Choosing Better Discrete Color Palettes for Molecular Models

Molecular modelers often need to visualize complex structures where clear, distinguishable visual components enhance interpretation. Whether you’re color-coding residues, chains, subunits, or datasets, using carefully designed color palettes is key. Poor palette choices can make important elements indistinguishable, especially for color-blind researchers or in grayscale publications.

SAMSON, an integrative molecular design platform, addresses this challenge through a robust set of discrete color palettes designed for distinction and aesthetics. Let’s explore these palettes and how they can help you communicate your models effectively.

What Are Discrete Color Palettes?

Discrete color palettes use a fixed set of distinct colors without gradients. These are perfect for categorical visualizations like:

• Highlighting amino acid types
• Coloring different chains or molecules
• Visualizing clusters

In SAMSON, you can choose from over a dozen built-in discrete palettes. Each one addresses specific visualization needs, from high-contrast schemes to artistically inspired sets.

Popular Discrete Palettes in SAMSON

Here are a few notable options, each with unique strengths:

1. Accent

Designed for clarity with moderately saturated tones that stand apart. This palette is useful for datasets with about eight categories.

2. Carto Vivid

High color contrast and vivid hues. Ideal for poster presentations or visualizations intended for screens.

3. Okabe-Ito

A colorblind-safe palette frequently used in scientific communication. Highly recommended when accessibility is a concern.

4. Set1 and friends (Set2, Set3)

Classic palette sets based on ColorBrewer. Widely recognized and compatible with many plotting tools.

5. tab10, tab20, etc.

Matplotlib-style palettes often chosen for consistency with code-based workflows. Provide plenty of distinct hues for large categories.

When to Use Which?

• For presentations: Go with high-saturation palettes like Carto Vivid or Set1.
• For publications: Use readable and tone-safe schemes like Okabe-Ito or Accent.
• If you have many elements: Try palettes like tab20 or Carto Prism which have extended color sets.

And here’s a tip straight from the documentation: you can create your own custom palette in the color palette dialog, or even reverse palette arms to better fit your background or visualization style.

Making subtle improvements to how you assign colors can make your models more intuitive and help others understand your ideas more quickly and clearly.

To learn more about the full range of available color palettes in SAMSON — including sequential, diverging, and HCL variants — visit the original documentation page here: https://documentation.samson-connect.net/users/latest/color-palettes/

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.