When working with complex molecular systems, clarity is essential. Whether you’re highlighting different protein chains, annotating functional domains, or distinguishing between ligands and cofactors, visual differentiation helps you and others understand your molecular model more effectively.
This is where discrete color palettes come into play. In SAMSON, the integrative molecular design platform, you can select from a rich range of discrete palettes specifically designed for clarity and distinction in your models. These palettes offer pre-arranged sets of colors that are purposefully chosen to be distinguishable from one another — especially useful when you need to color multiple parts of a system without confusion.
Why Discrete Color Palettes?
Discrete palettes are optimized for categorical distinctions. If you’re working with molecular components that have no inherent ordering — such as chains A, B, and C in a protein, or different ligands bound to the same site — using a sequential or gradient-based palette can confuse interpretation.
Instead, discrete palettes assign a unique, perceptually distinct color to each category. This makes them ideal for categorical data — like atom types, segments, domains, or molecular groups — ensuring that every item you color stands out on its own.
What’s Available in SAMSON?
SAMSON provides a variety of discrete color palettes. Here’s a sample of some commonly used ones:
- Accent: A bold and well-spaced palette useful for highlighting key elements.
- Carto Bold: Optimized for cartographic use, this one works well for models that will be printed or used in publications.
- Okabe-Ito: Carefully designed to be colorblind-friendly — great for inclusive visuals.
- Set1, Set2, Set3: These are classic palettes for categorical data visualization, widely used and recognized.
- tab10, tab20, tab20b, tab20c: Useful when you have many categories and need a palette that scales.
Here is an example of the Okabe-Ito palette:
This palette is especially helpful for collaborators or audience members with color vision deficiency, ensuring accessibility without sacrificing distinction.
Tips for Using Discrete Palettes in SAMSON
- You can assign discrete palettes through both the color palette and color scheme dialogs.
- If you want to reverse the palette order — for example, to shift focus from component A to component Z — that’s also possible from within the dialog.
- Create your own custom palette if none of the predefined ones fit your needs. This is particularly useful when working with known corporate or institutional color schemes for visual consistency in presentations.
When to Use Discrete Over Other Types
Discrete palettes are most helpful when colors are used to categorize items of equal importance. For example:
- Coloring by secondary structure elements (helix, coil, sheet)
- Marking different compounds in a multi-ligand complex
- Distinguishing chains in a protein-DNA complex
They are not well-suited for ordered data — that’s where sequential and diverging palettes are more appropriate.
Explore the range of discrete color palettes and see how they can improve both the aesthetics and clarity of your molecular scenes.
To view the full list and images of available discrete palettes in SAMSON, check out the original documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.