Finding the Right Look: Discrete Color Palettes in SAMSON

Choosing how to visually represent molecular structures is more important than it might first seem. Often, clarity and insight depend as much on color selection as on structure accuracy. When you’re comparing molecular parts, highlighting specific regions, or distinguishing components across models, the colors you choose have a real impact on interpretability.

This is where discrete color palettes in SAMSON can help. SAMSON is an integrative molecular design platform that enables users to explore, design and visualize complex molecular systems. For molecular modelers who often juggle atoms, residues, chains, and molecular assemblies — sometimes all at once — being able to effectively apply a consistent but distinct color scheme across multiple parts is essential.

Why Discrete Color Palettes Matter

Unlike sequential or diverging palettes (which imply some sort of order or gradient), discrete palettes are meant to assign clearly distinct colors to unrelated objects. This is perfect for:

  • Assigning unique colors to molecules, chains, or ligands.
  • Highlighting groups without implying a hierarchy or progression.
  • Visual differentiation across categories that have no natural order.

From a molecular modeling perspective, discrete palettes provide a way to “declutter” by making visual boundaries intuitive. For instance, when you’re analyzing a multi-subunit protein complex, color can tell you at a glance where one chain ends and another begins — without having to hover for tooltips or search through a sidebar.

Options Available in SAMSON

SAMSON comes with several pre-configured discrete palettes. Here are just a few examples:

  • Accent: A colorful, well-spaced scheme.
  • Carto series: Including Antique, Bold, Pastel, Vivid, Safe, and Prism versions for different levels of visual richness and accessibility.
  • Okabe-Ito: Particularly designed for colorblind safety.
  • Paired, Set1, Set2, Set3: Familiar from visualization libraries, offering balanced hues.
  • tab10, tab20, tab20b, tab20c: Useful for figures with many categories.

Here’s a glimpse at how some of these look:

Discrete - Carto Bold

Discrete - Okabe-Ito

Discrete - tab20c

Tips for Choosing a Palette

  • Number of Categories? Start with how many distinct entities you need to represent. Some palettes like tab10 or Paired work well with 8–10 categories, while tab20 can handle more.
  • Audience? If you’re publishing or collaborating, ensure accessibility —Okabe-Ito and Carto Safe are safer choices.
  • Consistency: Stick to the same palette across figures if you’re working on a publication or presenting to others.

Good color choices don’t just beautify your model — they improve communication. Viewers can instantly scan and understand relationships across molecular elements when color is used effectively.

To learn more about color palette types and customization options in SAMSON, visit the full documentation page.

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

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