One of the key challenges that molecular modelers face is keeping large biomolecular systems readable and informative during visualization. Whether presenting to collaborators or simply making sense of complex macromolecular structures themselves, researchers often struggle with visual clutter, indistinct representations, and inconsistent styling. Fortunately, color schemes in SAMSON offer flexible, intuitive ways to make your models clearer and more informative.
This post explores different types of color schemes in SAMSON, along with concrete examples of when and why to use them. Spoiler: a smart choice of color scheme can make your point instantly understandable – even to viewers unfamiliar with molecular biology. 🎨
Why Colorization Matters
Color isn’t just aesthetic; it’s functional. Whether you’re highlighting hydrophobic regions, showing charge distributions, or indicating chain boundaries, color gives immediate visual cues. Miscommunication or confusion in scientific visualization is often due to poor or inconsistent use of visual encoding.
SAMSON allows you to colorize both whole structures and individual parts (atoms, residues, chains) using either constant colors or attribute-driven schemes.
Types of Color Schemes in SAMSON
SAMSON offers three broad categories of color schemes:
- Constant Color: A uniform color applied to selected nodes. Quick and useful for grouping.
- Per Element: Default is the well-known CPK scheme (color by atom type). Variations exist, like custom carbon coloring per chain or model.
- Per Attribute: Based on node properties like chain ID, residue type, charge, hydrophobicity, or temperature factor. This is extremely helpful for biochemical insights.
When and How to Use Per-Attribute Coloring
Let’s say you are analyzing a protein complex and want to understand how hydrophobicity is distributed in active and surface regions. Applying a per-attribute color scheme such as Residue hydrophobicity (available under Visualization > Color > Per attribute) gives you an immediate visual representation. Cooler colors could represent hydrophilic residues, while warmer colors show hydrophobic ones.
You can also quickly switch between color schemes to view different properties (e.g., temperature factor, formal charge, secondary structure type), allowing for comparative analysis across multiple data layers.
Visualizing Chain Boundaries and Representing Structure
Use color schemes like Chain or Structural model when dealing with multi-chain complexes to assign different colors automatically. For presentations or print-ready visuals, the illustrative schemes mimic the hand-drawn style of David S. Goodsell and can make your images more communicative.
How to Apply a Color Scheme in SAMSON
There are multiple ways to apply a color scheme:
- Select a node and use the context toolbar (usually faster for constant colors).
- Go to Visualization > Color to choose per-attribute schemes.
- Use the Inspector to assign or change materials, color palettes, or their ranges.
Customizing and Resetting
SAMSON also provides options for customizing color palettes (HSV, HCL, Continuous or Discrete) and simulating how your palette looks to viewers with color vision deficiencies. When you’re done exploring, use Reset color to revert back to the default visualization.
Conclusion
Mastering color schemes in SAMSON can save time, improve communication, and offer deeper insights—without requiring programming or specialist rendering experience.
To explore all the options and examples in further detail, visit the full documentation page here: SAMSON Colorizing Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.