Color can significantly impact how molecular models are interpreted. Whether you’re analyzing electrostatic potential, comparing structural models, or making your visualizations publication-ready, selecting the appropriate color palette is essential. Yet, many molecular modelers overlook this crucial step or settle for defaults that may not effectively communicate their message.
In SAMSON, the integrative molecular design platform, color palettes are used alongside color schemes to map molecular properties to visual color gradients. If you’ve ever wondered how to choose a palette that’s both scientifically meaningful and accessible to diverse viewers, this post is for you.
Why color palettes matter
A color palette defines how numeric values—like partial charges, hydrophobicity, or temperature factors—are visually represented in a model. A good palette allows for:
- Clear differentiation of molecular regions
- Accurate perception of quantitative differences
- Accessibility for viewers with color vision deficiencies
Choosing the wrong palette, on the other hand, can obscure subtle yet important variations or confuse viewers with misleading contrasts.
Types of color palettes in SAMSON
SAMSON supports a variety of palettes, many of which are based on the HCL (Hue-Chroma-Luminance) color space, designed specifically for perceptual uniformity. These include:
- Qualitative palettes: Best for grouping discrete categories like chains or structural models.
- Sequential palettes: Ideal for variables that progress in one direction, such as occupancy or temperature factor.
- Diverging palettes: Useful when your data centers around a critical midpoint, e.g., a pH neutrality point.
- Discrete palettes: For specific residue types or classifications.
You can also use HSV palettes, the traditional RGB-style gradient model, but HCL options provide more perceptual consistency.
Customizing palettes and previewing results
To personalize your visualizations further, SAMSON lets you:
- Load default HCL palettes or define your own
- Reverse gradients to emphasize different regions
- Preview how the palette appears for people with color vision deficiencies
The Color Vision Deficiency Emulator lets you ensure that your visuals are accessible to a wider audience, which is particularly useful when preparing figures for talks, papers, or educational materials.
When adjusting palettes in the customizer, check the Auto update option to view real-time changes. This is especially handy for spotting visual artifacts or verifying interpretability before committing to a final render.
Saving and reusing your palettes
Once you’ve built a palette that meets your needs, SAMSON allows you to save it for later use. This makes it easier to maintain consistent branding or data representation protocols across different projects and teams.
To create your own palette:
- Select the Custom HCL palette option
- Tune the hue, chroma, and luminance parameters
- Save it with a meaningful name for future reuse
A better visualization experience
By tailoring color palettes to your data and audience, you can dramatically enhance its communicative power. This small change often results in clearer insight, increased reproducibility, and a stronger visual impression.
To learn more about how color palettes work in SAMSON, and how to create and manage them effectively, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.