When analyzing molecular structures, color is more than just a visual aid—it’s a key part of how we identify, compare, and communicate structural properties. Whether highlighting hydrophobic residues in a protein or displaying thermal motion via B-factors, effective color mapping helps transform abstract numerical data into intuitive visual cues. But how do you choose—and fine-tune—the right color palette for your specific visualization?
If you’re using SAMSON, the integrative platform for molecular design, you’re in luck: it offers extensive support for adjustable color palettes, empowering you to customize how structural data is visualized in ways that align with your research needs and personal preferences.
Choosing Meaningful Palettes
SAMSON provides multiple types of color palettes that pair with per-attribute color schemes. These are especially useful when colorizing atoms or residues based on values such as temperature factor, side chain polarity, or residue type.
Available options include:
- HSV (Hue-Saturation-Value): For continuous color transitions in standard RGB-style color blending.
- Discrete Palettes: Useful when categorizing data such as residue types or chain IDs.
- HCL (Hue-Chroma-Luminance): Designed for human perception, these palettes allow you to control how colorful and bright segments appear.
The HCL palettes are further separated into:
- Qualitative – Great for categorical data such as different chains.
- Sequential – Ideal for scalar values like B-factors or partial charges.
- Diverging – Effective for displaying values relative to a meaningful midpoint.
- Flexible Diverging – Offers more control over centerpoint and hue changes.
Customize Interactively
To explore and modify palettes in real time, use the Color > Custom… dialog. Simply select a structure, go to Visualization > Color > Custom…, and open the palette editor. There, you can:
- Switch between palette types
- Reverse palette directions
- Apply changes interactively with the Auto update option
Accessible Color Design
Colorblind-friendly design is built into the palette editor: the Color Vision Deficiency Emulator shows how your palette appears under various conditions like deuteranopia and tritanopia. This is especially important for figures intended for publications or presentations where audience visual abilities may vary.
Create Your Own Palettes
If the existing palettes don’t quite match your style or scientific needs, you can create your own in the HCL space. Just clone an existing one by checking Custom HCL palette, tweak the hue, chroma, and luminance properties, and save it locally for reuse.
Why It Matters
Being able to adjust palettes means better control over how your data is interpreted. A thoughtful color palette highlights structural features without distraction, reduces visual noise, and aids in accurate communication with collaborators—or your future self revisiting old results. Whether it’s for high-impact papers or insightful exploration, customizing your palette gives your molecular data the clarity it deserves.
To learn more about color palettes and how they interact with color schemes in SAMSON, visit the full documentation: https://documentation.samson-connect.net/users/latest/colorizing/.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.