If you’ve spent time repeatedly coloring atoms, toggling representations, and organizing your molecular scenes, you’re not alone. For many molecular modelers, one of the most frustrating tasks is having to redo the same visualization settings every time they open a new molecular structure. Whether it’s setting ribbons for proteins, spheres for ligands, or coloring by chain, it takes time – and can break your workflow.
This is where Visual Presets in SAMSON come in. They allow you to define once—and reuse forever—specific visualization styles, combining selections, actions, representations, and color schemes into a few simple clicks.
What makes a visual preset?
Each visual preset is built from a set of steps. Each step includes four customizable components:
- Selection of nodes (e.g., Ligands, Water, Receptor)
- Optional actions (e.g., Hide, Zoom on selection)
- Optional visual models (e.g., Van der Waals, Ribbons)
- Optional color schemes (e.g., Constant color, Per element)
Together, these make it possible to define highly specific views, ensuring that every time you visualize a protein-ligand complex or a polymer chain ensemble, it appears exactly the way you need it to.
Creating a custom visual preset
To create a visual preset in SAMSON, go to Home > Visual preset > Create… or Visualization > Visual preset > Create….
From there, you can:
- Click on
to add a new preset - Add steps by selecting Add step
- Choose your selection: default groups like “Receptor”, or custom ones using the Node Specification Language
- Apply actions like hiding solvent molecules or zooming on the ligand
- Choose the right visual model (e.g., Ribbons for proteins, Licorice for ligands)
- Color your selections meaningfully
You can use multiple steps to layer your visualizations. For example, the receptor can be shown as a ribbon and colored per chain, while the ligands appear as sticks with atom-based colors. This layered structure makes the visualization more informative.
Each step can also include edits: reorder, delete, or add new ones on the fly. Saving your custom preset will keep it available each time you launch SAMSON, as a personal favorite that boosts your productivity.
Why this matters
Visual presets are not just about aesthetics. For publication-quality images, quick exploration of new structures, or comparative visualization across datasets, consistent views are key. Presets help you avoid repetitive tasks and reduce errors, especially when dealing with large structures or collaborative projects.
Once you’ve created a set of presets that work for your workflow (e.g., one for proteins, another for small molecules, or one optimized for highlighting polar interactions), switching between them is instantaneous and makes your modeling environment feel more tailored and efficient.
Want to share or contribute?
If you think your visual style could help others, you’re encouraged to contribute it. Use the Send feedback button in SAMSON to get in touch and suggest your preset to be added to the defaults.
Learn more about visual presets here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.