A molecular structure can be scientifically rich and visually confusing at the same time. A rainbow of colors may look informative, but if you cannot tell what the colors represent—or if important differences disappear in the palette—the image is not helping you interpret the model. In SAMSON, colorization becomes more useful when you treat it as a deliberate mapping from a molecular property to a visual signal.
This workflow is especially helpful when you want to inspect a property such as temperature factor, residue type, chain, or hydrophobicity. The goal is not simply to make a structure colorful. It is to make the visual encoding clear enough that you can compare regions without losing sight of what the colors mean.
Start with a question, not a palette
Before choosing colors, decide what you want to see. Are you distinguishing chains? Comparing a continuous attribute across atoms? Highlighting residue categories? That choice determines which kind of color scheme is appropriate.
- For a single, consistent appearance: use Constant.
- For atom identity: use Per element (CPK), the default for structural nodes.
- For categories such as chains or residue types: choose a suitable per-attribute scheme.
- For a numerical property: choose its per-attribute scheme, such as Temperature factor or Partial charge.
For example, coloring by chain answers “which chain is this?” Coloring by temperature factor instead encodes a property that varies across atoms. Those are different questions, so they should not be expected to produce equally useful views.
Apply the color scheme to the right part of the model
Select the node you want to color, then apply a scheme through Visualization > Color, the context toolbar, or the Inspector. A useful detail to remember: a material applied to a node also affects its descendants. If the result looks broader than expected, check whether you selected a high-level node, such as a structural model, rather than a smaller component.
You can apply different schemes to different nodes, which is useful when one view needs to show multiple kinds of information. The Document view’s material icon indicates which nodes have materials applied.
Make the palette work for the data
A color palette controls how colors change with the value or category represented by the scheme. SAMSON provides HSV palettes, discrete palettes, and HCL palettes, including qualitative, sequential, and diverging options. In HCL, hue, chroma (colorfulness), and luminance (brightness) can be controlled more directly, making it a useful space to consider when choosing a palette for human perception.
For a per-attribute scheme, you can choose Color > Custom… to select both the scheme and its palette. You can also click the color bar in the Inspector to change the palette on an applied material. For numerical attributes, the Inspector also lets you adjust the minimum and maximum values. This is useful when you want the displayed color mapping to focus on a particular range—for example, when examining temperature factors. Treat range changes as an interpretive choice: check the values and the resulting view, rather than assuming a palette alone tells the whole story.
Check that the colors remain readable
When comparing palette options, enable Auto update in the palette window or use Update to preview the current system. Auto update may be slow for large systems. You can also reverse the left and right arms of a palette with the Reverse option.
Before settling on a palette, inspect it with the Color Vision Deficiency Emulator. This helps you see how the palette may appear to people with certain color vision deficiencies. It is a simple check that can make a structural figure easier for more readers to interpret.
A quick, repeatable check
- Select the node that should carry the visual information.
- Choose a color scheme that matches the question you are asking.
- Pick a palette, then adjust the range if the attribute and task call for it.
- Preview the result and check its appearance with the emulator.
- If the view becomes confusing, reset the colorization using Color > Reset color or clear the material in the Inspector. You can also undo with Edit > Undo.
A clear molecular view is not just a styling choice: it is a way to make the property you care about easier to inspect. For more details on schemes, palettes, and materials, see the SAMSON colorizing documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.