For many molecular modelers, producing high-quality visualizations from complex molecular systems is a time-consuming task. Whether for presentations, publications, or simply to better understand molecular structures, styling a model typically involves many steps — selecting components, choosing representations, applying color schemes, and organizing scenes. If you find yourself repeating these steps often, customizing visual presets in SAMSON can truly simplify your workflow.
In SAMSON, Visual Presets are sets of actions and visual styles saved together under a name. When applied, a preset instantly configures the visual representation of your molecular system. More importantly, you can create and customize your own presets to match your exact preferences or project requirements — and reuse them as often as needed.
Why Create Custom Visual Presets?
- Consistency: Ensure repeatable, publication-ready visualizations across different models.
- Efficiency: Save time by applying complex representation setups in just one click.
- Automation: Reduce manual steps and focus on your scientific insights.
Getting Started with the Visual Preset Editor
To create a new visual preset, go to Home > Visual preset > Create… or Visualization > Visual preset > Create…. This opens the Visual Preset Editor where you can define a series of steps. Each step can include:
- A node selection (e.g., Receptor, Ligands, Water)
- Any actions to apply (e.g., hide, label atoms, zoom)
- A visual model (e.g., Ribbons, Van der Waals)
- A color scheme (e.g., Constant, Per chain)
You can add multiple steps by clicking the + Add step button, creating a layered sequence of visual modifications. Each step is applied in order, allowing for comprehensive visual customization.
Example: Customizing a Ligand View
Let’s say you’re focusing on ligand interactions. You could set up a visual preset that:
- Selects ligand atoms
- Applies the Licorice visual model
- Sets a constant color (e.g., cyan)
- Zooms on the selection
This preset will instantly recreate your preferred ligand view, no matter which molecule you work on.
You can also define your own selectors using the Node Specification Language if the default categories do not match your needs.
Fine-Tuning Visual Styles
Further customization is just a few clicks away:
- Actions: Add multiple, sequential actions within a step
- Visual Models: Combine different representations in multi-step presets
- Color Palettes: Use default or define your own palettes
And if you wish to change your mind later, visual preset steps can be reordered, modified, or deleted. When you’re satisfied, click Apply. You’ll be prompted to save your new preset if you haven’t already.
Reusing and Sharing Presets
Once saved, your custom presets load automatically whenever you launch SAMSON. They appear alongside the default presets and can be shared within your team for consistent visual reporting.
To learn more or explore additional details, check the full documentation on visual presets.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.