When working in molecular modeling, quickly grasping the identity or role of individual elements—atoms, chains, ligands, or other entities—is essential. Yet, it’s surprisingly easy to get lost in a sea of similar shades when visualizing complex systems, especially when you’re using default or poor color mapping. That’s where discrete color palettes come into play.
In SAMSON, the integrative molecular design platform, discrete color palettes offer a powerful solution for assigning distinct, recognizable colors across different structural elements, helping you distinguish parts of your models at a glance. Whether you’re comparing multiple chains, visualizing molecular categories, or highlighting atom types, discrete color palettes enhance clarity in your work.
Why Discrete Palettes Matter
Visual confusion happens when colors are too similar or don’t contrast well. Discrete palettes are specifically designed to offer well-separated color values that maximize perceptual difference. This makes them ideal for categorical data—such as protein domains or molecular types—where clear distinctions are needed between groups.
Available Palettes in SAMSON
SAMSON comes with a variety of pre-defined discrete color palettes to suit different visual preferences and contexts. Here’s a selection:
- Accent – Soft but recognizable shades that work well in publications.
- Carto Series (Antique, Bold, Pastel, Prism, Safe, Vivid) – Series originally designed for cartography, offering stylish, contrasting hues.
- Okabe-Ito – A colorblind-friendly palette emphasizing accessibility.
- Paired – Designed to pair similar hues for connected categories.
- Dark2, tab20, Set1 – Derived from well-established color standards like ColorBrewer and matplotlib.
Each palette is accompanied by a visual bar so you can preview it directly. Here are a few examples:
Tips for Applying Them
Applying these palettes is simple within the SAMSON interface. When you’re in color palette or color scheme dialogs, you can:
- Select a named discrete palette for immediate visual classification.
- Customize or create your own palette based on specific project needs.
- Reverse palettes when needed for better contrast or thematic balance.
A Note on Accessibility
If you’re collaborating with a diverse team or preparing content for others to consume, it’s important to consider color accessibility. The Okabe-Ito palette, for example, was specifically designed to be readable by individuals with various forms of color vision deficiency.
Taking two extra minutes to choose a high-contrast, well-structured palette can save hours of misinterpretation later.
To explore the full range of palettes and preview them visually, visit the official SAMSON documentation.
To learn more about how SAMSON supports molecular design and visualization, read the full guides at the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at www.samson-connect.net.