Color is not just decoration in molecular modeling—it’s a way of encoding meaning and guiding perception. When visualizing complex structures, whether you’re comparing conformations, tracking changes in dynamics, or simply preparing a figure for publication, the color palette you choose can influence comprehension.
In SAMSON, molecular modelers have access to a wide set of color palette tools to fine-tune how color schemes reflect structural properties or attributes. This blog post explores how to use and customize color palettes in SAMSON—and why doing so can improve both scientific clarity and accessibility.
What is a color palette?
When applying a per-attribute color scheme (such as residue hydrophobicity, chain ID, atom charge, etc.), SAMSON uses a color palette to map attribute values to colors. For example, in a temperature factor color scheme, low B-factors might be mapped to one color, and high B-factors to another, with a gradient in between. The palette governs those mappings.
Why does the color model matter?
SAMSON supports color spaces like HSV (Hue-Saturation-Value) but also provides a more perceptually intuitive model: HCL (Hue-Chroma-Luminance). This model is generally better suited for scientific visualizations because it offers separate controls for color, dullness/intensity, and brightness—important when designing color ramps that need to make small differences visible.
Here’s an illustration of the Color Vision Deficiency Emulator tool available in SAMSON, which helps ensure your color choices remain effective for viewers with color vision deficiencies:
Insight: The default palette may not always be optimal. If you’re visualizing partial charges and the differences are subtle, a diverging HCL palette might provide better contrast than a sequential one.
How to customize a color palette
- Apply a per-attribute color scheme (e.g., Visualization > Color > Per attribute).
- Bring up the Inspector and click the color bar of the current material to open the palette settings.
- You can pick from several types: sequential, qualitative, diverging, and flexible diverging HCL palettes.
- Reverse the palette arms if needed for better correspondence with your attribute scale.
You can even create your own HCL-based palette by taking an existing one, checking the Custom HCL palette box, adjusting its hue and brightness settings, and saving it for later use. This becomes especially useful when you work on multiple projects and want consistency across visual outputs.
When visual clarity meets accessibility
SAMSON includes built-in support to emulate how your chosen palette will appear to users with various types of color vision deficiencies (e.g., protanopia, deuteranopia). This ensures your visuals communicate effectively to a broader audience—including evaluators, reviewers, and collaborators.
Whether you’re preparing publication figures or simply trying to analyze your structure more intuitively, being intentional with your color palettes can make a real difference in usability and accuracy.
To learn more about using and customizing color palettes in SAMSON, visit the official documentation: https://documentation.samson-connect.net/users/latest/colorizing/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.