As molecular modelers, we often rely on color to highlight important structural features, differentiate between chains, identify atom types, or signal changing properties across trajectories. But here’s a common challenge: how do you choose a color palette that’s both visually effective and perceptually distinct, especially when designing complex molecular representations?
SAMSON, the integrative molecular design platform, offers a wide selection of discrete color palettes to address this. Knowing how to use them can significantly improve clarity and aesthetic appeal in your presentations, simulations, and publications.
Where Discrete Palettes Excel 🎨
Discrete color palettes are ideal when you need to assign unique, contrasting colors to a limited number of categories: for example, representing different residues, protein chains, ligands, or clusters.
In SAMSON, here are some of the discrete palettes you can use:
- Set1, Set2, Set3: Traditional palettes suitable for general-purpose labeling.
- Paired: Good for showing paired elements with subtle differences.
- Okabe-Ito: Designed with colorblind accessibility in mind.
- Carto Vivid, Prism, Pastel: Distinct stylistic choices for publications or presentations.
Visual Comparison of Discrete Palettes
Here are a few examples of the discrete color palettes available in SAMSON:
Set1:
Okabe-Ito:
Carto Vivid:
Quick Tips for Effective Use
- Match palette choice to data type: Keep Set1 and Set2 for general labels; try Okabe-Ito for accessibility.
- Don’t use too many colors: If your data has many categories (e.g., > 10), consider re-grouping elements or switching to sequential palettes if appropriate.
- Preview before applying: Use the color palette dialog in SAMSON to preview color assignments before applying them to your full structure.
Pro Tip 💡
You can also create your own custom discrete palettes in SAMSON or reverse color orders using dialogs provided in the color palette tools. This is useful when trying to match the color asymmetry of a manuscript figure or adapting to a dark vs. light background.
Taking the time to select a fitting discrete color palette can make your visualizations easier to interpret and more visually pleasing without distracting from the science.
To learn more about all available palettes and customization options, visit the full SAMSON documentation on color palettes.
*Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.