If you’ve ever struggled with unreadable molecular models because the selected colors look too similar—or simply don’t stand out enough—then you’re not alone. In molecular modeling, visual clarity isn’t just about aesthetics. It’s essential for correct interpretation, communication, and publication.
SAMSON, the integrative molecular design platform, offers a rich collection of default discrete color palettes to help users avoid visual overlap and increase the interpretability of complex scenes. Whether you’re creating molecular animations, figures for publication, or collaborative visuals, selecting an appropriate color palette can significantly improve your work.
What are discrete color palettes?
Discrete color palettes are sets of clearly distinguishable colors, ideal for labeling different residues, chains, molecular groups, or selections in a model. Unlike gradient-based sequential palettes, discrete palettes avoid visual blending and are designed to provide quick visual differentiation between elements.
Why this matters for molecular modelers
In practice, it’s common to label atoms and residues using the default few shades of red, green, and blue. But this can quickly cause confusion when dozens of different elements are present. For molecular modelers working with large protein complexes, multi-subunit assemblies, or graphical abstracts, being able to switch to a well-designed discrete palette can make all the difference.
What options are available in SAMSON?
SAMSON comes with several built-in discrete palettes. Some include familiar scientific color schemes, while others are borrowed from cartographic and data visualization standards. Here are a few examples:
- Accent: A vibrant combination useful for up to 8 classes.
- Carto Safe: Optimized for colorblind accessibility.
- Okabe-Ito: A well-known palette for its clarity and vision-friendly colors.
- Tab10 and Tab20: Common palettes used by major plotting libraries like Matplotlib.
Here’s how a few of these look visually:
To change the color palette in SAMSON, open the color palette or color scheme dialog, and select the one that best fits your needs. Want mirrored color arms for left-right balance in diverging palettes? That’s possible too—just use the built-in control to reverse them.
When to switch palettes
Color palette choice often depends on your immediate task:
- Presentation and teaching: Opt for vibrant, distinct palettes like Vivid or Accent.
- Colorblind safety: Use palettes like Okabe-Ito or Carto Safe.
- High-contrast export: Dark2 or Set1 improve visibility when printed or exported.
One last tip
You’re not limited to the default palettes: SAMSON allows you to create your own HCL-based palettes for fine-tuned customization. Whether you need to match a journal’s guidelines or comply with institutional colors, there’s flexibility built in.
Discover all available options and visuals in the full documentation at this link.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.