Color is more than just a matter of aesthetics when it comes to molecular modeling. A good color palette can provide insight into structural and chemical properties, helping researchers interpret their data faster and more accurately. On the other hand, arbitrary or misleading colorization may obscure important features. If you’ve ever felt overwhelmed by color scheme options or unsure how to make your models more informative, this guide to using color palettes in SAMSON may help.
In SAMSON, color schemes define what gets colorized (e.g., atoms, residues, chains) and color palettes define how those properties are visually mapped using color. For example, you might colorize residues by hydrophobicity with a sequential palette that separates hydrophobic and hydrophilic residues using luminance or hue.
Why Color Palettes Matter
Not all color palettes work equally well. Many molecular properties—like temperature factors, partial charges, or hydrophobicity—are continuous or range-based. The right palette can highlight subtle transitions and boundaries more effectively. Moreover, for collaborative work or publications, accessible color representation (including for viewers with color vision deficiencies) becomes critical.
Types of Color Palettes Available in SAMSON
SAMSON provides several types of color palettes tailored to scientific visualization:
- HSV (Hue-Saturation-Value): A general-purpose palette useful for continuous data. Sometimes challenging for perceptual clarity.
- HCL (Hue-Chroma-Luminance): A perceptually uniform space, with palette categories like:
- Qualitative: Best for non-ordered categories (e.g., chain IDs).
- Sequential: Best for ordered data (e.g., occupancy values).
- Diverging: Effective for data centered around a midpoint (e.g., temperature factors).
- Discrete: Assigns separate fixed colors, often for categorical attributes.
Customizing Palettes
Not finding the ideal palette for your dataset? SAMSON lets you customize your own. You can tweak the hue, chroma, and luminance parameters, copy from existing palettes, and save your versions for future reuse. This can be useful for applying a consistent color scheme across a project or lab group, or to meet journal-specific formatting guidelines.
Previewing and Validating Your Palette Choices
Choosing a palette is not only about personal preference — it’s also about accessibility. The color palette interface in SAMSON includes an embedded Color Vision Deficiency Emulator that helps you see how your palette might look to individuals with different types of color vision deficiencies. This is a useful tool for researchers preparing figures for broad audiences.
Applying Palettes in SAMSON
You can apply color palettes through the Inspector or via the Color > Custom… menu. Enabling the Auto update setting helps you rapidly preview how different palettes affect the model in real-time — a valuable feature when fine-tuning your visualizations.
Whether you are preparing a presentation, publishing a paper, or simply analyzing molecular structures, taking the time to choose (or create) the appropriate color palette can significantly improve the clarity and impact of your visualizations.
To dive deeper into color palettes and visualization tools in SAMSON, visit the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.