Visualizing molecular systems accurately is crucial for effective communication and interpretation. But what if the color scheme you’re using is misleading, hard to read, or inaccessible to people with color vision deficiencies? Many molecular modelers underestimate the impact of color palettes on their visualizations. In SAMSON, color isn’t just decorative—it’s functional.
This post explores how to choose and customize color palettes in SAMSON to improve the clarity and accessibility of your molecular models.
🎨 What is a color palette in SAMSON?
A color palette defines how the colors appear in per-attribute color schemes—these include representations based on residue type, temperature factor, side-chain polarity, and more. Each scheme has a default palette, but you can tailor it to your needs for better visual communication.
🚶 Why modelers should care
- Highlight specific molecular features: Focus attention on charge distribution, hydrophobic regions, or secondary structures using intuitive color gradients.
- Improve accessibility: Use SAMSON’s built-in Color Vision Deficiency emulator to choose palettes that are visible to all viewers.
- Enhance comparisons: Sequential and diverging palettes allow you to spot subtle differences across attributes like B-factors or occupancies.
🔧 Customizing your palette
In SAMSON, you can access color palette customization when selecting Color > Custom…. You’ll be presented with a dialog box to choose the color scheme and then a suitable palette. There are several palette types available:
- HSV (Hue-Saturation-Value): Good for linear gradients.
- Discrete palettes: Useful for categories like chain ID or residue type.
- HCL (Hue-Chroma-Luminance): More perceptually uniform and customizable.
For advanced uses, you can select the Custom HCL palette option and tweak parameters directly. Even better, save your palette for later use—it will be stored locally in your SAMSON configuration.
⏱️ Live preview and flexibility
Need to compare several palettes quickly? The palette selection window includes an Auto update option that refreshes your visualization live as you switch between palettes. This gives you immediate feedback to see which color set communicates your data most effectively (though note it might be slower for large systems).
🔁 Reversible gradients
If the visual emphasis doesn’t work as expected, check the Reverse option to flip the palette direction. This is handy if, for instance, you want low charges in red rather than blue, or to invert hydrophobicity mapping.
🧪 Final thoughts
The right color palette doesn’t just make your model prettier—it makes your data more understandable and your insights more shareable. Whether you’re publishing a paper, presenting in a lab meeting, or simply organizing your thoughts, taking the time to refine your color palette can make a real difference.
Learn more in the full SAMSON documentation on colorizing.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.