Choosing the right color palette is essential when building or analyzing molecular models, especially when attempting to convey complex information clearly. Whether you’re preparing figures for a scientific publication, explaining results during a presentation, or exploring molecular systems visually during your research, having a visually balanced and informative color scheme matters.
In SAMSON, the integrative molecular design platform, choosing the right colors for molecular structures and properties doesn’t have to be a guessing game. That’s because SAMSON comes with a wide range of default HCL-based color palettes that are optimized for clarity, interpretability, and visual differentiation.
What’s HCL and why does it matter?
HCL color palettes are based on a perceptually uniform color space. This means that changes in color correspond more closely to changes in how human vision perceives differences. HCL color palettes help avoid misinterpretations due to color intensity differences or poor contrast.
For molecular modelers, this translates to more accurate and accessible visualizations—especially when mapping data such as atomic properties, energies, or structural differences.
Spotlight: Sequential HCL Color Palettes
Sequential color palettes are helpful when visualizing ordered data (e.g., electrostatic potential maps, pLDDT confidence values, solvent exposure levels). These palettes typically range smoothly from light to dark or transition clearly between two colors, helping you spot trends or outliers in your data.
Here are some sequential palettes available in SAMSON:
- Blue-Green-Yellow – excellent for gradient maps, with a gentle transition of hues
- Inferno – a high-contrast option for grayscale printing and low-light environments
- Plasma and Viridis – favorites in scientific visualization for clarity and colorblind-friendliness
- pLDDT – tailored for protein structure confidence values
These palettes can be applied through SAMSON’s color palettes or color scheme dialogs. For example, when visualizing molecular properties, you can map low confidence areas to cooler hues and high-confidence areas to warmer ones—improving your model’s readability instantly.
Bonus tips 🧠
- Flip the palette direction if the data representation feels counter-intuitive. You can do this directly in the palette dialogs.
- Create your own palettes if you have specific needs! SAMSON’s interface allows for custom HCL palette creation.
- Use perceptually uniform palettes (like Viridis) to ensure clarity for colorblind users or when exporting grayscale images.
Choosing wisely saves time and improves clarity
Color choices in molecular visualization are often overlooked, but a thoughtful palette can instantly make your systems easier to understand. If you want to better communicate your data through clear, perceptually adaptive visualization, start experimenting with the HCL-based sequential color palettes next time you open SAMSON.
Browse all available palettes and learn more about using color in SAMSON here: https://documentation.samson-connect.net/users/latest/color-palettes/
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.