Creating high-quality molecular visualizations can be time-consuming. Colorizing individual residues, selecting rendering styles, tweaking lighting—we’ve all spent too much time on that perfect image. If you’re preparing figures, presentations, or simply trying to better understand a molecular structure, you probably wish there were an easier way to get good-looking, informative visuals.
That’s where visual presets in SAMSON come in. They offer a fast and efficient way to get clear, professionally styled representations of your molecular systems using predefined style presets. In just a few clicks, your model can be ready for a presentation or publication—no need to micromanage visual model settings.
What are visual presets?
Visual presets are predefined groups of styles and color schemes that can be easily applied to a molecular system within SAMSON. They modify several aspects at once: from how atoms and bonds are displayed, to color mapping, to which visual models are used (like ribbons or van der Waals) — all without having to adjust each parameter manually.
In SAMSON, you can apply a visual preset by navigating to Visualization > Visual preset and selecting from the available options. These presets include styles tailored for protein-ligand complexes, RNA strands, illustrative animations, and more.
The most common use case? Rapidly cleaning up messy molecular structures into easy-to-read graphics. Take, for instance, the “Protein-ligand” preset—designed to immediately spotlight ligands in their protein environment with appropriate visualization styles and coloring that enhance clarity.
Example: Using the “Protein-ligand” preset
Here’s how the “Protein-ligand” visual preset transforms the visualization of PDB 1AA1:
As you can see, the preset automatically applies appropriate models and color schemes to highlight the interaction, reducing clutter and making key components stand out.
Going further: Custom presets
In addition to using built-in presets, SAMSON lets you create and save custom visual presets. This is helpful if you often work with specific molecule types or have a preferred visual style. You can build a visual setup once, and reuse it as often as needed.
If you tweak an existing visual preset or set up your own combination of models and styles, you can simply save that configuration and apply it instantly in future sessions.
Best practices
- Use visual presets early in your workflow. They provide a clean baseline to build from.
- Combine visual presets with rendering effects such as fog, ambient occlusion, and lighting for even better results.
- Create custom presets for repeated figure types or journal submissions to maintain consistent visuals.
Visual presets in SAMSON are a small feature that can save a lot of time. Whether you’re preparing figures for a report or trying to understand a molecular interaction better, these presets offer a solid starting point—or even the final finish—without the usual manual setup.
To explore more options and learn how to apply or create your own visual presets, visit the Visualization documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.