Color plays a crucial role in molecular modeling, beyond aesthetics. It communicates information clearly when exploring complex systems. But what if the default coloring schemes in your visualization software don’t match what you’re trying to express or understand?
That’s a common issue for molecular modelers—especially when trying to communicate specific properties like temperature factors, hydrophobicity, or chain distinctions. Fortunately, SAMSON provides a deeply customizable approach through its support for tailored color palettes in the Hue-Chroma-Luminance (HCL) color space.
Why Customize a Color Palette?
The right color palette can:
- Reveal patterns more clearly (e.g., regions with highly flexible residues)
- Improve accessibility, especially for users with color vision deficiencies
- Match publication or institutional color standards
The Color Palette system in SAMSON lets you control how values are mapped to colors when using per-attribute color schemes. For example, you can visualize temperature factors using a diverging palette to highlight deviations from a baseline, or use sequential palettes to emphasize gradients.
Types of Color Palettes in SAMSON
In SAMSON, color palettes come in several forms, most based on perceptual principles:
- HSV (Hue-Saturation-Value) – A basic color wheel, suitable for familiarity but not perceptually uniform
- Discrete palettes – Useful when you want to assign distinct colors to categories (e.g., chains)
- HCL-based palettes – Designed for perceptual uniformity, with various types:
- Qualitative – For unrelated categories
- Sequential – For ordered data (e.g., hydrophobicity)
- Diverging – For values diverging around a midpoint
- Flexible diverging – Advanced control for complex gradients
Creating and Modifying Color Palettes
SAMSON lets you not only select from built-in color palettes but also create your own. In the Custom Color Palette dialog:
- Choose between default HCL types
- Adjust hue, chroma, and luminance ranges to define color intensity and brightness
- Reverse the palette mapping for better contrast or visual emphasis
- Preview how the palette will look on your system using Auto update
- Use the Color Vision Deficiency Emulator to check accessibility for users with protanopia, deuteranopia or tritanopia
Saving and Reusing Palettes
If you tune a palette that works particularly well for your needs, you can save it locally for future use. It becomes part of your SAMSON environment and can be applied to other systems, or shared across projects.
A Real-World Example
If you’re analyzing a protein with flexible and rigid regions, applying a per-attribute color scheme (like temperature factor) with a diverging HCL palette quickly highlights hotspots of motion. By tuning the value range and color scale, your visualization becomes both scientifically relevant and easier to interpret.
Want to explore further?
To learn more about color palettes in SAMSON and how to make the most of them, visit the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.