When working with complex molecular systems, properly distinguishing between structures, regions, or types of data is critical. One challenge that comes up often in molecular modeling: how do you make your models visually clear and easy to interpret at a glance?
This might sound like a small usability tweak, but effective coloring is essential during model exploration, presentations, and publication preparation. In SAMSON, the integrative molecular design platform, a useful solution lies in the wide array of discrete color palettes available by default.
Discrete color palettes are especially handy when you’re visualizing categorical data. Whether you’re depicting different residues, chains, atom types, or other non-continuous classifications, using a good palette improves clarity and reduces misinterpretation.
What are Discrete Color Palettes?
As the name suggests, discrete color palettes provide a set of individually distinct and non-gradient colors. Unlike sequential or diverging palettes that are built around intensity or central neutral tones, discrete palettes aim to visually separate categories without implying order.
Here are some examples of discrete color palettes available in SAMSON:
- Accent: A subtle and accessible set of colors.
- Carto series: Includes options like Carto Antique, Carto Pastel, Carto Vivid—ideal for presentations where visual appeal matters.
- Okabe-Ito: A colorblind-safe palette, great for inclusivity without compromising contrast.
- Dark2 and Set1–3: Borrowed from standard scientific color palettes, offering high saturation and defined hues.
SAMSON embeds previews of each palette, making it easy to select the most readable one for your dataset. For instance:
When to Use Discrete Palettes
Use discrete palettes when dealing with categorial variables such as:
- Protein chains (A, B, C…)
- Ligand or drug types in docking simulations
- Regions in a segmented cryo-EM map
- Selection groups or annotations
Choosing the correct palette improves both aesthetics and interpretation efficiency. If you’re presenting or sharing your model, the right colors reduce viewer fatigue and improve comprehension, even for those unfamiliar with the molecular structure shown.
Tip: Custom and Reversible Palettes
You can also create your own custom discrete palettes if you need a specialized visual language for your research. Additionally, SAMSON provides options to reverse palettes, which can subtly change the perception of figure foreground/background relationships.
For more details on how SAMSON handles colors, check out the full documentation: Color palettes in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.