Color can make or break the interpretation of molecular models. For researchers and designers working in molecular science, the right color palette isn’t just aesthetic—it’s essential for accurate, effective communication. Whether you’re analyzing large biomolecular systems or visually presenting molecular interactions, identifying clear regions, domains, or atom types can quickly become messy with inadequate color schemes.
One common problem faced by molecular modelers is the challenge of assigning distinctive colors to different elements, molecules, or groups in visualization platforms—especially when dealing with many categories simultaneously. Similar shades can easily get confused. Worse still, some palettes can be unintuitive or difficult to distinguish for colorblind users. SAMSON offers a valuable solution with its collection of discrete color palettes designed precisely to address this.
What Are Discrete Color Palettes?
Discrete color palettes are sets of categorical colors—each distinctly different from the others. They’re ideal when elements being colored don’t follow a magnitude or order, such as distinguishing between atoms in a ligand and protein backbone, or differentiating conformational states in a simulation.
These palettes are not gradients, but rather separate and visually contrasting colors to ensure clarity.
Top Discrete Palettes Available in SAMSON
Here are a few popular examples:
- Accent: A bold palette with varied hues
- Carto Pastel / Vivid / Safe: Excellent for thematic presentations with careful color planning
- Set1, Set2, Set3: Widely used in scientific illustrations for categorical comparisons
- Okabe-Ito: Colorblind-friendly and sharpened for distinction
- Dark2: A richly contrasted palette, good for dark backgrounds
Below you can see an example of the Carto Vivid palette in SAMSON:
Tips for Molecular Designers
- Consistency matters: Use the same palette across comparative studies to avoid confusion.
- Consider accessibility: Okabe-Ito is one of the best for audiences with color vision deficiencies.
- Balance color load: Avoid using more colors than the palette comfortably supports. Set3, for instance, offers up to 12 distinct colors.
- Preview before applying: In SAMSON, you can visually preview palettes, helping you choose with clarity.
Custom Colors?
SAMSON also allows creation of custom discrete palettes. Though beyond this post’s scope, the documentation shows how to define your own palette based on specific hues and luminance levels. This can be especially useful for adapted scientific visuals, lab-specific standards, or publications.
To explore the full list of discrete palettes (including tab10, tab20, and more), and to view palette images, visit the official documentation.
Color may not change your model’s chemistry—but it does shape how others understand your work. Whether you’re preparing visuals for a conference, a publication, or simply organizing your visual workspace, choosing the right discrete palette helps keep things crisp, readable, and professional.
Learn more about all the available color palettes in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.