Color can be a powerful tool when visualizing molecular systems, but choosing the right color palette is often underappreciated. For molecular modelers examining subtle variations in structure, properties, or dynamics, the difference between an adequate and a well-chosen color scheme can have a measurable impact in interpretation, communication, and presentation.
In SAMSON, color schemes are not just about aesthetics—they help distinguish atomic elements, chains, residue types, charges, and more. But what if the default palettes don’t quite align with your preferences or the clarity you need when conveying meaning during presentations or publications?
Why Customizing Palettes Matters
When coloring structures based on attributes like residue hydrophobicity, temperature factor, chain ID, or partial charge, using the right palette can drastically improve the ability to interpret and analyze key patterns or outliers. More importantly, certain palettes are more accessible—for example, some palettes are optimized for color vision deficiencies.
Types of Palettes You Can Use
SAMSON supports a variety of palette formats:
- Standard HSV (Hue-Saturation-Value) palette, offering a broad range of vibrant transitions.
- Discrete palettes for segmenting categories like chain IDs or residue types by sharply distinct colors.
- HCL (Hue-Chroma-Luminance) palettes, which align better with human perception—especially relevant if your work will be published or shared visually.
HCL Palettes Breakdown
- Qualitative: For unordered categories.
- Sequential: For ordered values (e.g., occupancy or temperature factor).
- Diverging: To highlight deviation from a central point (e.g., deviations from neutrality).
- Flexible diverging: More customizable diverging gradients.
How to Create Your Own
Via the Color > Custom… option, you can open a dialog window where you choose both a color scheme and your preferred palette. Selecting Custom HCL palette lets you fine-tune hue, chroma, and luminance parameters. You can reverse arms of diverging palettes and preview appearance with the Auto update option.
A Color Vision Deficiency Emulator is also included. This allows you to see how your palette would appear to users with certain types of color blindness—helpful when sharing results in multi-disciplinary teams or student groups.
Saving and Reusing Palettes
After customizing, save the palette—it gets saved to your local configuration and can be reused across different sessions or projects. This is ideal for establishing visual consistency across your work or within team collaborations.
When Custom Palettes are Especially Useful
- When preparing figures for publications.
- If default colors don’t meet accessibility or clarity standards.
- To visually emphasize a specific gradient or threshold in molecular properties.
- For education, where clarity and pedagogy rely on precise visual contrasts.
More Than Just Looks
Switching palettes isn’t about style—it equips the molecular modeler with tools to better interpret and share insights that otherwise might remain hidden in uniform or poorly contrasted visuals. With HCL palettes, you’re not just assigning color—you’re structuring the user’s perception of data.
To learn more, visit the full documentation page on colorizing in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.