When visualizing molecular models, clarity and interpretability are everything. If you’re working with large biomolecules or need to present complex data about structural attributes (like residue polarity or temperature factors), the way those attributes are color-mapped can make a big difference. Poor color choices can obscure meaning, impair accessibility, or simply confuse your audience.
That’s where color palettes in SAMSON come in. Whether you’re colorizing atoms by charge, visualizing hydrophobicity, or distinguishing chains, SAMSON provides a variety of color palette types that allow you to present data clearly, accurately, and accessibly.
Perception matters: the HCL color space
A key feature of SAMSON’s color palette system is its use of the Hue-Chroma-Luminance (HCL) color space. Unlike HSV or RGB, which are commonly used but not perceptually uniform, HCL is tailored to human visual perception. This means better contrast between similar values and more intuitive visual gradients.
There are several types of HCL palettes provided in SAMSON:
- Qualitative: for categorical data (e.g., different chains)
- Sequential: for ordered data (e.g., temperature factor)
- Diverging: for bipartite data (e.g., positive and negative charges)
- Flexible diverging: a customizable version of the above
These palettes produce cleaner heatmaps and distinguishable labels, especially when you view your molecules in different lighting or background contexts.
Customizing and previewing color palettes
In SAMSON, applying a custom color palette is interactive. When you select Color > Custom…, a dialog opens where you can choose:
- What attribute to map the color to
- Which type of color palette to use
- Whether to reverse the color gradient
You can also preview the effect of different palettes in real time by selecting the Auto update option. This is especially useful for finding the right balance between visual appeal and data clarity.
Accessibility: Seeing through different eyes
Color accessibility is an often-overlooked topic in scientific visualization. SAMSON includes a Color Vision Deficiency Emulator at the bottom of the color palette dialog. This lets you see how your current palette looks to people with different types of color vision deficiencies, such as deuteranopia or protanopia.
Create your own palette
If none of the default palettes are quite right, you can create your own. By copying parameters from an existing palette and modifying attributes like hue range or chroma, you can craft exactly the visual style you need. These custom palettes can be saved locally for reuse across projects.
Conclusion
Color is more than decoration — it’s a functional part of how we interpret molecular data. Thanks to SAMSON’s flexible color palette system and its emphasis on perceptual design, you can adapt your visualizations for both scientific rigour and broader accessibility.
To learn more, explore the full documentation page on colorizing in SAMSON: https://documentation.samson-connect.net/users/latest/colorizing/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here: https://www.samson-connect.net