For molecular modelers, data visualization is not just aesthetic—it’s functional. The way atoms, residues, and molecules are colored can directly impact the clarity of your interpretations, the speed of your decision-making, and even the persuasiveness of your publications or presentations. Yet, color conventions are often overlooked or handled inconsistently.
That’s why SAMSON includes customizable default color palettes—a subtle yet powerful feature that enhances molecular clarity, consistency, and communication across projects.
What Are Default Color Palettes in SAMSON?
The Default color palettes in SAMSON allow you to define how atoms, residues, secondary structures, and other molecular elements are visually represented. These palettes are used across different visualization modes and editors. Whether you’re inspecting molecular orbitals, protein structures, or simulation results, SAMSON ensures color consistency throughout.
Why It Matters: A Common Pain Point
If you’ve ever worked on a molecular modeling project with collaborators or across different platforms, you’ve probably encountered mismatched visuals. Colors that were meaningful in one file might be confusing or incorrectly interpreted in another. Sharing screenshots or videos becomes harder when colors aren’t intuitive. And if you’re preparing figures for a paper, recreating visuals manually can waste hours.
That’s where color palette settings in SAMSON come in—the platform lets you tailor and reuse visual standards with ease.
How to Access and Modify Default Palettes
Access your color preferences in SAMSON through the Preferences page at:
https://documentation.samson-connect.net/users/latest/color-palettes/
You can define colors for the following key elements:
- ATOM TYPES: Adjust based on atomic number or hybridization state.
- RESIDUES: Customize coloring of amino acids and nucleotides for easier secondary structure identification.
- SECONDARY STRUCTURES: Highlight helices, sheets, and coils with different tones.
- SELECTION STATES: Change how selected atoms or groups are colored to improve visibility during workflows.
Tips for Effective Color Use
- Be consistent across projects: Define a preferred palette and reapply it whenever possible.
- Use contrast wisely: Avoid palettes with colors that are visually close, especially when showing multiple selections.
- Test for accessibility: Some viewers may be color blind. Use color-blind safe palettes to increase accessibility.
- Match common conventions: For example, oxygen = red, carbon = grey/black, nitrogen = blue. That helps others quickly understand your visualizations.
Exporting and Sharing Consistent Visuals
Once your palette is customized, it will be consistently applied during molecular visualization, animations, and even exported images or movies. This consistency saves time in post-processing and simplifies collaborations.
Even better: since color presets are saved as part of user preferences, you can export them and share with colleagues—ensuring consistent figures across labs or publications.
To learn more about how to modify and use color palettes in SAMSON, check the full reference documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.