When building molecular models, one of the recurring challenges is color choice. Molecular modelers often use color to indicate atom types, molecular properties, interactions, or structural information. But picking colors isn’t just about aesthetics — it’s about clarity, contrast, and accessibility.
In SAMSON, a wide range of discrete color palettes is available to help researchers visually differentiate between entities. These are designed to represent categories — for instance, viewing different molecular chains, domains, atom types, or simulation states. Choosing a well-suited discrete palette can make a significant difference in how easily patterns and anomalies are detected in a 3D model or during a presentation.
Why default palettes matter
Manually assigning colors every time can be tedious and time-consuming. Moreover, when not using carefully designed palettes, there’s a risk of low contrast or poor visibility for users with color vision deficiencies. The default discrete palettes in SAMSON are designed to mitigate these issues.
Here’s a brief description of some of the discrete palettes available in SAMSON:
- Accent and Set1–Set3: These are classic palettes originated from data visualization libraries like ColorBrewer, providing good visual separation of up to 8–12 categories.
- Okabe-Ito: A palette designed for clarity and accessibility, especially for users with color blindness.
- Carto series: These include variants like Carto Bold, Carto Pastel, and Carto Vivid, tailored for cartography and adapted here to provide sharp or soft contrasts depending on the version.
- tab10 and tab20: From Matplotlib, these palettes are balanced and eye-friendly, often used in publications and scientific plots.
Below is a selection of available discrete color palette previews from SAMSON:
Tips for using palettes effectively
- Use high-contrast palettes when labeling many categories or when the model will be used in presentations.
- Check color accessibility: Okabe-Ito and some Carto palettes offer alternatives useful for colorblind-friendly representations.
- Customize: You may also add or create your own discrete HCL (Hue-Chroma-Luminance) palettes for total control over your visualization style. See tips in the Color Palettes or Colorizing sections of SAMSON documentation.
By choosing the right palette from SAMSON’s built-in options, you make your models more intuitive, inclusive, and visually informative — all critical factors in both research and communication.
To explore the full list of discrete color palettes and how to use them in SAMSON, visit the SAMSON color palettes documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.