For molecular modelers, visual clarity is essential. When dealing with complex molecular structures, even the smallest details can make the biggest difference. Color palettes play a crucial role in making those details stand out, helping researchers to identify and interpret structural elements quickly and accurately.
Default color palettes made simple
In SAMSON, the integrative molecular design platform, default color palettes bring a systematized approach to colorizing structures. With these palettes, you can achieve consistency and precision in visualizations—key aspects that molecular modelers often strive for.
In this blog post, we will explore different types of default color palettes available in SAMSON and their most common uses, including tips to customize your workflows for even better results.
Four main categories of color palettes
The default color palettes in SAMSON are neatly divided into four categories based on their intended use:
- Discrete color palettes: These are ideal for categorical data, like differentiating between distinct molecular groups. Examples include the vivid Carto Vivid palette or the high-contrast Okabe-Ito, which is also color-blind friendly.
- Sequential HCL palettes: Use these when you need to represent gradients or progressions, such as heat maps or intensity scales. Examples include Blue-Green-Yellow or the evocative Inferno.
- Qualitative HCL palettes: Best suited for visual comparisons, these palettes—like Green2Red Dark or Harmonic—are designed to help identify patterns and contrasts in qualitative datasets.
- Diverging HCL palettes: Perfect for showcasing data with two opposing trends, such as pH shifts. Examples include Berlin or Blue-Red palettes.
Tips for enhanced workflows
While the default palettes are robust and versatile, SAMSON offers options to make your visualizations even more impactful:
- You can reverse the arms of diverging palettes to emphasize gradients from left to right or vice versa. This is especially helpful for switching perspectives mid-analysis.
- If the default palettes aren’t quite what you need, you can even create your own custom HCL palettes. The ability to tailor a palette to your dataset ensures that your visualizations will be uniquely suited to your study.
For example, the “Accent” discrete palette is useful for grouping molecular entities at a glance, whereas the “Blue-Yellow-2” sequential palette might be selected to track density or frequency changes across a gradient.
Note: The concept of HCL (Hue-Chroma-Luminance) ensures perceptual uniformity, meaning color changes are proportionate to the human visual system’s interpretation. This scientific basis makes HCL palettes a superior choice for precise molecular visualizations.
If you’re ready to see exactly how these palettes look, here’s an example of the Discrete – Carto Prism palette:
Learn more
Using SAMSON’s default color palettes not only simplifies molecular design but also enhances clarity. If you’d like to explore these palettes in more depth, we invite you to consult the complete documentation at https://documentation.samson-connect.net/users/latest/color-palettes/.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.