Visualizing complex molecular structures can quickly become overwhelming — atoms, residues, chains, secondary structures all tangled together in 3D. For many molecular modelers, getting lost in this jungle of atoms is a familiar pain.
What if you could color your models not just by default, but based on real biological or chemical properties? Attributes like chain ID, residue type, hydrophobicity, charge, or even occupancy? With SAMSON’s color schemes, you can — and doing so can reveal subtle patterns, anomalies, or trends at a glance.
Why it matters
Whether you’re preparing a model for publication, teaching, or just trying to understand how a protein behaves, choosing the right color scheme can instantly transform raw structural data into actionable insights. For example:
- Colorizing by hydrophobicity can highlight hydrophobic cores or surface-exposed polar regions.
- Colorizing by secondary structure type (e.g., helix, sheet, loop) gives an immediate sense of the fold.
- Colorizing by temperature factor (B-factor) can quickly illustrate flexible vs. rigid parts of molecules.
How it works in SAMSON
SAMSON supports a range of per-attribute color schemes, allowing you to color structural nodes (atoms, residues, etc.) based on specific biological or structural attributes. Here’s what’s available out of the box:
- Chain and Chain (illustrative)
- Residue type, Residue index, and Secondary structure type
- Partial charge, Formal charge
- Temperature factor, Occupancy
- And others like side chain polarity, structural model ID, or even custom attributes
You can also combine these with different color palettes (including perceptually uniform HCL palettes) to build visualizations that are both meaningful and colorblind-friendly.
Sample usage
Let’s say you’re visualizing a protein and want to see which residues are polar vs. hydrophobic. In SAMSON:
- Load a protein structure, such as one from the RCSB PDB.
- Select the structural model in the Document view.
- Go to Visualization > Color > Per attribute > Residue hydrophobicity.
SAMSON will apply a color scheme that reflects the hydrophobicity of each residue. Areas of high hydrophobicity pop out, helping you spot regions likely to be buried or participate in interactions.
Switching palettes
For fine-tuned control, open Color > Custom…. Here, you can pick from several palette families including sequential, diverging, and discrete palettes using the HCL (Hue-Chroma-Luminance) color space. This space is more suited to human vision than traditional HSV or RGB — an important consideration for accessibility.
You can also simulate how each palette appears to users with color vision deficiencies using the built-in Color Vision Deficiency Emulator.
Conclusion
The ability to color molecular models based on structural and biochemical attributes is more than a visual upgrade — it’s a better way to analyze molecular systems. If you’ve ever found yourself squinting at complex models trying to find patterns, per-attribute color schemes might be the answer.
To learn more about color schemes and palettes in SAMSON, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.