If you often find yourself applying the same sequence of visualizations when working on molecular systems—setting colors, choosing representations, focusing on ligands—you are not alone. Consistency in visualization is key for insights, collaboration, and publication. But endlessly repeating the same steps wastes time and adds room for error.
What if you could turn those repeated steps into a single click?
That’s exactly what SAMSON’s Visual Presets offer. More than just a convenience, customizing visual presets can significantly streamline your molecular modeling workflow by letting you define how structures appear and behave, including selections, actions, visual representations, and color schemes. Here’s a deeper look into how this system works and how to create your own presets for faster, consistent molecular visualization.
What Is a Visual Preset?
A Visual Preset in SAMSON is a combination of steps that define how specific parts of a molecular system should be presented. Each step contains:
- A selection of nodes (e.g., ligands, receptors, solvents)
- Optional actions (like hiding, labeling, or zooming)
- Optional visual models (e.g., van der Waals, ribbons, licorice)
- Optional color schemes (e.g., per chain, constant color)
This means you can, for example, define a preset that automatically highlights the ligand in licorice style with per-element coloring, hides water molecules, and zooms on the receptor-ligand complex—all without a single manual adjustment after loading your molecule.
How to Create Your Custom Preset
To begin, go to Home > Visual preset > Create… or Visualization > Visual preset > Create…. You can either start with a blank slate or modify an existing preset.
From there, click the 
Add step button. For each step you can:
- Select a node type: Choose from default categories like receptors or ligands, or create your own involving specific criteria using the Node Specification Language
- Apply actions: Want to hide water or zoom to your ligand? Add that action here
- Add a visual model: Pick how you want the items to appear—e.g., Van der Waals spheres for ligands
- Choose colorization: Color by chain, by element, or use a constant color for clarity
If you want to fine-tune a selection, scroll to the bottom of the selector list and click More… to open the Find window. Here, you can define custom queries using the Node Specification Language to pinpoint exactly what you want to manipulate in your system.
You can also apply multiple actions within a single step and easily re-order or remove them. Visual models and color schemes are similarly flexible—choose from many presets or define your own palettes through a dialog window.
Once satisfied with your Visual Preset, click Save visual preset so it’s available next time you work on a molecule. Users working across projects or collaborating with others will appreciate how custom presets ensure a consistent, easy-to-recognize visual standard—and speed things up in the process.
Why It Matters
Creating custom visual presets may only take a few minutes, but it can save hours over the course of large projects. Whether you’re preparing figures for publication, teaching students, or reviewing complex systems, having the right visuals at the ready makes a big difference.
To learn more, visit the full documentation page: 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.