Colors aren’t just visual flair in molecular modeling—they are crucial tools for understanding. When dealing with complex molecular structures, reaction networks, or simulation results, using clear, distinguishable colors helps avoid confusion and supports better decision-making.
In SAMSON, discrete color palettes serve this need by assigning distinct colors to separate elements in your models—atoms, residues, chains, domains, or even different simulation frames. But with so many palette options available, how do you pick one that fits your data best?
What are discrete color palettes?
Discrete color palettes are designed to split the visual spectrum into clearly separable chunks. Unlike sequential palettes (which are suited for continuous data), discrete palettes help you easily differentiate categories: e.g., protein chains or groups in a clustering result. Whether you’re colorizing by molecule name or assigning unique colors to selection sets, discrete palettes are tailored for clarity.
Palette options in SAMSON
SAMSON provides more than a dozen pre-defined discrete color palettes. Each one comes with a unique character to suit your specific visualization goals:
- Accent: Soft but diverse hues, good for labeling up to eight categories.
- Carto Palettes (Antique, Bold, Pastel, Prism, Safe, Vivid): Inspired by cartographic mapping, offering stylish blends of readability and aesthetic coherence.
- Okabe-Ito: A colorblind-friendly choice optimized for distinctiveness even in grayscale printouts.
- Set1, Set2, Set3: Balanced and bright palettes from the ColorBrewer project, commonly used in plotting software.
- Paired / tab10 / tab20: Widely used in data visualization libraries like Matplotlib and D3.js, offering harmony for larger sets of categories.
Here’s a peek at a few of them:
Carto Prism
Okabe-Ito
tab20
Tips for choosing the right palette
Here are a few considerations when picking a discrete palette for your next project:
- Number of categories: Check whether the palette provides enough unique colors. For small numbers, any will work; for >10, consider tab20 or Carto Prism.
- Accessibility: If sharing or publishing results, opt for Okabe-Ito or Carto Safe to accommodate readers with color vision deficiencies.
- Style consistency: Match with your lab’s or publication’s visual identity—Carto Pastel offers a muted, professional look, while Vivid feels modern.
Customization and flexibility
Can’t find a palette that fits perfectly? SAMSON lets you create your own palettes or reverse palette directions if needed. Just open the color palette dialog and get started. You can even save custom schemes for reuse.
Using the right discrete palette can truly make a difference in interpretation and communication of your molecular data. Clear visuals enhance clarity—not only for yourself, but also for collaborators and audiences.
To learn more, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net