Choosing the right colors when visualizing complex molecular systems is not just a matter of aesthetics—it’s a key part of communicating scientific insights clearly. Whether you’re preparing a figure for a publication, sharing a model with a colleague, or simply trying to understand molecular interactions at a glance, well-designed color schemes can make a big difference. This is where the Default Color Palettes in SAMSON come in.
In this post, we explore how molecular modelers can leverage SAMSON’s pre-defined color palettes to rapidly produce effective, understandable molecular visualizations. We’ll look at how you can access these palettes, what they’re best used for, and why they simplify your modeling workflow.
Why Color Palettes Matter in Molecular Modeling
Colors help encode key properties such as atom types, residue classifications, and interaction types at a glance. Inconsistencies or unclear color choices can mislead or confuse viewers. Standard color conventions—like carbon being grey, oxygen red, and nitrogen blue—are often used, but different visualization tools use different defaults, and switching back and forth slows down workflows.
SAMSON solves this by offering clear, consistent color palettes tailored for molecular modeling, designed to follow conventions and optimize readability.
What’s in SAMSON’s Default Color Palettes?
SAMSON includes a variety of color schemes suitable for atoms, residues, and other molecular entities. Among the most useful palettes:
- CPK—based on the Corey-Pauling-Koltun convention, this standard palette uses familiar colors for atoms and is ideal for general molecular visualization.
- Chain-based palettes—useful in protein structures to make each polymer chain visually distinct.
- Secondary structure palettes—color-code alpha helices, beta sheets, and loops to highlight protein folding and conformational features.
These palettes support both small molecules and macromolecules and can be applied either to the full model or selectively to parts, offering modeling flexibility.
When Should You Use Default Palettes in SAMSON?
If you’re moving quickly through visual screening or need to rapidly prepare consistent imagery for reports, using SAMSON’s built-in palettes ensures common standards are met while saving time. They’re also ideal for educational settings or collaborative work, where clarity and shared visual conventions are essential.
Applying Color Palettes in SAMSON
To apply a default palette in SAMSON, choose your molecular representation, go to the visual properties panel, and select a palette from the dropdown. Palettes can be adjusted further if needed—ideal when you want to highlight active sites or mutations while keeping the rest of the molecule easy to interpret.
Final Thoughts
Default color palettes are a simple but powerful part of the molecular modeling toolkit. By aligning with visual conventions and making molecular elements easy to distinguish, SAMSON’s palettes enhance clarity without adding complexity.
Learn more about SAMSON’s default color palettes in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.