Color can be more than visual appeal when modeling molecules—it communicates information, separates regions, and reveals trends. But choosing a color palette that fits your goals can be difficult, especially when you want clarity across complex molecular assemblies. If you’re using SAMSON, understanding how to control color palettes can make your models more insightful and easier to interpret.
The challenge: One of the common frustrations among molecular modelers is interpreting or presenting data where color schemes do not align with the information being conveyed. A color map that doesn’t accommodate different types of data, such as polarity or hydrophobicity, can lead to confusion or even misinterpretation of molecular properties.
In SAMSON, each color scheme—especially the per-attribute ones—comes with a default color palette. But what if you want to customize colors so they stand out more for specific attributes or better match color vision needs?
Understanding Color Palettes in SAMSON
Each per-attribute color scheme (e.g., residue hydrophobicity, temperature factor) uses a corresponding color palette to map values to colors. These palettes are visual gradients or collections of discrete colors that make differences across attributes more noticeable.
By default, SAMSON provides various color palette types:
- Standard HSV gradient palettes
- Discrete color palettes (ideal for categorical data)
- HCL-based palettes (Hue-Chroma-Luminance), optimized for human perception:
- Qualitative
- Sequential (single- and multi-hue)
- Diverging
- Flexible diverging
Why Use HCL Color Palettes?
The HCL color space is designed with user perception in mind, offering control over hue (color), chroma (saturation), and luminance (brightness). These palettes are especially useful when visualizing data that needs to consider color distinguishability—or when your viewers may have color vision deficiencies.
SAMSON makes it easy to experiment with different palette types. In the Custom color dialog, activating the Auto update option allows you to preview how the colorization will appear live, which is handy for larger systems—just note that it can slow down performance on complex molecules.
To ensure accessibility, there’s even a Color Vision Deficiency Emulator at the bottom of the color palette window. It previews what your visualization might look like to someone with color blindness (e.g., deuteranopia or protanopia). This is very helpful when presenting or publishing your work.
Create and Reuse Your Own Palettes
Sometimes, none of the built-in palettes are quite what you need. For those cases, SAMSON lets you create your own HCL-based palettes. Start by copying an existing palette, checking the Custom HCL palette box, and modifying the settings. When you’re happy with the result, save it—SAMSON will store it in your local configuration so you can use it in future projects.
Preserving Consistency
Another useful option is the ability to reverse color palette arms. This means you can flip how colors are assigned across your value range, which is especially valuable in diverging color schemes where interpretation may depend on directionality (e.g., high vs low temperature).
With these settings, SAMSON goes beyond just colorizing—it gives you control to match your visualization to your dataset, making your molecular models more explanatory and accessible.
To explore all the color palette options and see how to integrate them into your workflow, visit the full documentation: https://documentation.samson-connect.net/users/latest/colorizing/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.