When working with complex molecular systems, one common challenge modelers face is clearly distinguishing between different components. Whether you’re highlighting various molecular chains, atom types, ligands, or interaction groups, color plays a critical role in aiding perception and communication.
SAMSON, the integrative platform for molecular design, provides a wide range of default color palettes to streamline visualization tasks. Among these, discrete color palettes are particularly useful when you need to assign distinct, easily differentiable colors to a finite set of elements.
What Are Discrete Color Palettes?
Discrete color palettes define a set of separate, non-gradient colors. They’re particularly helpful in situations where visual separation is more important than representing numerical magnitude—like representing atom or residue categories, protein chains, or different molecular structures in a scene.
SAMSON includes a variety of such palettes, many of which are sourced from well-established visualization libraries and cartographic standards, ensuring perceptual clarity and accessibility.
Examples of Discrete Palettes in SAMSON
Here are some of the discrete palettes available in SAMSON with examples:
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Accent
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Okabe-Ito (Colorblind-safe)
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Set1
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Carto Prism
How to Choose the Right One
Choosing the best palette often depends on your use case:
- Colorblind Accessibility: Okabe-Ito is designed to be distinguishable for users with color vision deficiencies.
- Data with Limited Groups: Palettes like Accent or Set1 provide high-contrast schemes ideal for visualizing up to 8 categories.
- Maps or Diagrams: Carto* palettes (e.g., Carto Pastel, Carto Prism) give visually pleasant combinations inspired by cartography.
- Large Numbers of Categories: For scenarios needing many distinct colors, palettes such as tab20 or Set3 are more suitable.
Tips for Using Color Palettes in SAMSON
- You can apply discrete palettes through the color palette or color scheme dialogs accessible in the interface.
- Reversing left/right arms of palettes is possible, giving more flexibility when matching colors to molecular groups.
- There’s also the possibility to create your own custom palettes if your visualization needs are very specific—see the documentation on colorizing for more.
By strategically selecting the appropriate discrete color palette in SAMSON, you can drastically improve readability and communication in molecular scenes, making presentations clearer and analysis more effective.
Learn more about all color palettes available in SAMSON in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.