Choosing the Right Discrete Color Palette in Molecular Modeling

One of the less discussed, but surprisingly important aspects of molecular modeling is color perception. Visualizing molecular structures clearly is essential when working with complex systems, and when you’re layering atoms, molecules, or domains, using the right color palette can determine whether you catch subtle patterns or miss vital details.

This is where discrete color palettes in SAMSON become especially useful. These palettes consist of a limited set of distinguishable colors, ideal for labeling categories such as molecular chains, atom types, or residue families.

Why Discrete Palettes Matter

If you’ve ever shown someone your model and heard “I can’t tell those apart,” you know what poor color choices feel like. Overlapping hues, low contrast, or inaccessible design for colorblind viewers can lead to confusion. That’s why SAMSON includes a wide variety of built-in discrete palettes, many of which are designed to improve clarity and accessibility.

Exploring Your Options

SAMSON offers over 18 discrete color palettes, all available through the color palette or color scheme dialogs. Here are a few highlights:

  • Okabe-Ito: Designed to be colorblind-friendly by avoiding easily-confused hues.
  • Accent: A more expressive palette that works well when you need stronger separation between categories.
  • Carto Series: Including Antique, Bold, Pastel, Vivid, and others — originally designed for maps, these palettes prioritize contrast and clarity on screen.
  • tab10 and tab20: Taken from scientific plotting libraries, they provide evenly spaced colors which scale well with multiple categories.

Here’s a sample of the “Carto Bold” palette:

Carto Bold Palette Example

Use Cases

Here are some concrete applications where the discrete palettes can boost your modeling clarity:

  • Residue coloring: Assign each amino acid type a unique hue in comparative studies.
  • Chain identification: Quickly discern different molecular chains in large assemblies.
  • Data segmentation: Label molecules based on simulation results like clustering analyses or domain predictions.

Tips and Flexibility

In addition to using the default options, keep in mind that:

  • You can revert the left and right arms of palettes in the dialog windows if the gradient direction matters for clarity.
  • You’re free to create your own custom HCL palettes.

Choosing the right color palette isn’t about artistic expression—it’s about clarity, communication, and comprehension.

To explore the full selection of available color palettes in SAMSON, including sequential and diverging types, visit the official documentation.

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

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