Color is more than just aesthetics. For molecular modelers, colorization is often key to revealing the underlying story of a structure. Whether you’re inspecting protein stability, analyzing charge distribution, or presenting a clean visual for publication, an effective use of color can make molecular features stand out—or disappear into confusion.
One of the most powerful and flexible ways to manage molecular appearance is through per-attribute color schemes in SAMSON. This approach lets you assign colors based on properties like temperature factor, residue type, hydrophobicity, and more. It’s a technique that serves both analysis and communication purposes.
What Are Per-Attribute Color Schemes?
Per-attribute color schemes allow you to map structural features or simulation data to visual elements. For example, you can:
- Color residues based on hydrophobicity to identify interaction surfaces
- Apply a gradient based on B-factors to assess flexibility
- Visually distinguish secondary structures within proteins
Using meaningful and consistent color schemes enhances clarity—especially when working with complex biomolecular assemblies. It can also support accessibility when chosen correctly, e.g., using HCL color palettes that are perceptually uniform and colorblind-friendly.
How to Apply Per-Attribute Color Schemes in SAMSON
To apply a per-attribute color scheme:
- Select a structural model from the Document view.
- Navigate to Visualization > Color > Per attribute and choose the desired property, such as Residue hydrophobicity.
- The molecule will be instantly colorized based on that attribute.
This can be done more quickly using the context toolbar for frequently used attributes.
Customizing Color Palettes
Each attribute comes with a predefined color palette, but SAMSON lets you tailor it further. By clicking on the color bar in the Inspector, you can:
- Switch between HSV, HCL, or discrete palettes
- Reverse color scales (useful for charges, where blue-to-red or red-to-blue is standard)
- Enable the Color Vision Deficiency Emulator to preview perception under colorblind constraints
For researchers preparing visuals for presentations or publications, adjusting color palettes helps maintain consistency and clarity across figures.
Use Case: Visualizing Protein Hydrophobicity
Proteins often show hydrophobic cores and hydrophilic surfaces. By applying the Residue hydrophobicity color scheme to your protein, you can instantly gain insights on folding, surface exposure, or potential interaction sites.
These visualizations can be instrumental when engineering binding sites, understanding membrane interaction potential, or comparing homologous structures.
Conclusion
Per-attribute color schemes in SAMSON provide molecular modelers with a flexible toolkit to highlight key structural or functional features. Whether refining figures for a paper or analyzing structural dynamics, using meaningful coloration can make your scientific story clearer.
Learn more about colorizing in SAMSON in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.