If you’ve tried making sense of molecular data in 3D, you know how fast your screen can turn into a tangled visualization that’s difficult to interpret. Whether you’re exploring structural models or protein properties, the way colors are applied can make a huge difference in the clarity of your results. That’s where SAMSON’s color schemes can help.
In SAMSON, color schemes aren’t just aesthetic—they reveal underlying molecular patterns and properties with precision. You can color atoms, residues, chains, and structures based on attributes like partial charge, hydrophobicity, secondary structures, or even custom values. Here’s how that can become a daily tool for your interpretation workflows.
When Color Tells a Story
Let’s say you’re analyzing a protein and want to understand temperature fluctuations across its residues. Instead of scrolling through values database-style, choose the Temperature factor color scheme. With one click under Visualization > Color > Per attribute > Temperature factor, you’ll see a gradient that visually highlights the hotspots and stable zones across the molecule.
The same goes for properties like formal charge, side chain polarity, occupancy, or structural model ID. These aren’t just labels—they can directly inform your decisions on mutations, docking experiments, or structure-based predictions.
Per Attribute, Per Benefit
Per-attribute schemes in SAMSON come with default color palettes. While these defaults offer a quick glance, you can adjust them precisely in the Inspector to fit your research context. Maybe a diverging HCL palette brings better insight when comparing extremes in charge or hydrophobicity. Or perhaps discrete palettes make it easier to illustrate residue types for educational presentations.
Tuning Palettes for More Than Color
When you switch to Color > Custom..., SAMSON opens up a color palette dialog window where you can pick from a variety of palettes in HSV or HCL color spaces. You can reverse color axes, experiment with color vision deficiency previews, or even create your own HCL-based palette tailored to your publication style or lab standard.
Being able to associate color to data ranges helps pinpoint activity across structure: high occupancy regions in your small molecule? Highlighted instantly. Negative regions of side chain charge? Immediately distinguishable.
A Quick Note on Accessibility
Coloring should work for everyone—that’s why SAMSON includes a Color Vision Deficiency Emulator. It helps you see whether your chosen palette remains readable for users with various types of colorblindness. This aligns well with the increasing focus on accessibility in scientific communication.
Why It Matters
Even if you’re not an expert in HCL or HSV models, working visually with reliable, interpretable, and customizable colorizations makes pattern recognition faster and communication clearer. And for large, complex systems where numbers alone get overwhelming, this saves time along with cognitive effort.
So the next time you open a model, don’t just look at atoms—see the data they carry, expressed through meaningful color. It’s not just visualization. It’s molecular insight.
👉 Learn more in the official SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.