When visualizing molecular models, color is more than aesthetic—it’s a communication tool. Whether you’re highlighting atom types, representing molecular groups, or differentiating between molecular chains, selecting the right color palette helps make your models intuitive and easier to interpret. But with so many options available, how do you choose the right one?
In SAMSON, the integrative platform for molecular design, users have access to a wide range of discrete color palettes designed to support clarity and accessibility. These palettes are especially useful when you are distinguishing categorical data, such as residue types, ligands, or interacting molecules.
When Should You Use Discrete Color Palettes?
Use discrete color palettes when your data categories are distinct and unordered. For instance:
- Coloring protein residues by type (e.g., aliphatic, aromatic, charged…)
- Highlighting multiple ligands bound to a protein
- Displaying different chains in a macromolecular complex
The goal is to ensure each category is represented by a clearly distinguishable color, even in complex scenes.
Overview of Available Discrete Palettes
SAMSON provides a variety of discrete color palettes, including widely known scientific palettes designed for clarity, accessibility, and aesthetic balance. Here are a few highlights:
- Accent: A colorful palette for high contrast between a small number of categories.
- Okabe-Ito: Carefully designed for color vision deficiency; ideal for communicating results to broader audiences.
- Set1, Set2, and Set3: Common palettes from ColorBrewer often used in scientific visuals.
- Carto Safe: Another palette optimized for universal accessibility.
- Dark2 and Paired: Useful for creating strong contrasts, particularly in presentations.
Below is an example of how these discrete palettes appear visually:
Okabe-Ito palette: designed for colorblind-friendly visualizations
Having a visual preview makes it easier to explore which palettes support your storytelling best—whether you’re preparing a publication figure, teaching a concept, or analyzing a structural phenomenon.
Tips for Effective Palette Use
- Check for perceptual distinctness: Colors should remain distinguishable at small sizes or after exporting to grayscale.
- Keep the category count in mind: Choose palettes with enough distinct colors for your dataset. Some palettes are limited to 8–10 easily distinct colors.
- Consider accessibility: Favor palettes like Okabe-Ito or Carto Safe if your visuals will be seen by people with color vision deficiencies.
- Stay consistent: Use the same palette throughout your project to maintain visual harmony and avoid confusion.
To explore all available discrete color palettes in SAMSON, and see how each looks with real color swatches, visit the full documentation page on color palettes.
For a complete overview of all color options in SAMSON, including sequential, qualitative, diverging, and custom palette creation, explore the full documentation here: Color Palettes Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.