If you’ve ever spent more time formatting a molecular visualization than analyzing it, you’re not alone. Adjusting colors, toggling visibility, setting rendering parameters—all these steps add up, especially when working with large systems or during presentations. Fortunately, there’s a shortcut built into SAMSON that many users overlook: visual presets.
Visual presets in SAMSON let you instantly apply a full set of visual styles and color schemes to your molecular system in just a couple of clicks. Whether you’re preparing figures for a publication, slides for a talk, or just trying to interpret complex structures more clearly, visual presets help you get results fast—and consistently.
What are visual presets?
Visual presets are predefined templates that combine visual representations (like ribbons or Van der Waals models) with color schemes, all intelligently based on the molecule’s properties such as chain ID or residue type. Best of all, these can be applied to your structure without fussing with individual rendering settings.
How to use them
Applying a visual preset is simple:
- Click on Visualization > Visual preset.
- Choose one of the existing presets from the list.
The changes are instantly visible in the viewport, allowing you to focus on the science, not the formatting. Here’s what the Protein-ligand preset looks like on PDB entry 1AA1:
Create your own presets
In addition to the default set, SAMSON lets you create and save your own visual presets. This is especially helpful if you often visualize the same type of structure (e.g., ligands in active sites) and want to maintain consistency across sessions or collaborations.
Your custom presets can include:
- Multiple visual models per structure
- Color schemes based on chain ID, residue types, or atomic attributes
- Rendering options like transparency or illustrative effects
Illustrative styles for publications
If you’re preparing publication-ready images, SAMSON offers an illustrative preset inspired by David Goodsell’s iconic Molecular Landscapes. You can apply this by selecting:
- Visualization > Visual preset > Illustrate… for shapes and colors
- Visualization > Presets > Illustrative to match rendering settings like lighting and outlines
When are visual presets useful?
Here are a few scenarios where visual presets can save you time and effort:
- Finalizing a figure: Quickly switch between high-quality and illustrative styles to see what works best.
- Live demos: Adjust a molecular presentation on-the-fly without diving deep into rendering menus.
- Consistent team visuals: Share presets among colleagues to ensure visual consistency.
Visual presets are one of those features that quietly remove friction from your workflow. Once you start using them, it’s hard to go back to manual adjustments.
To learn more about visual presets—how to apply, customize, and share them—visit the SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.