One common obstacle molecular modelers encounter is the visual clutter that arises when representing complex molecular systems. With multiple chains, ligands, functional groups, or protein domains in a scene, choosing clear and consistent colors becomes more than a matter of aesthetics—it’s essential for comprehension and communication. If you’ve ever struggled to find a color scheme that distinguishes elements without overwhelming your visualization, you’re not alone.
Fortunately, SAMSON provides a diverse collection of discrete color palettes tailored to help you segment and identify different molecular parts clearly. These are especially useful when you need to represent a set of distinct categories—like protein chains, different residues, or unique structural components—without implying any numerical order or gradient.
Why Use Discrete Color Palettes?
Discrete palettes assign distinctly different colors to a fixed number of categories. In other words, each item gets its own unique, easily separable color. This is much more effective than continuous gradients when it comes to categorical data.
In SAMSON, you can choose from a variety of predefined discrete palettes under the Color Palettes section in the software. These include popular standards such as Set1, Accent, Dark2, and Okabe-Ito, each designed with accessibility and clarity in mind.
Examples of Available Palettes
Here are a few examples with previews to help you decide which might best suit your needs:
Set1
A bright, high-contrast palette suitable for distinguishing up to 9 categories.
Okabe-Ito
Designed to be colorblind-friendly and effective in both print and screen environments. Useful for up to 8 categories.
Accent
Designed for visual accessibility; draws clear distinctions even in complex scenes.
Carto Vivid
Visually appealing and vivid palette originally designed for cartographic use. Can handle many categories with strong color variety.
Tips for Getting the Most Out of Discrete Palettes
- Use Okabe-Ito if accessibility is a concern—especially if your visuals will be presented to a broad audience.
- Try Carto Antique or Carto Pastel if you’re aiming for a more subdued look in your visualizations.
- Set3 and tab20 work well for large numbers of categories but may sacrifice contrast between similar hues.
And remember—you can always add your own custom palettes in SAMSON if needed. This can be especially valuable for branding, publications, or comparative studies where consistency across models is important.
To explore the full list of discrete color palettes and learn more about how to customize them for your molecular design projects, visit the color palettes documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.