When visualizing complex molecular models, clarity matters. Whether you are analyzing molecular surfaces, electrostatic potentials, or volumetric maps, color palettes are not just cosmetic—they’re critical tools that can make or break your interpretation of a structure. But selecting a good color palette isn’t always obvious.
One set of options to consider are the Sequential HCL color palettes available in SAMSON. These palettes vary in chroma and luminance systematically, enabling scientists to emphasize the gradation in values—be it density, temperature, or confidence scores. If you’re working with scalar fields like electron density maps or pLDDT confidence scores from AlphaFold structures, you should absolutely know about these palettes.
While SAMSON includes dozens of palettes, the Sequential HCL sets are particularly suited to continuous datasets. Here’s why:
- They guide attention gently from low to high values using perceptually uniform transitions. 👁️
- They’re accessible for color-impaired viewers.
- You avoid misleading visual interpretations (no artificial “clusters”).
Let’s take a look at some of the most helpful Sequential HCL color palettes:
1. Viridis
Viridis starts with dark blue, moves through green, and ends in yellow. It’s a great general-purpose palette: neutral and well-balanced. It’s also one of the defaults in tools like matplotlib for a reason.
2. Inferno
If you want to highlight high-value regions (e.g., regions of high density), Inferno provides strong luminance contrast that draws the viewer’s eye toward regions of interest.
3. Blue-Yellow 2
This is a classic diverging-style palette wrapped into a sequential format. Excellent for heatmaps and continuous properties requiring clear contrast between low and high values.
4. Heat
Intuitively communicates increasing values through a warm spectrum. Ideal for data types mimicking natural temperature distributions or activity gradients.
When to Use Sequential Palettes?
Use sequential palettes when mapping scalar values over a molecular model, for example:
- Mapping RMSD over protein structure alignment
- Visualizing per-residue conservation scores
- Coloring atoms by occupancy or B-factor
Tips from the SAMSON Documentation
- You can revert the direction of color palettes in the color scheme dialog if needed.
- Want more control? You can also create your own custom HCL color palettes.
Every dataset is different—choosing the right palette can improve your storytelling, make your images more intuitive, and reduce misinterpretation of molecular measurements.
Learn more about all available palettes (discrete, qualitative, diverging, and more) in the color palettes section of the SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.