As molecular modelers, we often deal with complex structures, from proteins to nanomaterials. When visualizing these assemblies, color plays a critical role in separating elements, highlighting features, or simply making models easier to interpret. But selecting colors manually each time can be time-consuming and inconsistent—especially when trying to match accessibility standards or keep visuals clear across different presentations.
SAMSON, the integrative platform for molecular design, provides an extensive collection of predefined color palettes made specifically to aid scientific visualization. In this post, we’ll focus on the Discrete color palettes available in SAMSON, which are ideal when dealing with categorical data—such as different residues, chains, or domains.
Why Discrete Color Palettes?
Use discrete palettes when your goal is to draw clear distinctions between separate groups of elements. Each category is assigned a single, easily identifiable color. For example: different secondary structure types, protein chains, or ligand types.
SAMSON includes several built-in discrete palettes, each following different visual philosophies to adapt to your unique modeling needs. Below are some notable examples:
- Accent: Offers a high-contrast set of colors—ideal when you’re visualizing a small number of categories and need immediate distinction.
- Carto Safe: Designed to be colorblind-friendly and printing-safe. Helpful for publication-quality visuals or when presenting to wide audiences.
- Set1, Set2, Set3: Based on ColorBrewer schemes, commonly used in mapping and scientific communications. Clean and professional.
- Okabe-Ito: Popular for providing distinguishable colors even for colorblind users.
Here’s what some of these palettes look like:
Palette Examples
Tips for Usage
- You can easily switch between these palettes in SAMSON’s color palette dialog.
- Use the “invert arms” option when applying diverging or customized palettes to reverse color order if needed.
- Develop your own palette for custom workflows or visual identity—just click the “Add” or “Create” button in the palette dialog.
Keep in mind that clarity should be your top priority. While vibrant and stylish palettes can look attractive, the best visualization is one that’s both legible and tells your data’s story effectively. A well-chosen discrete palette can subtly elevate how people engage with your model—whether in research meetings or lectures.
Explore all the available discrete color palettes and more in the SAMSON documentation: https://documentation.samson-connect.net/users/latest/color-palettes/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.