Molecular visualizations communicate complex structural information. But if you’ve ever found your protein coloring scheme hard to interpret—or worse, misleading—you’re not alone. Poor color choice can obscure relevant features, strain the eyes, or confuse colleagues with color vision deficiencies. Fortunately, SAMSON provides a well-structured, flexible toolset for applying and customizing color palettes in meaningful ways.
This post walks you through how to choose or create optimized color palettes when using per-attribute color schemes in molecular models—allowing your visualizations to be both scientifically relevant and accessible.
Why Color Palettes Matter
In SAMSON, per-attribute color schemes let you visualize data like residue hydrophobicity, atom charge, or secondary structure. Each scheme comes with a default color palette, but modifying that palette can be crucial when:
- You’re highlighting critical differences in a dataset (e.g., charge distribution).
- You want to match a consistent style across multiple models.
- Your audience includes people with color vision deficiencies.
Types of Color Palettes in SAMSON
SAMSON offers several color palette types suited for different visualization needs:
- HSV (Hue, Saturation, Value): Useful for gradient color scales; intuitive control over hue and brightness.
- Discrete: Helpful for categorical data like chain identifiers.
- HCL (Hue, Chroma, Luminance): Designed for human perception. Includes:
- Qualitative
- Sequential
- Diverging
- Flexible Diverging
You can switch between these to suit your data’s nature.
Hands-On: Customizing Palettes
To try it yourself:
- Select a structural model in your scene.
- Choose a per-attribute color scheme (e.g., Residue hydrophobicity).
- Go to: Visualization > Color > Custom…
The dialog that appears lets you:
- Choose a base color scheme.
- Select or reverse a color palette (switching left and right arms).
- Preview your changes with Auto update.
- Test how your palette appears to users with different color vision deficiencies using the built-in emulator:
Advanced Option: Build Your Own Palette
Sometimes, default palettes don’t quite fit your data or stylistic preferences. Click Custom HCL palette, tweak hue and luminance parameters, and save your new palette to reuse later:
This user-centered design not only refines your visuals but also ensures accessibility for everyone viewing your work.
Conclusion
Careful colorization can make your molecular themes clearer, more data-driven, and easier to understand—particularly in collaborative settings. Next time you’re preparing a figure or presentation, take a few extra minutes to explore SAMSON’s color palette options.
Learn more in the official SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.