For many molecular modelers, the first step in gaining insight from a structure is being able to see it clearly. But visualizing complex biomolecular systems can be time-consuming. Choosing how to represent atoms, bonds, chains, ligands, and setting rendering parameters like lighting and fog can quickly become a repetitive task—especially when jumping between different structures.
That’s where visual presets in SAMSON can make a difference. With just a few clicks, SAMSON users can transform raw molecular data into meaningful visualizations tailored for analysis, presentation, or publication. Whether you’re working with proteins, ligands, nucleic acids, or large molecular assemblies, visual presets offer predefined combinations of representations and color schemes that reduce setup time and improve readability.
Why use visual presets?
Visual presets are a way to apply curated visual styles to molecular systems in SAMSON. These styles automatically define how atoms, residues, and chains are displayed, which visual models are used (e.g., secondary structures, van der Waals surfaces), how elements are colorized, and how rendering effects are configured.
For example, you can quickly apply a “Protein-ligand” preset to show the protein backbone with ribbons and color chains by ID, while highlighting the ligand using a different representation. This visual context helps you immediately grasp molecular interactions without spending time setting each style manually.
How to apply a visual preset
In SAMSON, applying a preset is straightforward:
- Go to Visualization > Visual preset
- Select from the list of available presets (e.g., “Protein-ligand”, “Illustrate…”, etc.)
The selected preset will be instantly applied to the structure in the viewport.
Illustrative style – For publications and teaching
If you’re preparing figures for a presentation or manuscript, SAMSON also includes an “Illustrate…” preset inspired by Molecule of the Month illustrations by David S. Goodsell.
This preset combines van der Waals models with high-contrast coloring per chain or component, and can be paired with a matching rendering preset under Visualization > Presets > Illustrative. The result is a clean, sketch-like visual style that emphasizes structural features without overwhelming shading or effects.
Making your own presets
Have a visual style you use frequently? You can create and save your own visual presets. After customizing a visualization, save it under a name and reuse it later with one click. This is especially useful if you’re analyzing a series of similar structures or sharing consistent views across a project team.
When presets aren’t enough
While presets are powerful, they are just starting points. You can still manually add visual models, adjust rendering styles, or colorize specific residues as needed. SAMSON is designed for flexibility, and visual presets help you get to that point much faster.
To learn more about visual presets and see step-by-step usage examples, visit the Visualization section of the SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.