If you’ve ever struggled to distinguish between important parts of a molecular model due to color confusion or visual overload, you’re not alone. A common pain point in molecular modeling is using color schemes that are either too harsh, too similar, or not perceptually uniform. This makes it hard to interpret data, compare structures, or create figures that are both clear and publication-ready. Fortunately, SAMSON, the integrative molecular design platform, offers a wide variety of well-designed Qualitative HCL color palettes to help solve this problem.
Why qualitative HCL palettes? HCL stands for Hue–Chroma–Luminance, a color space designed to match human color perception. Qualitative palettes are particularly useful when you want to show differences between categories that don’t have a natural order—like different chains in a protein, atom types in a molecule, or domains in a biomolecular complex.
These palettes are crafted to ensure:
- Distinguishable hues – adjacent colors are easy to differentiate
- Consistent luminance – ensures legibility across all regions of the model
- Colorblind safety – some palettes (like Okabe-Ito in other sections) are particularly mindful of accessibility
In SAMSON, you’ll find a diverse list of qualitative HCL palettes, including:
- Blue2Green and Green2Red – useful for binary or opposing group comparisons
- Dynamic and Pastel – visually appealing when clarity matters for presentations
- Red2Blue Dark and other dark variants – excellent for models rendered on dark backgrounds where standard palettes may not offer enough contrast
Here’s an example of the Blue2Red qualitative HCL palette:
Each palette is visually previewed in the SAMSON documentation, allowing you to click through and see exactly how it will impact your molecular scenes. This takes the guesswork out of choosing a palette, especially when preparing visual content for scientific communication.
🎯 Pro Tip: If you’re working on color-heavy visualizations like protein interaction maps or ligand binding pockets, choosing a qualitative HCL palette can improve visual clarity without overwhelming the viewer. Paired with appropriate atom or residue selection, the right palette can make your models more interpretable at a glance.
And here’s a final bonus—SAMSON also allows you to create your own HCL color palettes. Custom palettes can be especially useful if your team adopts a visual standard or if you have specific visual requirements for teaching or publication.
To explore more palettes and learn how to customize your own, visit the full documentation here: https://documentation.samson-connect.net/users/latest/color-palettes/
SAMSON and all SAMSON Extensions are free for non-commercial use. Get started at https://www.samson-connect.net.