Color is more than just aesthetics in molecular modeling. When examining complex biomolecular systems, color can reveal structural patterns, highlight molecular properties, or help detect issues hidden in raw structures. A common challenge for molecular modelers is choosing suitable color schemes and palettes to consistently and clearly convey molecular features. This is especially true when presenting data to colleagues, preparing visuals for publications, or analyzing properties like charge, hydrophobicity, and temperature factor.
In SAMSON, an integrative platform for molecular design, users can fully control how molecular elements are colorized — from the choice of color scheme to the subtle properties of color palettes. Understanding how to tweak these settings is key to visually accurate and interpretable molecular representations.
What’s a Color Palette?
A color palette defines how values (such as atomic charge or residue index) are mapped to colors. For instance, if you’re using a color scheme that visualizes partial charge, the associated color palette will determine the hue assigned to atoms with positive or negative charge values.
Each color scheme in SAMSON comes with a default palette, but users have the flexibility to change these through the Inspector or by selecting Color > Custom… in the visualization menu. This is particularly helpful when the default palette doesn’t distinguish values adequately, or when specific visual standards are required (e.g. colorblind-friendly palettes).
Palette Types at a Glance
SAMSON offers several types of palettes:
- HSV (Hue–Saturation–Value): A standard model effective for broad applications.
- Discrete palettes: Best for categorical data like chain IDs or residue types.
- HCL (Hue–Chroma–Luminance) palettes
- Qualitative: Ideal for unordered categories.
- Sequential: Good for continuous scale data, like occupancy or temperature factor.
- Diverging: Useful when visualizing deviations from a central value (e.g., zero charge).
- Flexible Diverging: Allows more control over how values are distributed across colors.
Color for All Eyes: Accessibility Tools
SAMSON includes a Color Vision Deficiency Emulator at the bottom of the custom color palette dialog. This tool allows you to preview your color mapping as it would appear to users with various types of color blindness, such as Deuteranopia or Protanopia.
This can be especially important when sharing models in collaborative environments or when preparing materials for educational content.
Create and Save Custom Palettes
Need a specific visual style? You can create your own HCL-based palette by modifying an existing one. Just check the Custom HCL palette option, alter parameters like hue range and chroma, and save the new palette. Saved palettes are stored in your SAMSON configuration for future use.
This gives you complete control over the look of your molecular representations, tailored to your scientific context, collaboration needs, or publication requirements.
To learn more and explore step-by-step instructions, visit the official documentation page on colorizing in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.