When working with complex molecular systems, effective visualization isn’t just about generating eye-catching graphics — it’s about clarity, interpretation, and communication. A common challenge many molecular modelers face is choosing color schemes that not only highlight specific properties of a structure but also communicate data accurately and accessibly. In SAMSON, color palettes go beyond basic colorization and offer customizable schemes designed for human perception. This post dives into how you can harness color palettes in SAMSON to improve the way you visualize molecular information.
Why color palettes matter in molecular modeling
The way color is used can greatly impact your understanding of a biomolecule’s structure and functions. Whether you’re highlighting temperature factors, residue hydrophobicity, or chain ID, the palette you choose can either enhance or hinder communication. Traditional RGB or HSV color systems often fall short when it comes to subtle data variations or accessibility for people with color vision deficiencies.
SAMSON’s solution: perceptually-optimized color palettes
SAMSON offers color palettes implemented in a more perceptually balanced color space: HCL (Hue-Chroma-Luminance). This space is particularly suited for scientific visualization because it allows you to control hue (color), chroma (vividness of the color), and luminance (brightness) independently. The result is color schemes that are not just visually appealing but also easy to interpret.
Types of color palettes available in SAMSON
Here’s an overview of the types of color palettes you can choose from:
- HSV: The widely-used Hue-Saturation-Value system.
- Discrete palettes: Assign distinct colors to categories (e.g., chains A, B, C…).
- HCL Qualitative: For representing categorical data like residue types.
- HCL Sequential: Single- or multi-hue schemes useful for attributes like temperature factor or hydrophobicity.
- HCL Diverging: Good for highlighting deviations from a median (e.g., charge distributions).
- Flexible Diverging: Advanced version of diverging palettes with fine-tuned control.
Visualizing data with the right palette
To apply a color palette:
- Select the molecule or node type in the Document view.
- Go to Visualization > Color > Per attribute and choose the appropriate scheme (e.g., occupancy, chain ID).
- Select Color > Custom… to open a dialog and fine-tune your color palette.
Accessibility and customization options
SAMSON includes a Color Vision Deficiency Emulator in the palette dialog box. This is especially helpful if your visuals will be shared with collaborators or students who may have color vision deficiencies. It helps preview how your protein or molecular system will appear to users with different types of color blindness.
Additionally, advanced users can design their own color palettes in HCL space. You can create a custom palette by copying and modifying an existing one, adjusting parameters like hue angles, chroma ranges, and luminance span. These can be saved locally for future sessions.
Tips to improve your visualization workflow
- Use sequential palettes for gradient data like occupancy or temperature factor.
- Use qualitative palettes for non-ordered categories like residue type or structural model.
- Toggle the Auto Update option in the palette window to preview changes instantly (note: this may be slower for large systems).
- Use the Reverse option to invert left and right arms of diverging palettes — useful for flipping emphasis in your visualization.
Choosing the right color palette in SAMSON can significantly enhance both your understanding and presentation of molecular systems. For more on this topic, visit the full documentation page: https://documentation.samson-connect.net/users/latest/colorizing/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.