Molecular modeling often involves visualizing complex datasets and structures, but ensuring clarity and precision can be a challenge. This is where the color scheme tools in SAMSON simplify the process, offering a powerful way to enhance the visualization of your models.
Why are color schemes important?
When studying molecular systems, representing data through appropriate use of color improves both understanding and communication. For example, structural nodes like atoms, residues, or chains can be colored based on specific characteristics like formal charge, temperature factors, or residue type. This not only highlights critical details but also helps convey the story of your model to others.
Versatile Color Scheme Options in SAMSON
SAMSON offers numerous predefined color schemes:
- Constant: Apply a uniform color to nodes for simplicity.
- Constant Illustrative: Depict a molecule in an artistic style, inspired by David S. Goodsell’s molecular illustrations.
- Per-Element (CPK): Use the traditional Corey-Pauling-Koltun color scheme for atom types, customizable with options like per-chain carbons.
- Per-Attribute: Color structures based on chain ID, temperature factors, residue polarity, hydrophobicity, and much more.
An example is the “Residue Hydrophobicity” color scheme, where residues in a protein are visually differentiated based on their hydrophobic nature. This is helpful for protein analysis and better understanding molecular interactions.
How to Apply a Color Scheme
Applying a color scheme in SAMSON is intuitive and can be done in several ways:
- Use the Context Toolbar material options after selecting a structural model.
- Navigate through Visualization > Color in the menu.
- Leverage the Inspector to change materials directly.
For example, to apply a “Residue Hydrophobicity” color scheme, simply select a structural model, open the Visualization menu, and choose Color > Per Attribute > Residue Hydrophobicity. SAMSON automatically colorizes residues according to their hydrophobic properties, as illustrated in the image below:
Using the Inspector for Further Customization
Customization doesn’t stop at color schemes. By using the Inspector, you can tweak materials and palettes further. For instance:
- Modify or reset the color scheme via the Inspector visuals.
- Adjust the range for per-attribute color schemes, such as narrowing the displayed range for temperature factors.
- Enable auto-update of palettes when testing different visual representations.
Creating Custom Color Palettes
If you need further flexibility, you can create custom color palettes in SAMSON using the intuitive Hue-Chroma-Luminance (HCL) color space. This provides finer control over parameters like brightness and “colorness” to better suit your visualization needs. An option to emulate how your color palette appears to those with color vision deficiencies ensures your presentation maintains universal accessibility.
Conclusion
Color schemes in SAMSON empower users to create informative, visually appealing molecular models. By applying or customizing these schemes, you can emphasize unique data points, communicate ideas more effectively, and bring clarity to complex systems.
Ready to dive into SAMSON’s colorization tools? Learn more at the SAMSON documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get started here.