Color plays a crucial role in molecular modeling. Whether you’re presenting a simulation, analyzing protein structures, or preparing material for a publication, the ability to clearly distinguish different molecular entities and properties can make a significant difference in communication and understanding.
One challenge many researchers face is choosing meaningful, readable, and visually appealing colors — especially when dealing with complex systems involving many components. Eye strain, color repetition, and indistinguishable tones can all reduce the effectiveness of your representations.
If you’ve run into this problem using poor or default color settings, SAMSON offers a practical way out: Discrete Color Palettes. These predefined sets of distinguishable colors are specifically designed to help you color code data effectively, even across many molecular groups.
What are Discrete Color Palettes?
Discrete color palettes are collections of individual colors that do not vary in a continuous gradient but instead provide separate, distinct colors. These palettes are perfect for categorizing different atoms, residues, chains, or molecules that shouldn’t be confused with one another.
SAMSON includes a variety of discrete palettes such as:
- Accent – bold colors for distinct classes
- Carto variants (e.g. Bold, Pastel, Prism, Vivid) – designed for mapping and readability
- Okabe-Ito – colorblind-friendly
- Set1, Set2, Set3 – from RColorBrewer, balanced for clarity
- Dark2, Paired, tab20 – great for presentations on dark or light backgrounds
For example, here is what the popular Set3 palette looks like:
When and Why to Use Discrete Palettes
If you’re visualizing categories without an inherent order — say types of ligands, chain IDs in a protein complex, or different molecule classes — discrete palettes are your best bet. Compared to gradients, they avoid implying a progression that doesn’t exist.
Some discrete palettes, like Okabe-Ito, are specifically designed to be distinguishable by people with color vision deficiencies — a key accessibility feature if your visualizations will be shared broadly.
Tips for Using Discrete Palettes in SAMSON
- You can apply a discrete palette via the color scheme dialog.
- Different palettes can be previewed before application.
- You can even create your own custom palettes and reuse them.
SAMSON also allows you to revert the order of elements in a palette if needed — useful when you want to emphasize a specific molecular category.
Better Clarity Leads to Better Communication
In science, visuals are not just pretty pictures — they help transmit ideas. Making molecule types stand out with thoughtfully chosen colors improves both your own understanding and the clarity of your presentations. If you’ve been spending too much time tweaking color values manually, discrete palettes can be a quick and reliable solution.
To explore the full list of discrete palettes available in SAMSON (with preview images), visit the original documentation page: https://documentation.samson-connect.net/users/latest/color-palettes/.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.