Visual clarity is essential when working with complex molecular models, especially when highlighting differences such as binding affinities, charge distributions, or simulation deltas. But using the wrong color scheme can cause confusion—or worse, misinterpretation of critical regions. If you’ve ever struggled to clearly visualize a property that varies around a central reference (e.g., negative to positive values, or low to high deviation), diverging color palettes might become your go-to solution.
SAMSON, the integrative molecular design platform, includes specialized HCL diverging color palettes tailored to help you highlight contrast around a central value. These diverging HCL palettes generate balanced color transitions around this midpoint—providing a natural and intuitive way to represent molecular differences.
Here are the diverging HCL palettes currently available in SAMSON:
- Berlin
- Blue-Red
- Blue-Red 2
- Blue-Red 3
Each palette offers a visual gradation from one hue to another through a desaturated center point, ideal for visualizing bidirectional data variations. For example, applying these palettes to electrostatic potential maps lets you visually discern regions of like charge—helpful in docking simulations or molecular interaction studies.
When to Use Diverging Color Palettes?
Diverging palettes are best used in scenarios where the data varies around a meaningful midpoint, like zero or a neutral value. Here are some use cases within molecular modeling workflows:
- Comparing RMSD values to a reference structure
- Mapping charge distributions or electrostatic potential
- Visualizing difference maps from simulations
- Marking binding affinities on a molecular surface
Palette Breakdown
Berlin: A soft diverging scheme offering a gentle contrast, great for subtle differences.
Blue-Red series: More vivid transitions for when you want high-impact visuals. Versions 2 and 3 offer more nuanced gradations depending on the intensity of difference you want to show.
Practical Tips
- You can reverse the left and right color arms in SAMSON’s color palette dialogs if you want to switch the direction of your data gradient.
- If none of the default diverging palettes fit your needs perfectly, you can create your own custom HCL palettes.
These tools make it easier to tailor your visualizations for clarity and consistency, especially when sharing results with collaborators or preparing figures for publication.
Learn more in the official documentation: SAMSON Color Palettes Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Try it today at https://www.samson-connect.net.