A molecular model can contain all the information you need and still be hard to read. When chains, residues, and atoms share one default appearance, it is difficult to spot where one part ends and another begins—or to see how a property changes across a structure. The fix is not simply to add more color. It is to choose a color scheme that answers a specific visual question.
In SAMSON, color is part of a material, which can also include appearance settings such as metallic, roughness, and transmission. Applying a material to a node affects its descendants, so applying one to a structural model can color the contents beneath it. You can also apply different schemes to different nodes, which is useful when you want to distinguish one part of a scene without recoloring everything.
Start with the question you want the image to answer
Before choosing a palette, decide what you are trying to see. Is the goal to distinguish chains, identify residue types, inspect charge, or show a property such as temperature factor? The scheme should make that feature easier to interpret—not just make the model more colorful.
- To separate chains: choose Chain. This assigns colors by chain ID and can make a multi-chain structure easier to parse.
- To see residue categories: try Residue type or Secondary structure type.
- To inspect an atom-level property: use schemes such as Formal charge, Partial charge, Occupancy, or Temperature factor, when those attributes are present in your structure.
- To emphasize a single object: apply a Constant color. This is also a straightforward way to give a selected model or visual object a distinct appearance.
For example, coloring a protein by residue hydrophobicity can make variation across residues easier to inspect than a uniform color. The point is to map a meaningful attribute to color, so the image communicates something about the structure.
Apply the scheme to the right node
Select the node you want to affect, then apply a scheme through the context toolbar, Visualization > Color, or the Inspector. A useful habit is to check the Document view for the material icon: it indicates which nodes already have materials. This can help explain why a color change affects more—or less—of the scene than expected.
Because a material affects a node’s descendants, applying a scheme high in the structure can color many objects below it. If you need a more targeted result, select a lower-level node instead. You can also apply different schemes to different nodes, such as using a constant color for one object and an attribute-based scheme for another.
Choose a palette that preserves the meaning
A color scheme decides what is mapped to color; a palette decides how the colors change across values or categories. SAMSON includes standard HSV palettes, discrete palettes, and HCL palettes, including qualitative, sequential, and diverging options. For a continuous property, a sequential palette can help show a progression. For values that vary around a meaningful midpoint, a diverging palette may be more suitable. For categories, a qualitative palette can help keep groups visually distinct.
Use Color > Custom… to select both a scheme and a palette. In the palette dialog, you can preview changes with Auto update or Update; large systems may take longer to refresh. The Color Vision Deficiency Emulator can also help you check how the current palette may appear to people with certain color vision deficiencies. If needed, reverse the palette’s left and right arms, or create and save a custom HCL palette for later use.
Refine, compare, and reset
After applying a scheme, use the Inspector to adjust its material. For a constant scheme, you can change the color; for a per-attribute scheme, you can change the palette and, where available, the minimum and maximum range. Adjusting that range can be useful when you want to focus the mapping on a particular interval—for example, for temperature-factor coloring. If the result becomes confusing, reset the colorization from the context toolbar or Visualization > Color > Reset color, or clear the material in the Inspector. You can undo an operation with Edit > Undo.
A simple workflow is: identify the feature you want to inspect, apply the corresponding scheme to the appropriate node, choose a palette suited to the data, and check whether the result is still readable. That turns color from decoration into a practical guide through a complex molecular model.
For details and additional examples, see the SAMSON colorizing documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.