When working with complex molecular models, color is much more than just aesthetics. It plays a critical role in distinguishing between atoms, molecules, conformations, and other elements of a model. An effective color palette can help make a visualization understandable at a glance, while a poorly chosen one may lead to confusion or misinterpretation.
SAMSON, an integrative platform for molecular design, provides a robust set of default color palettes to help molecular modelers communicate data clearly and accurately. In particular, discrete color palettes are essential when assigning distinct colors to categorical variables — for example, different residues, molecular domains, or molecules in a system. These palettes ensure that labeled groups are clearly separated visually.
Why Discrete Color Palettes Matter
In many molecular systems, you’ll be visualizing elements that should be perceived as logically distinct: say, RNA chains in a ribosome, or ligands binding to different sites. Each of these items should ideally be assigned a unique, distinguishable color. Discrete color palettes are collections of individual colors with enough perceptual difference to be used in such contexts.
Using well-designed palettes avoids colors that are too similar (especially problematic in grayscale printing or for color-blind viewers), and can also take into account context and cultural associations (for example, red often signals importance or danger).
Palette Options Available in SAMSON
SAMSON offers a range of discrete color palettes that vary in tone, contrast, and design purpose. Here are some examples:
- Accent – A high-contrast palette ideal for emphasizing up to 8 items.
- Carto Series – A variety of palettes for different moods, such as Pastel, Bold, Antique, and Vivid. These are inspired by cartographic conventions and maintain good visual differentiation.
- Dark2 – A palette with rich, saturated colors that work well against light backgrounds.
- Okabe-Ito – A colorblind-safe palette often used in scientific publishing.
- R4 – A more compact set, useful for highlighting just four categories.
- Set1/Set2/Set3 – Classic palettes from ColorBrewer designed for maps and data visualization — also widely used in scientific plotting tools.
- tab10/tab20 series – Inspired by Tableau’s color schemes, suited for dashboards and data-heavy visuals.
Below is a visual example of the “Carto Vivid” discrete palette:
Choosing What Works for You
While many users default to the same palette out of habit, it’s worth experimenting with alternatives to find those best-suited for your specific visual goal. Here are a few general recommendations:
- Use Vivid, Bold, or Accent palettes when visual contrast is needed to differentiate components in a dense model.
- Prefer Pastel variants for presentation materials where softer tones may be easier on the eyes.
- For publications or accessibility, choose the Okabe-Ito palette for its colorblind-safe properties.
You can also customize your own color palettes (via dialogs in SAMSON), which is helpful when branding or standardization is needed across multiple projects.
View the full list of options, including sequential, qualitative, diverging, and flexible diverging palettes, in the documentation.
To learn more about using color in molecular visualizations with SAMSON, visit the official documentation: Color Palettes in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.