Color is more than aesthetics in molecular modeling – it’s a key part of communication. Whether you’re distinguishing chains in a biomolecular complex or visualizing multiple residues, choosing the right discrete color palette can make your visualizations clearer and easier to interpret.
SAMSON, the integrative molecular design platform, provides a wide range of discrete color palettes that are particularly useful when working with categorical data – for example, when you need to assign a distinct color to each atom type, residue category, or chain in a protein.
What Are Discrete Color Palettes?
Discrete color palettes in SAMSON consist of a fixed number of distinct, visually separated colors. They’re especially helpful when:
- You are mapping a limited number of categories or labels to colors.
- You want to ensure each entity is easily visually distinguishable.
- You’re preparing figures for publication or presentations where clarity is important.
SAMSON includes popular palettes like Set1, Dark2, and Accent, as well as domain-specific sets like Okabe-Ito, known for its colorblind-friendly design. Here’s a quick preview of some options:
Set1
Okabe-Ito (colorblind-friendly)
Carto Vivid
Dark2
Tips for Effective Use
- If you are working with a dataset that includes many categories, opt for palettes like tab20 or Set3 which offer more distinguishable colors.
- For enhanced accessibility, especially in teaching or public presentations, try using Okabe-Ito which is optimized for clarity and colorblind compatibility.
- You can change or reverse color order via the palette dialogs in SAMSON if you want to adjust the visual emphasis.
- Need a personalized look? SAMSON allows you to create or import your own palettes. You can learn more about custom palette creation in the Color palettes section.
When to Use Discrete Palettes
Use discrete color palettes when your molecular visualization involves:
- Chiefly categorical data (e.g., atom types, residues, domains)
- No quantitative values on a continuous scale
- A limited set of distinct elements you wish to highlight
This ensures each category stands out clearly without overlapping color tones that could create confusion.
Whether you’re building complex biomolecular systems or teaching molecular structure visualization, selecting the right color palette contributes greatly to the clarity and professionalism of your work. Want to explore the full set of discrete palettes and see how they look?
Browse the complete listing in the documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net