When working with complex molecular models, color plays a bigger role than you might think. Color can help distinguish between molecular groups, highlight structural features, and enhance overall legibility—particularly in presentations, publications, or educational content. But picking colors manually can be tedious, inconsistent, and prone to visual confusion (e.g., using similar tones for distinct elements).
That’s where discrete color palettes in SAMSON come in. These pre-defined color palettes are specially designed to help you visualize molecular objects clearly and consistently. Whether you’re colorizing residues, atoms, chains, or entire molecules, discrete palettes give you a clean, visually distinct selection of colors that work well together.
Why Use Discrete Palettes?
Discrete palettes are helpful when you need to assign categorical colors—i.e., when each color represents a different group or type. In molecular modeling, this can apply to different residues, ligands, chains, or atom types. By using a discrete palette, you ensure that categories don’t get visually mixed up due to subtle color differences.
SAMSON currently offers a wide range of discrete palettes, including:
- Colorblind-friendly options like Okabe-Ito and Set2.
- Design-inspired themes like Carto Antique, Carto Pastel, and Carto Vivid.
- Common data visualization palettes like Accent, Paired, and Dark2.
- Standard plotting palettes you might recognize from Matplotlib or R, such as tab10 and tab20b.
The Carto Vivid palette offers high contrast colors suitable for presentations.
How to Apply a Discrete Palette in SAMSON
To apply a discrete color palette in SAMSON:
- Open the Color Palette or Color Scheme dialog (depending on what you’re visualizing).
- Select one of the discrete palettes from the list.
- If needed, reverse the palette direction directly in the dialog using the reverse arms option.
Creating Consistency and Clarity
Using a pre-defined palette keeps your models consistent across projects and sharing contexts. If you’re working in a team, deciding on a color palette ahead of time makes collaboration easier and results more visually reliable. It also helps your viewers focus on the science rather than adjusting to new color conventions.
And if none of the existing palettes suit your needs, remember: you can create your own custom palette. This makes it possible to tailor visualizations to match branding requirements, accessibility needs, or personal preferences. See the full documentation for more information on how to create custom HCL color palettes.
To explore the full list of color palettes available in SAMSON, including sequential and diverging palettes, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.