A molecular model can be visually clear and still hide the information you need. A single color may make a structure look tidy, but it cannot distinguish chains, highlight residue properties, or show how an atomic value changes across a model. The key is to treat color as a way to inspect and communicate structure—not just as decoration.
In SAMSON, color is applied through a material. A material contains a color scheme and 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 colorize the nodes beneath it. You can also apply different schemes to different nodes when you want to compare parts of a scene.
Choose a scheme that answers a question
Start by deciding what you want the colors to help you see. For a neutral view of atom types, use the default Per element scheme, also known as CPK. To distinguish chains or structural models, choose a per-attribute scheme such as Chain or Structural model. To explore a molecular property, use a scheme based on an attribute—for example, temperature factor, partial charge, residue type, or secondary structure type. The documentation’s example uses residue hydrophobicity to color a protein by residue property.
This choice matters: a palette that separates categories is not necessarily the right choice for values that vary across a range. SAMSON offers qualitative, sequential, and diverging HCL palettes, among other types. In broad terms, qualitative palettes help distinguish categories; sequential palettes show progression; and diverging palettes can help show values on either side of a meaningful midpoint. Pick a palette whose visual structure matches the data you are trying to inspect.
A practical colorization workflow
- Select the node you want to affect. For example, select a structural model in the Document view.
- Apply a useful scheme. Use Visualization > Color, the context toolbar, or the Inspector. For an attribute-based scheme, select an appropriate option under Per attribute.
- Check whether the result is readable. If the colors are difficult to distinguish, try another palette. Use the palette dialog’s Reverse option if you want to swap the palette’s ends.
- Adjust the range when needed. In the Inspector, per-attribute materials allow you to change the minimum and maximum values. This can be useful when you want to focus the color mapping on a specific range, such as a temperature-factor range.
For a custom combination, use Color > Custom… to choose both the attribute scheme and its palette. You can preview palette changes with Auto update or the Update button; the documentation notes that updates may be slow for large systems.
Make the colors easier to interpret
A vivid palette is not automatically a useful one. SAMSON includes a Color Vision Deficiency Emulator in the palette window, so you can check how the current palette may appear to people with certain color vision deficiencies. HCL palettes are also designed around perceptual dimensions—hue, chroma, and luminance—which can make it easier to reason about differences in color and brightness.
If a result becomes confusing, reset the colorization from the context toolbar or through Visualization > Color > Reset color. You can also remove or change the material in the Inspector. And if you are experimenting, remember that SAMSON supports undo through Edit > Undo.
A helpful habit is to ask, before choosing a color scheme: What relationship should someone be able to see at a glance? Matching the scheme and palette to that question makes a molecular image more informative—and helps prevent color from implying distinctions that the visualization was not meant to show.
For details on available schemes, palettes, and material controls, see the SAMSON colorizing documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.