Color is more than visual flair in molecular modeling — it’s a vital tool for interpretation, annotation, and storytelling. Especially when handling large systems, molecular modelers often need to distinguish between specific chains, ligands, or molecular properties at a glance. But manually picking colors every time can be tedious, inconsistent, and occasionally confusing. Wouldn’t it be easier to rely on a consistent color logic that communicates meaning intuitively?
This is exactly where discrete color palettes in SAMSON come in handy. Discrete palettes assign distinct colors to categorical data — like atom types, residue names, or molecule selections — making them ideal for quick classification.
What Makes Discrete Palettes Useful?
Imagine visualizing several protein chains or different ligands in a large complex. If each selection ends up with a color that’s too similar to another, it becomes hard to distinguish between them. Discrete palettes provide clear differentiation to prevent that.
SAMSON includes a comprehensive set of discrete palettes that cover a wide range of use cases, from accessibility-aware schemes to palettes suited for publications or dark-mode themes. Here’s a glance at some of the most useful ones available by default:
- Accent – A compact yet vibrant set of colors, great for emphasizing key selections.
- Carto palettes (Antique, Bold, Pastel, Prism, Safe, Vivid) – Originally designed for cartography, these palettes offer both aesthetic variation and clarity, useful for dividing complex selections.
- Set1, Set2, Set3 – Popular palettes often found in data visualization libraries.
- Okabe-Ito – A colorblind-safe palette designed to ensure accessibility for all viewers.
- tab10, tab20, tab20b, tab20c – Excellent choices when labeling many categories.
Example: Carto Bold
Wondering what Carto Bold looks like in action?
As you can see, each color is easily distinguishable from the others. This makes it perfect for visualizing up to 10 categories without overwhelming the viewer.
Tips When Using Discrete Palettes
- You can quickly switch between palettes using the Color Palette dialog in SAMSON.
- Need to emphasize a group? Pick a bolder palette like Vivid or Set1.
- If working with a colleague who has color vision deficiency, use Okabe-Ito or Carto Safe.
- Colors can also be reversed directly from the dialogs for visual optimization.
Consistency Matters
Using structured palettes can also help maintain naming conventions or align visual themes across multiple projects. Whether you’re preparing figures for a publication or sharing molecular models in presentations, relying on predefined discrete palettes saves time and improves clarity.
Better yet, you can define your own palette if your project requires specific branding or a domain-specific scheme.
To view all default discrete palettes and try them out, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.