Color is an essential tool for molecular modelers. Whether you’re communicating structural insights, visualizing properties like hydrophobicity or temperature factors, or simply enhancing the aesthetic clarity of a molecular scene, choosing the right color scheme makes a big difference. But what happens when the default color palettes don’t align with your needs?
In SAMSON, color schemes are powerful and flexible—but what many users overlook is the ability to customize color palettes. This feature allows you to fully control how molecular attributes map to color, dramatically improving the accuracy and communicative power of your visualizations.
What Are Color Palettes in SAMSON?
A color palette in SAMSON defines how colors are assigned based on a molecular attribute, such as residue type, chain ID, or temperature factor. Each color scheme has its own default palette, but these defaults might not always fit your context—especially if you’re tailoring visuals for accessibility or preparing figures for publication.
Customize with Precision
When applying per-attribute color schemes, you can customize the palette in two ways:
- By changing the palette in the Inspector via the color bar
- By using the Color > Custom… option in the visualization menu
This opens a dialog where you can:
- Select the color scheme
- Choose from multiple palette types: HSV, discrete, and several types of HCL (Hue-Chroma-Luminance) palettes
- Enable auto-updating to preview your palette while switching
- Simulate how color palettes will be perceived by users with color vision deficiencies
Even More Control
You’re not limited to the built-in palettes. SAMSON enables you to create your own HCL palette. Just copy the parameters of an existing palette, check the Custom HCL palette box, and tailor it by adjusting hue, chroma, and luminance settings.
Once you’re satisfied, you can save the palette, which becomes available in your local SAMSON installation. It’s a flexible way to build a consistent visual language across all your molecular projects.
Improving Accessibility
If you collaborate with colleagues or audiences with color vision deficiencies, you’ll appreciate the Color Vision Deficiency Emulator at the bottom of the customization dialog. It helps ensure your visuals remain informative and distinguishable for more viewers.
Why It Matters
Custom color palettes help avoid misleading visuals and increase clarity, especially when working with complex systems. They become crucial in publications, presentations, and user interfaces where color plays a communicative role.
To explore further, visit the full SAMSON colorizing documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.