For many molecular modelers, visual clutter and unclear structural representations slow down analysis and discovery. Colors that aren’t well chosen can obscure rather than reveal important differences in structures—such as charge distributions, chain boundaries, or hydrophobic patterns. That’s where fine-grained control over color schemes becomes an underrated superpower in molecular design platforms.
In SAMSON, a flexible colorization system lets you assign specific color schemes to different structures (atoms, residues, chains, structural models, etc.). These schemes are not just cosmetic. They convey meaningful data directly into your molecular designs and help uncover patterns that might otherwise go unnoticed.
Why Color Schemes Matter
Imagine trying to study how a drug binds to a receptor without being able to visually distinguish hydrophobic regions from polar ones. Or analyzing secondary structures in a protein without a clear visual cue signaling helix versus sheet elements. Proper colorization can make these distinctions immediate and intuitive—crucial when working with large datasets or collaborating across interdisciplinary teams.
In SAMSON, color schemes are part of a broader concept called materials, which include not only color but surface properties like metallic appearance, transparency, and roughness. Applying a material to a node affects all its descendants, so you can easily colorize whole structures with just a few clicks.
Types of Color Schemes
SAMSON offers several types of built-in color schemes:
- Constant: Assign a single color to a selection.
- Per Element (CPK): Use the classic CPK coloring for atom types.
- Per Attribute: Color based on properties like chain ID, temperature factor, residue type, hydrophobicity, and many more.
- Illustrative: Inspired by the hand-drawn look of scientific illustrations (e.g., David S. Goodsell).
Here’s an example of different per-attribute color schemes as applied in SAMSON:
Applying a Color Scheme
You can apply a color scheme to selected nodes in several ways:
- Select the node and use the context toolbar to choose a material.
- Use the menu path Visualization > Color to apply a scheme.
- Use the Inspector for more control, including modifying associated color palettes.
In this image, a protein’s residues are colorized using the hydrophobicity scale. Visualizing such properties instantly provides structural and functional insights.
Quick Reset
Not happy with the visualization? It’s easy to revert to the default by selecting the node and using Color > Reset color or clearing the material in the Inspector.
A Time-Saving Bonus
SAMSON color schemes are not static. You can:
- Switch palettes for better visibility
- Create your own color palettes in the HCL space
- Use presets for specific appearances
- Preview color schemes using a color vision deficiency emulator
Having this kind of flexibility removes friction from your workflow and makes it easier to communicate scientific data visually—essential when collaborating or publishing figures.
Explore the documentation for more ways to customize your visual models using color schemes: https://documentation.samson-connect.net/users/latest/colorizing/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.