When building molecular models, effective visual distinction between different structures, chains, atoms, or datasets is essential for clarity. But how often have you found yourself stuck with default colors that just don’t work — whether they’re too similar to distinguish easily or simply not visually pleasing?
SAMSON, the integrative molecular design platform, offers a full set of discrete color palettes for precisely this reason. These palettes allow you to assign clearly differentiated colors to distinct categories — perfect for use cases like visualizing different residues, ligands, or molecular chains without ambiguity.
In this post, we’ll take a closer look at the Discrete color palettes available in SAMSON and provide guidance on when you might want to use each. The palettes are accessible in the color palette and color scheme dialogs in SAMSON, and they cover a wide range of aesthetic styles, from functional to artistic.
What are discrete color palettes useful for?
- Highlighting different chains or residues in a protein complex
- Color-annotating molecular fragments or conformations
- Defining groups in simulations or multi-component systems
- Teaching or demonstrations requiring easily distinguishable colors
Available Discrete Color Palettes
Each palette has unique color characteristics. Here are some popular choices, with visual examples below:
- Accent: A set of moderate pastel tones with good contrast.
- Carto Series (e.g., Carto Antique, Carto Bold, Carto Prism): Inspired by cartographic coloring practices — great for aesthetic visuals in publication visuals.
- Dark2 and Set1, Set2, Set3: Commonly used in data visualization, these provide well-spaced categorical colors.
- Okabe-Ito: A colorblind-friendly palette specifically designed for scientific figures.
- tab10/tab20: Borrowed from Matplotlib, very practical for consistent, well-tested visualizations.
Visual Examples
Below are some of the palettes you can find in SAMSON. Click to see in larger format:
Tips when using discrete palettes
- You can reverse the order of colors in the palette, which can be handy if you want to maintain a consistent logic across different datasets or structures.
- SAMSON also lets you create your own custom palettes using the same interface, for absolute control.
- Not all palettes support a large number of categories. For models involving many groups, consider using tab20 or Set3.
To explore all the discrete color palettes and find the best match for your content, browse the full list in the official documentation: SAMSON Color Palettes Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at https://www.samson-connect.net.