When modeling complex molecular structures, visualization often feels like tackling a puzzle with too many pieces. How can you easily decode structural attributes like residue type, chain IDs, or hydrophobicity at a glance? The answer lies in mastering color schemes. SAMSON, the integrative molecular design platform, provides an array of color schemes that not only streamline your visualization but significantly enhance your understanding of molecular structures.
Revealing Insights Through Color Schemes
In SAMSON, color schemes let you apply colors to molecular nodes (atoms, residues, chains) or visual models, enabling dynamic insights into your molecular data. For instance:
- Use the Constant scheme to assign a uniform color to nodes for clean visualization.
- Apply Per atom element schemes to color nodes based on atom types using the Corey-Pauling-Koltun (CPK) convention.
- Decode structural nuances with Per attribute schemes, such as residue hydrophobicity, temperature factors, or chain IDs.
Combined with SAMSON’s interactive visualization tools, these schemes facilitate the effortless exploration of molecular properties.
Applying Color Schemes
Applying color schemes in SAMSON is an intuitive process designed to suit different workflows. Here are three methods to get you started:
- Select a structural model and click the material in the context toolbar to apply a color scheme.
- Choose Visualization > Color in the main menu for further options, such as selecting attributes like residue hydrophobicity.
- Head to the Inspector interface to customize an existing material or assign new ones.
Once a scheme is applied, interact with your model to witness how it transforms visualization into actionable insights.
Customizing Colors with Color Palettes
The true power of color schemes in SAMSON lies in the accompanying color palettes. These define how colors vary based on structural properties. SAMSON supports a wide range of palettes, such as discrete palettes, sequential HSV (Hue-Saturation-Value) palettes, and perceptually optimized HCL (Hue-Chroma-Luminance) palettes.
You can further enhance your experience by creating custom palettes via the Custom… option. Need to highlight subtle hydrophobicity differences or achieve a visually distinct view for presentations? Simply tweak the palette parameters and save it for future use.
Improved Accessibility with the Color Vision Deficiency Emulator
Incorporated into the color palette editor, the Color Vision Deficiency Emulator ensures your visualizations remain accessible to individuals with color vision deficiencies. Preview how your molecular model appears under different vision conditions and make adjustments for enhanced inclusivity.
Streamlining Molecular Modeling Workflows
Once you’ve mastered applying and customizing color schemes, resetting and switching visuals becomes a breeze. Need to revert to default colors or explore new schemes for a specific analysis? With simple commands via the toolbar or Inspector, you gain full control over your molecular visualization workflow.
Explore more details and examples on the official SAMSON documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON from https://www.samson-connect.net.