Choosing the right color palette when visualizing molecular structures can have a significant impact on how data is interpreted, especially when dealing with large biomolecules or complex simulation results. With SAMSON, molecular modelers can apply and customize color palettes to enhance clarity, distinguish properties, and even improve accessibility for viewers with color vision deficiencies.
One common pain point in molecular modeling is the difficulty of interpreting large datasets due to unclear or inconsistent color schemes. For example, structural properties such as hydrophobicity, temperature factor, or residue type can be visualized in color—but which palette communicates the data best?
This is where SAMSON’s color palette functionality becomes valuable. It offers a diverse set of palettes based on both the traditional HSV (Hue-Saturation-Value) model and the perceptually optimized HCL (Hue-Chroma-Luminance) model. The HCL color model aims to be more intuitive and effective for human perception, offering better contrast and consistency across data distributions.
Color Palettes in SAMSON
When using per-attribute color schemes (e.g., by chain, charge, or temperature factor), SAMSON allows users to either stick with default palettes or tailor them through the Inspector or the Color > Custom… menu.
Types of color palettes available include:
- Standard HSV palettes: Good for simple use-cases but less effective for data-driven distinctions.
- Discrete palettes: Useful for categorical attributes like chain ID or residue type.
- HCL palettes:
- Qualitative – Best for categorical data.
- Sequential – Ideal for ordered data such as temperature or occupancy.
- Diverging – Useful for values that deviate from a midpoint (e.g., charge).
- Flexible diverging – Offers more fine-tuned divergence settings.
Previewing and Testing Your Palette
In the palette dialog window, you can preview how your visualization will appear using different palettes. Turn on Auto update to see real-time feedback when toggling between options. For complex systems, this might slow things down slightly, but it helps ensure you’re making the best choice.
Making Accessibility a Priority
A standout feature of SAMSON’s palette customization is the Color Vision Deficiency Emulator. This tool shows how your chosen palette will appear to users with various types of color vision deficiencies. Ensuring your scientific visuals are inclusive not only makes your work more accessible but can also help when preparing figures for broader audiences or publications.
Creating Your Own Palettes
If built-in palettes don’t meet your visualization needs, you can create your own HCL-based palette by modifying parameters like hue range, chroma depth, and luminance directly in SAMSON. Once customized, users can save their palette locally for reuse in future projects.
Choosing the right color palette isn’t just about aesthetics—it can sharpen your scientific insights and help make critical data trends more apparent. Whether you’re visualizing temperature gradients in protein structures or residue polarity, SAMSON’s palette system gives you the control and flexibility you need.
To explore the feature in more detail, visit the official SAMSON documentation on colorizing.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.