Color is more than just visual appeal in molecular modeling — it’s a language. When you’re working with complex biomolecular assemblies, subtle conformational changes, or trying to communicate your results clearly, the default color palettes you apply to your models can make all the difference.
Many molecular modelers—especially scientists preparing publications or presentations—spend hours tweaking visuals to make them more legible or informative. A common pain point is ensuring consistency across images or making sure certain atom types, residues, or molecular regions stand out. If you’ve found yourself battling with manual color assignment or inconsistent representations, SAMSON’s default color palettes can help streamline your workflow.
What is a Default Color Palette in SAMSON?
In SAMSON, default color palettes define how various molecular elements—atoms, chains, residues, etc.—are colored when loaded or visualized. These palettes are pre-defined schemes that can assign consistent and meaningful colors throughout your session, freeing you from manual adjustments and improving visual consistency.
Why Use Them?
- Clarity: Highlight structural regions, chemical groups, or interaction patterns with better contrast.
- Efficiency: Save time by not recoloring new elements during editing or modeling.
- Communication: Enhance visuals for teaching, publishing, or collaboration, where clarity matters.
- Customization: Create visual consistency tailored to your needs or institution’s style.
Common Palettes and When to Use Them
SAMSON includes several built-in palettes you might find useful depending on the goal of your work:
- Element-based: Assigns standard colors used in many chemistry visuals (e.g., oxygen as red, carbon as gray/black). Great for publications or cross-platform consistency.
- Chain/Ribbon-based: Colors polymer chains differently, helpful in protein-ligand complexes or multi-subunit assemblies.
- Residue-based: Highlights amino acids and nucleotides, ideal for educational purposes and structural analysis.
How to Apply or Change Palettes
Applying a color palette in SAMSON is intuitive:
- Right-click on the element or group (such as a node or selection of atoms).
- Navigate to
Visual > Color > Apply palette. - Select the desired palette from the list.
Additionally, you can define your own palettes, save them, and reuse them in different projects. This is especially useful in collaborative environments where standards are required.
Advanced Tip: Combine Palettes with Visual Presets
If you want to go a step further, try combining color palettes with Visual Presets. Presets control lighting, shading, and other appearance parameters for more polished and publishable images without requiring additional editing.
Best Practices
Here are a few tips to get the most out of color palettes in SAMSON:
- Be consistent: Use the same palette for all related figures in a publication.
- Use explanatory legends: Especially when sharing visuals without interactive elements.
- Test for color blindness accessibility: Choose palettes that remain legible across visual impairments.
Color isn’t just style—it’s part of the science. A smart use of color palettes can help others quickly spot patterns, understand complex arrangements, and trust the clarity of your explanations.
To learn more, visit the full SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.