Visualizing molecular structures clearly and distinctly is central to effective molecular modeling. Whether you’re representing different atom types, residues, domains, or simulation states, your ability to communicate data visually with accuracy and ease can make a significant difference. But here’s a common problem: it’s incredibly easy to pick color palettes that look good in general but fail in scientific visualization.
Colors that are hard to distinguish, inaccessible to color-blind users, or inconsistent across models can quickly introduce confusion. That’s where discrete color palettes come in—or rather, choosing the right ones for molecular design platforms like SAMSON.
What Are Discrete Color Palettes?
Discrete color palettes consist of a fixed set of distinct colors used to represent categorical data—perfect for assigning colors to specific molecule components. In SAMSON, you have multiple built-in options, each serving different use cases. Here are some highlights:
- Okabe-Ito: Designed for accessibility, this is a color-blind safe palette ideal for universal sharing and presentations.
- Carto Safe: Another palette with good perceptual differentiation, useful in environments where color perception might vary widely (e.g., classrooms, printed outputs).
- Accent: Includes more vibrant and contrasting colors, good when representing a small number of key structural features.
- Paired and Dark2: These palettes offer extended ranges and moderate contrast, useful when categorizing more than ten categories with clear labels.
Here are a few examples right from the SAMSON documentation:
Okabe-Ito palette:
Carto Safe palette:
When to Use Which Palette?
Use high-contrast palettes like “Accent” and “Carto Vivid” for educational or visual media. These palettes have vivid, saturated colors that can make structures pop. However, avoid them in color-critical applications like printing or in accessibility-sensitive contexts.
Use color-blind safe palettes like “Okabe-Ito” for collaboration and publishing. These palettes ensure that data is interpreted correctly across different audiences, regardless of visual differences in color perception.
Use more subdued palettes like “Carto Antique” for overlays or when working with complex scenes. These won’t distract from core visual elements and are good for layered representations.
Maximizing the Value of Color Palettes
You can fully configure your palette choice in SAMSON dialogs. Here’s a bonus tip: you can reverse the color arms in palette settings. This is especially helpful when you want to align the visual scale with the directionality of a simulation or transition (e.g., high to low vs. low to high activity).
And if the defaults don’t cut it, SAMSON allows for full customization. You can create your own HCL friends in the color palette interface using intuitive tools made for visual predictability.
Choosing the right color palette doesn’t solve all visualization challenges, but it’s a low-effort, high-impact decision that improves clarity, accessibility, and even aesthetic appeal.
To explore the complete list of available palettes and use cases, visit the official SAMSON color palettes documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.