When studying complex molecular systems, clarity is key. Whether presenting research, teaching, or navigating your own data-rich models, the ability to differentiate components visually can make all the difference. This is where color palettes play a crucial role. SAMSON provides a diverse set of discrete color palettes designed to help you differentiate between categories or types of items, such as chains, residues, or ligands.
But with over a dozen options to choose from, how do you pick the right one for your project?
What Are Discrete Color Palettes?
Unlike sequential or diverging palettes that represent ordered values or deviations from a midpoint, discrete palettes are meant for categorical data. These are particularly useful when labeling distinct chains in a large biomolecular complex, or when visualizing different ligands, cofactors, or molecules in a multi-structure scene.
Palette Options in SAMSON
Here are some of the discrete palettes available in SAMSON, each with its own style and use case:
- Accent – A colorful palette with high contrast, well-suited for differentiating elements in figures.
- Carto Antique and Carto Bold – Stylized palettes often appreciated for presentations and publications.
- Carto Prism and Okabe-Ito – Designed for color blindness accessibility, especially helpful in teaching or public communications.
- Set1, Set2, Set3 – Inspired by the ColorBrewer project, these palettes are familiar to data visualization practitioners.
- tab20 series – Great when you need many distinct colors without overwhelming contrast.
Here’s a visual comparison to give you an idea of what these look like:
Best Practices
When choosing a discrete palette, consider the following guidelines:
- Number of categories: Some palettes support more categories better than others. For example, tab20 can distinguish up to 20 groups.
- Accessibility: Palettes like Okabe-Ito have been tested for color vision deficiencies.
- Consistency: Use the same palette across figures or slides to maintain coherence.
Customizing and Reversing Palettes
SAMSON also allows you to reverse the left and right arms of a palette directly in the dialogs. This can subtly change the implication of a visual hierarchy or help align with pre-existing figure conventions.
You’re not limited to what’s preloaded, either. The platform allows you to create and add your own custom palettes. This is helpful if your organization has branding guidelines, or you’re working with a colorblind colleague.
To learn more about how to work with all types of color palettes in SAMSON, including sequential and diverging palettes, or how to create your own, visit the full documentation page.
Learn more about SAMSON’s color palettes.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at https://www.samson-connect.net.