One of the subtle pain points in molecular modeling is choosing effective colors that communicate your data clearly. Whether you’re differentiating chains in a protein, visualizing atom types, or building figures for publications, poor color choices can easily confuse viewers or obscure important information.
To address this, SAMSON comes with a rich set of discrete color palettes built into its platform. Discrete palettes are made for categorical data—items that don’t have a natural order. This makes them ideal for differentiating things like molecular components, binding sites, or individual simulation trajectories.
Here’s an overview of what SAMSON offers to help you pick discrete color palettes intelligently.
What Does “Discrete” Mean in This Context?
Discrete palettes assign a unique color to each distinct item. These colors are picked to be visually distinct, even for users with color vision deficiencies. This is key when clarity matters, such as in educational materials, publications, or collaborative work.
Highlighted Palettes
SAMSON includes several predefined discrete palettes. Here’s a look at a few notable ones:
- Accent: Bright and diverse colors, suitable when you need to highlight differences sharply.
- Okabe-Ito: Designed to be colorblind-friendly. Ideal for accessibility-focused visualization.
- Carto Antique / Safe / Vivid: From the Carto family, these stylish palettes bring both aesthetic value and readability.
- Set1 / Set2 / Set3: Well-known palettes borrowed from established data visualization standards. Balanced and readable.
Here’s what they look like:
Example of the Okabe-Ito palette (colorblind friendly)
Carto Vivid palette, designed for crisp differentiation
How to Use These in Practice
When using SAMSON’s discrete palettes:
- Open the Color Palette dialog in your project.
- Select a predefined discrete palette from the list.
- Assign colors automatically to molecular components or manually adjust if needed.
- Use the flip left/right arms feature if it helps with your visual composition.
Use discrete palettes when elements like chains, ligands, and atom types carry categorical meaning (i.e., their order is irrelevant). Avoid using sequential palettes for these tasks; they are more suited for data on an interval scale like electrostatic potential or B-factors.
Bonus: Shareable Visuals
Using clean, accessible color palettes makes it easier for colleagues and readers to interpret your visualizations. This increases the sharability and readability of your work, particularly important when crafting posters, slides, or collaborative documentation.
To learn more and see the full list of discrete palettes available in SAMSON, visit the Color Palettes documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get started at https://www.samson-connect.net.