One of the key challenges in molecular modeling isn’t only about building accurate models — it’s about understanding and communicating complex structures efficiently. Visual clarity plays a huge role, and for many researchers and students, that means making each atom or residue instantly meaningful through color coding.
That’s where SAMSON’s color palettes come in — especially the HCL (Hue-Chroma-Luminance) color space palettes. Unlike standard RGB or HSV color schemes, HCL was designed with human visual perception in mind, making it uniquely suitable for scientific visualization.
Why HCL Color Palettes?
The HCL color space gives you precise control over three components:
- Hue: the evident color itself
- Chroma: the intensity of the color
- Luminance: the perceived brightness
This control ensures that visualizations remain equally intelligible to different viewers, including those with color vision deficiencies. This is critical when your visualizations are part of publications or presentations.
In SAMSON, you can choose between several HCL palette types including:
- Qualitative: distinct colors for categorical data
- Sequential: a smooth gradient to represent ordered data (e.g., temperature factors)
- Diverging: two contrasting hues with a neutral midpoint (e.g., hydrophobic vs. hydrophilic residues)
- Flexible diverging: more control over the midpoint and gradient range
Using and Customizing HCL Palettes
To apply or customize a color palette in SAMSON:
- Select a structural node (e.g., a molecule or protein chain).
- In the main menu, go to Visualization > Color and choose a per attribute color scheme (e.g. Residue Hydrophobicity).
- In the color dialog, click on Custom… to select and edit a color palette.
You’ll then be able to:
- Preview how the palette will look with real-time updates
- Reverse the color gradient direction
- Test for accessibility using the Color Vision Deficiency Emulator
- Create your own palette based on existing parameters and save it for reuse
All of this ensures that your models are not just technically accurate, but also clear and communicative to others — whether in peer-reviewed papers, collaborative work, or educational settings.
When to Use Custom Palettes
If the default palette isn’t clearly separating your values or if you’re working with a quantity outside the default min–max range, it’s worth switching to a custom HCL palette. For example, in residues with subtle differences in hydrophobicity, a tailored diverging palette can improve contrast.
Whenever you use a per-attribute color scheme in SAMSON, you can click the palette color bar in the Inspector to tweak its min/max range or assign a better suited palette.
Summary
HCL color palettes in SAMSON are a powerful way to precisely and accessibly encode complex molecular data. Whether you’re visualizing occupancy, charge, or structural models, using the right palette enhances both scientific understanding and communication.
To learn more, visit the official SAMSON documentation on colorizing.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download it at https://www.samson-connect.net.