For molecular modelers, visual clarity is essential. Whether you’re interpreting a protein-ligand interaction, preparing data for publication, or explaining a molecular mechanism to a broader audience, being able to generate clean, meaningful images can make a big difference.
But carefully selecting visual styles, color schemes, and rendering parameters manually for each molecule can be time-consuming. What if you could apply a professional-looking visualization in just a single click? That’s exactly what visual presets in SAMSON allow you to do.
What are visual presets?
Visual presets are predefined combinations of visual representations and color schemes that apply instantly to a molecular system. They take care of choosing the most appropriate visual models for different molecular elements—proteins, ligands, ions, etc.—as well as lighting, shading, and coloring options.
For instance, the built-in Protein-ligand preset automatically represents the protein using ribbons, highlights the ligand using van der Waals spheres, and applies a distinctive color scheme that brings forward relevant interactions. Here’s what applying that looks like on a molecule with PDB code 1AA1:
How to apply a visual preset
To try it yourself in SAMSON:
- Go to Visualization > Visual preset.
- Select one of the available presets (e.g., Protein-ligand, Illustrate…, etc.).
The changes are immediately reflected in your viewport.
Do presets take away your control?
Not at all. You can think of presets as a powerful starting point. Once applied, you can tweak individual visual models, change colors, or adjust rendering effects to suit your specific needs.
SAMSON includes a library of built-in presets, but you can also create your own based on how you prefer to display certain molecular systems.
If you often work with similar types of structures, saving your own preset can save you time and ensure consistency across your projects.
Illustrative style inspired by scientific art
If you’re looking to generate eye-catching molecular illustrations like those featured in the RCSB’s Molecule of the Month, SAMSON includes an Illustrate visual preset that mimics that minimalistic, high-contrast style:
Pair this visual setting with the Illustrative rendering preset to optimize shadows, lighting, and background contrast:
This dual-preset approach is ideal for both educational content and high-quality figures.
Customizing and creating your own presets
You can clone any visual preset, modify the representations and color schemes, and save it as your own custom preset. This is especially useful for labs that want to maintain a visual style across multiple figures or for researchers producing consistent snapshots for simulations over time.
To learn how to build your own preset, check the Visual Presets documentation.
Conclusion
Whether you’re a novice looking for quick, reliable visualization defaults or an experienced user striving for efficiency and consistency, visual presets in SAMSON provide a practical solution that saves time and enhances clarity.
You can explore more visualization tools and visual presets in the official SAMSON documentation: https://documentation.samson-connect.net/users/latest/visualizing/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.