Color is more than aesthetics in molecular modeling—it’s a visual language. Whether you’re distinguishing between protein chains, highlighting functional groups, or visualizing molecular dynamics, choosing the right color palette has a practical impact.
However, many molecular modelers struggle with inconsistent coloring schemes across datasets or find that the default palette lacks clarity, especially when dealing with complex molecules or presentations. One frequent challenge is selecting distinct yet harmonious colors for categorical elements—like residues, atom types, or chains.
If you’re using SAMSON, the integrative molecular design platform, there’s a structured solution to this: the Discrete Color Palettes. These predefined palettes are carefully curated to improve differentiation, contrast, and accessibility in molecular scenes.
What Are Discrete Color Palettes?
Discrete palettes are sets of distinct colors used mainly for categorical data. In molecular modeling, this might apply when assigning unique colors to different chains or molecule types for comparison.
SAMSON provides a diverse collection of discrete palettes—everything from cartographic schemes to color-safe variants and those designed specifically for accessibility (e.g., Okabe-Ito). Here’s a quick overview of some available palettes:
- Accent: Good for emphasizing specific residues or selections.
- Carto Vivid: A vibrant option derived from mapping visualization techniques.
- Dark2: Offers deep and rich hues—ideal against lighter backgrounds.
- Okabe-Ito: Designed to be colorblind-safe (CVD-friendly).
- Set1, Set2, Set3: Widely used multi-hue palettes from scientific publications.
Here’s a visual example of the Set1 palette:
When to Use Discrete Palettes
Use discrete palettes in scenarios where:
- You need to color multiple distinct molecular chains for comparison.
- Displaying different atom types or molecular instances side-by-side.
- Exporting publication-quality figures with repeatable, readable colors.
Each palette is previewed in SAMSON’s color palette dialogs, so you can visually select the best option for your current visualization. You can even reverse the order of colors or design your own palette if needed.
What’s the Okabe-Ito Palette?
This palette deserves special attention. Created with color vision deficiency in mind, Okabe-Ito ensures contrast between colors remains distinguishable even for viewers with red-green color blindness. If you’re preparing figures for publication or broader audiences, this is a useful choice:
Tips for Best Use
- Use fewer colors when possible to avoid visual overload.
- Pair with consistent molecular annotations for clearer interpretation.
- Test your visuals under grayscale or CVD simulators when working on presentations.
Discrete color palettes may seem like a small feature, but they can significantly enhance clarity in your molecular visualizations. Try experimenting with a couple of palettes in your next layout—you might find that one fits your workflow better than your current default.
To explore the full list of options and see previews of all palettes, visit the official documentation page on color palettes in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.