When exploring molecular structures, color can be much more than decoration—it can be a powerful tool to convey chemical properties, improve clarity, and communicate findings. But with so many options, how do you choose the right color palette?
In SAMSON, the molecular design platform, users can apply a wide range of color palettes to their models, from simple constant colors to detailed attribute-based schemes. Understanding how and when to use color palettes can help molecular modelers quickly interpret structural features and improve the visual presentation of data.
Why Color Palettes Matter
Color helps distinguish different molecular components, such as chains, residues, or charge distributions. When working with large or complex systems, visual overload can hinder interpretation. That’s where color palettes become most useful—they provide a way to encode meaningful variations across the model in a legible, perceptually accurate format.
Types of Color Palettes in SAMSON
SAMSON includes several palette types. Here’s a quick guide:
- HSV (Hue-Saturation-Value): Offers a standard circular color distribution. Useful for quick visual differentiation.
- Discrete Palettes: Useful for encoding a limited number of categories—e.g., chain IDs or residue types.
- HCL (Hue-Chroma-Luminance): Recommended for scientific visualization. These palettes improve readability and color perception across different viewers and devices.
Customize and Compare with Ease
SAMSON provides a simple way to switch and test different palettes. Use the Color > Custom… menu to explore palette and color scheme combinations in a dedicated window. You can even preview how the palette will look for users with different types of color vision deficiencies, thanks to a built-in simulator:
By enabling Auto update, you can preview changes live on your model. This is particularly helpful when tweaking custom palettes to highlight specific structural features.
Creating Your Own Color Palettes
Need something more tailored? You can create custom palettes in the HCL space. Just select a starting palette in the Custom dialog, turn on the Custom HCL palette option, and modify parameters like hue, chroma, and luminance. When you’re satisfied, save it for future projects.
When to Use Which Palette
- Qualitative HCL palettes: Great for discrete variables like chain ID or residue type.
- Sequential palettes: Best for scalar data like temperature factors or hydrophobicity.
- Diverging palettes: Ideal when you have values around a central reference point, such as zero formal charge.
Why HCL?
Unlike RGB or HSV, the HCL color space is based on perceptual uniformity—changes in parameters produce perceived changes in color. This helps ensure your visual encodings are easily distinguishable, even in grayscale print or by viewers with vision deficiencies.
To explore this topic in more detail, visit the full resource on the SAMSON documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.