Save time by eliminating repetitive tasks when dealing with different proteins, ligands, or assemblies
Imagine always showing ligands in licorice style with chain-based coloring, while water is hidden and the protein backbone is shown as ribbons in neutral gray. Once you set this up as a visual preset… click once, and it’s done.
How to Make a Visual Preset in SAMSON
Go to Home > Visual preset > Create… or Visualization > Visual preset > Create…. You’ll see an editor where you can:
- Add new steps with
Add step - Choose node selections like “Ligands” or “Receptor” — or define custom selections using the Node Specification Language
- Apply actions (Zoom, Hide, etc.)
- Select a visual model and apply colorization
Each step is flexible: mix and match actions, visuals, and colors. Steps are executed in order, so you can build dynamic visual sequences.
When and Where It’s Useful
- Running repetitive analyses on structure series (e.g., docking results)
- Teaching: you can create simpler, cleaner visuals for certain systems
- Demonstrating specific features (e.g., highlighting polar contacts in ligands)
You can also update presets anytime—just open them, change steps or sequences, and save. SAMSON stores your presets along with the default ones and loads them each time you start it.
If you’d like your visual setup to become a standard in SAMSON, you can even submit your visual preset via the Send feedback button in SAMSON’s interface.
Want step-by-step instructions with more images? Visit the full documentation on this topic in the official SAMSON Visual Presets page.
*Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.