Color is more than just visual flair—it can be the key to clarity. When working with complex molecular models, effective color schemes reduce visual clutter and help communicate atomic properties, selections, dynamics, and structural hierarchies. In SAMSON, the integrative platform for molecular design, default color palettes make this easier for modelers and researchers.
Why color palettes matter in molecular modeling
A big challenge in visualization is consistency. Different structures might use inconsistent coloring for atoms, residues, or interactions. This makes it harder to compare molecules, communicate findings, or spot patterns. Whether you’re creating educational content, preparing a publication, or analyzing data, having a shared visual language matters. Default color palettes in SAMSON provide that foundation.
The default palettes in SAMSON
SAMSON provides several pre-made color palettes that can be applied to different node types (atoms, molecules, chains, etc.). These palettes are designed with readability and interpretability in mind. For example:
- Chain-based palettes help distinguish polymers like proteins and nucleic acids by assigning unique colors to different chains.
- Element-based palettes follow conventional schemes (e.g. C in grey, O in red, N in blue), which are widely recognized by chemists and molecular biologists.
- Residue-based palettes differentiate amino acids for analyzing binding sites or mutational effects.
When and how to use them
Imagine you’re visualizing a protein-ligand complex that includes DNA, protein domains, and a small molecule inhibitor. Instead of manually setting up colors for each component, you can apply SAMSON’s default palettes with just a few clicks. For example:
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Right-click on a node > Appearance > Use default color palette |
This automatically assigns colors based on node types or structural hierarchy, producing a clean, informative view in seconds.
Tips for effective use
- Use element-based coloring when you want to highlight atomic composition or charge distribution.
- Use chain- or residue-based coloring to analyze domains or variations across biomolecular assemblies.
- Combine palettes with Visual Presets in SAMSON to switch quickly between views (e.g. cartoon view + chain colors).
For video and image exports
The default palettes are especially useful when exporting molecular scenes for communication or publication. A consistent and recognizable coloring scheme improves readability in slides, posters, or animations.
Conclusion
Instead of spending time adjusting colors manually, consider using SAMSON’s default color palettes to streamline your workflow and improve visualization quality. Clear visuals lead to clearer insights.
To learn more, visit the official documentation page on Default color palettes, or explore the full SAMSON documentation reference.
SAMSON and all SAMSON Extensions are free for non-commercial use. Try it yourself by downloading SAMSON at https://www.samson-connect.net.