If you’ve ever struggled to interpret or share molecular models effectively due to unclear or inconsistent coloring, you’re not alone. Color plays a critical role in structure analysis—whether you’re trying to identify hydrophobic versus hydrophilic residues, distinguish chains, or highlight temperature factors. Choosing the right color palette can make complex structures easier to understand and present.
SAMSON offers powerful color palette tools, especially tuned for scientific accuracy and clarity, including palettes in the Hue-Chroma-Luminance (HCL) color space. This blog post explores how to use color palettes effectively in SAMSON and how they can enhance your molecular models.
Why Color Palettes Matter in Molecular Modeling
When visualizing molecular data, it’s not just about making the model look appealing. Different molecular attributes (residue types, temperature factors, charges, etc.) have real scientific meanings. Choosing an appropriate color scale can prevent misinterpretations and improve communication with your colleagues. Additionally, customizing palettes allows you to meet specific journal or presentation requirements, or make the visualization accessible to color-blind viewers.
Exploring the Color Palette Options in SAMSON
In SAMSON, each per-attribute color scheme uses a default palette. But you can easily switch it or create your own. Here’s an overview of what’s available:
- HSV (Hue-Saturation-Value): A standard color space where you manually control hue rotations.
- HCL (Hue-Chroma-Luminance): A perceptually uniform space ideal for scientific illustration and accuracy.
- Discrete palettes: Useful when visualizing categorical data like chains, residues, or models.
- Sequential and Diverging palettes: Designed for continuous data such as temperature or charge. Use diverging palettes to emphasize both high and low extremes.
How to Use Custom Palettes
To fine-tune your color schemes:
- Select a structural node in the Document View.
- Go to Visualization > Color > Custom…. This will open the custom color palette configuration dialog.
- Choose a color scheme (e.g., “Residue hydrophobicity”).
- Select a palette from the dropdown. Want more control? Click Custom HCL palette to define your own.
You can also reverse color gradients using the Reverse checkbox—handy when you want blue to represent high values instead of low, for instance.
Accessible Visualization: Color Vision Deficiency Emulator
Color blindness affects an estimated 1 in 12 men and 1 in 200 women. SAMSON includes a Color Vision Deficiency Emulator within the palette configuration tool, allowing you to preview how your visualization appears under different types of color blindness. This ensures your work remains interpretable to a wider audience.
A Note on Saving Your Palettes
Once you’ve customized a palette, you can save it to your local SAMSON configuration. This means you can quickly apply it to future projects without remaking it from scratch.
By aligning color choices with specific goals and audiences, you can better communicate the insights within your molecular models. Whether you’re preparing a publication, a presentation, or working with a team, SAMSON gives you the flexibility to colorize your data meaningfully.
To learn more and explore all options, visit the full SAMSON Colorizing documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.