When working with complex molecular models or large biomolecular systems, one common source of frustration is the lack of visual clarity. At some point, everything is color-coded in a way that makes it hard to tell atoms, chains, or functional groups apart. Whether you’re analyzing a protein-ligand complex or setting up a figure for publication, a thoughtful choice of color palette can make a big difference in readability—and even prevent errors in interpretation.
In SAMSON, discrete color palettes offer a handy way to assign distinctive colors to categorical elements like residues, molecule types, or domains. These palettes assign unique but visually balanced colors to each category, which is particularly important when you have tens or even hundreds of grouped elements.
What Are Discrete Color Palettes?
Discrete color palettes are best suited for categorical data: things that fall into distinct, non-sequential groups. For example, if you want to distinguish between multiple molecules in a system (e.g., water, ligand, receptor, counter ions), discrete palettes help make each component visually distinct without implying a gradient or numerical relationship.
Explore the Options
SAMSON currently offers over 18 discrete color palettes, adapted from widely-used schemes in scientific visualization. Examples include:
- Okabe-Ito: Colorblind-friendly palette.
- Carto Bold / Pastel / Vivid: Designed for maps, great for high contrast or muted tones.
- Set1 / Set2 / Set3: Popular palettes used in data visualization tools like ggplot2 in R.
- Dark2: Good for darker backgrounds with strong contrast.
- tab10 / tab20 / tab20b / tab20c: From the Tableau color systems.
Here’s an example of the Carto Vivid palette:
How to Use These Palettes Effectively
When selecting a palette, consider the following tips:
- Number of Groups: Some palettes look great with up to 10 distinct categories; beyond that, colors might become similar.
- Background Color: If you’re working with a dark background, opt for brighter palettes like Set1 or Carto Bold.
- Colorblind Accessibility: Use palettes such as Okabe-Ito to ensure accessibility.
- Print Media: For figures intended for print, avoid too many similar hues, and test visibility on grayscale printers if needed.
Quick Tip: Reverse Palette Arms
Did you know you can also reverse the left and right arms of an HCL palette in SAMSON? This is useful when you want to flip the emphasis from one end of the color spectrum to another. You can do this directly from the color palette or color scheme dialogs.
Create Your Custom Palette
If none of the default palettes satisfy your needs, you can also create your own custom discrete palette. Just go to the Color Palettes settings and define a set of handpicked colors tailored for your system or branding style.
For a full overview of available palettes and how to use them, visit the documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.