Choosing the right color palette might seem like a small detail when setting up a molecular visualization, but it can make a significant difference—especially when working with large, complex systems or preparing visuals for publication. In SAMSON, the integrative molecular design platform, you can use advanced color palette mechanisms to create better, clearer molecular representations.
This blog post shows how to leverage SAMSON’s color palette system to improve visual clarity, highlight molecular properties, and enhance accessibility.
Why color palettes matter 🧬
Molecular modelers often need to encode complex properties such as hydrophobicity, charge, temperature factor, or secondary structure into a single image. The right palette makes these attributes more understandable at a glance, but not all palettes are equally suitable for visualization. SAMSON helps by offering carefully designed palettes, including those based on Hue-Chroma-Luminance (HCL), a color space optimized for human perception.
How it works in SAMSON
When you apply a per attribute color scheme in SAMSON—such as chain ID, residue type, or partial charge—you get access to SAMSON’s default color palettes. These palettes map attribute values to colors, helping you visualize trends, groupings, or outliers across a structure.
You can choose palettes in several ways:
- Use the Inspector to change the palette of an already-applied material
- Start from Visualization > Color > Custom… to set both the color scheme and the palette at once
Understanding HCL-based palettes
One of SAMSON’s strengths lies in its use of HCL color palettes. Unlike traditional HSV (Hue-Saturation-Value) palettes, HCL palettes are perceptually uniform. This means differences in values are more consistently represented by differences in colors, making your molecular visuals less ambiguous.
You can choose between types of palettes:
- Qualitative: for categorical data (e.g. chain ID)
- Sequential: for continuous values that grow in one direction (e.g. temperature factor)
- Diverging: for continuous values with a meaningful central reference (e.g. charge)
These palettes can be reversed for convenience by checking the Reverse option, and you can preview changes in real time using the Auto update toggle.
Accessibility built-in 🎨
Color vision deficiency is a common challenge in scientific visualization. SAMSON includes a Color Vision Deficiency Emulator at the bottom of the palette dialog window. This feature shows how your current palette looks to viewers with various types of color blindness, helping you choose more accessible representations.
Creating your own palette
If the default palettes don’t quite suit your dataset, SAMSON allows you to create custom HCL palettes. Start by copying parameters from an existing palette, then adjust hue, chroma, and luminance to fit your needs. These palettes can be saved locally for future use.
Summary
SAMSON’s color palette system doesn’t just make structures look better — it makes them clearer and more informative. Whether you’re preparing a graphic for research, teaching, or publication, using perceptually tuned color palettes helps ensure your message is not lost in visualization.
To learn more, check out the original SAMSON documentation on colorizing molecules.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.