One of the most common challenges molecular modelers face is visual overload—too many atoms, residues, or chains can make it nearly impossible to focus or communicate your scientific point effectively. Whether you’re preparing a publication figure or simply trying to follow a protein’s folding pathway, poor visuals make for poor science.
Fortunately, SAMSON offers a flexible colorization system that provides more than just aesthetic control. It helps enhance structural clarity, reveal molecular properties, and tailor the visualization to exactly what you need—even when working with complex biomolecular systems.
Context Matters: Why Is Colorization So Useful?
Imagine you’re looking at a multi-chain protein. Identifying hydrophobic versus hydrophilic residues? Hard. Locating charged areas or thermal fluctuations? Time-consuming. These are pains faced by structural biologists and computational chemists alike.
SAMSON provides per-attribute color schemes that let you instantly encode this kind of information into your molecular visualizations—no scripting required. You can color residues by hydrophobicity, atoms by partial charges, or structures by temperature factors, among others.
How It Works: Assign Meaningful Colors with a Few Clicks
The system is based on materials, which you assign to nodes—these can be atoms, residues, chains, or larger molecular models. Each material includes a color scheme and visual properties like metallic reflection and surface roughness.
When you apply a color scheme (through Visualization > Color or the context toolbar), it cascades to all descendant nodes for consistent rendering. This means one click applies colorizations down the molecular hierarchy where needed.
The image below shows an example of color scheme options for per-attribute mapping, including useful properties like side chain charge, temperature factor, and secondary structure:
Looking to focus on a specific property? Try selecting ‘Residue hydrophobicity’ from the menu to visualize how exposed versus buried regions present themselves. Here’s how such a color application looks in practice:
Customize Your View
If the default palettes aren’t ideal for your needs or audience, especially when considering color vision deficiencies or presentation standards, SAMSON lets you change them. Open the Inspector and select an existing material. You’ll find the option to switch palettes, reverse them, or assign your own HCL-based palette.
That flexibility means you can make your visualization more than just functional—you can make it understandable to diverse audiences, including non-scientists, reviewers, or students.
You Can Always Undo
Worried about messing it up? Just hit Edit > Undo or use the classic Ctrl+Z / Cmd+Z. You can also reset a node to its default color scheme at any moment via the toolbar or Inspector.
To learn more about SAMSON’s colorization system, visit the original documentation page here: https://documentation.samson-connect.net/users/latest/colorizing/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.