One of the key challenges in molecular modeling is accurately and intuitively representing molecular properties. Whether you’re analyzing protein hydrophobicity, temperature factors, or charge distribution, visual clarity matters. This is where color palettes in SAMSON come into play.
If you’ve ever found yourself struggling to distinguish between attributes or just wanted to produce clearer visuals for a publication or presentation, custom color palettes might be the solution.
What Are Color Palettes in SAMSON?
Color palettes in SAMSON define how colors change based on the values associated with a particular color scheme. For example, if you colorize a molecule by temperature factor, the color palette determines how low and high values are displayed visually.
Each per attribute color scheme in SAMSON comes with a default color palette—but you’re not limited to those. You can also customize palettes or use a variety of predefined ones in HSV or HCL color spaces.
Types of Color Palettes
- HSV (Hue-Saturation-Value): The standard option, adaptable for general use.
- Discrete: Useful when categories are discrete (e.g., different chains).
- HCL (Hue-Chroma-Luminance): Designed for enhanced human perception. These include:
- Qualitative
- Sequential (single- and multi-hue)
- Diverging
- Flexible diverging
The HCL space allows better control of parameters like hue, intensity, and brightness, leading to more readable representations.
Why Change the Palette?
By default, color schemes work well for many cases. But when your system is large, complex, or you’re trying to emphasize specific molecular properties, altering the color palette can make insights visible at a glance.
For example, adjusting the range of the color palette can help you better highlight subtle differences in temperature factor or partial charge. You can also reverse palettes or try various schemes to see which provides the best clarity.
Creating a Custom Palette
To go beyond the default options, simply use the Color > Custom… menu in the context toolbar or Inspector. You’ll be able to:
- Select a color scheme
- Pick a pre-existing HCL palette
- Modify HCL parameters manually or copy from an existing one
- Save your new palette for later use in your local SAMSON configuration
Don’t forget about accessibility! SAMSON also includes a Color Vision Deficiency Emulator at the bottom of the palette dialog. This lets you simulate how your color choices appear to individuals with different types of color blindness, helping ensure your visuals are inclusive.
Tips for Palette Optimization
- Use Auto update to preview how different palettes affect your model in real-time.
- Reverse the color direction using the Reverse toggle if it improves contrast.
- Limit the color range to enhance visibility of specific value intervals.
Color isn’t just aesthetic—it’s a tool to communicate molecular meaning clearly and effectively. Mastering SAMSON’s palette features allows you to create representations that are not only beautiful but also analytically precise.
To learn more, explore the full colorizing documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.