A molecular model can contain a lot of information, but a color scheme that does not match the information can make the structure harder to read. A common modeling headache is choosing colors because they look appealing, then realizing the result does not clearly distinguish molecular parts or show how a value changes across a structure.
A useful starting point is to ask: What does each color represent? SAMSON’s default palettes are grouped into types that help answer that question. These groups are not just different looks; they offer a practical way to match a palette to the kind of information you are showing.
For separate categories, choose distinct colors
If colors identify separate items—such as different chains, components, or groups—you generally want colors that are easy to tell apart, rather than a smooth progression from one color to another. In SAMSON, the discrete palettes include options such as Accent, Carto Bold, Okabe-Ito, Paired, Set1, and tab10.
Think of this as labeling, not measuring: the colors should help viewers recognize that two things belong to different categories. A gradient can accidentally suggest that one category is “more” or “less” than another, even when the categories have no order.
For values that progress, use a sequential palette
When color represents an ordered quantity that runs from low to high, a sequential palette is a natural place to start. SAMSON includes palettes such as Viridis, Plasma, Inferno, Blue, Green, and Gray. A sequence helps communicate that the colors correspond to positions along one scale, rather than unrelated groups.
Before applying one, decide what the endpoints mean. For example, identify which end represents the lower value and which represents the higher value, and make sure the legend or accompanying explanation makes that mapping clear. The palette alone cannot tell readers what a value measures.
For values on either side of a reference point, consider diverging
Some data are best understood relative to a meaningful center: below versus above a reference, or one direction versus another. A diverging palette can make that structure visible by using contrasting arms around a central point. SAMSON lists diverging palettes such as Berlin and Blue-Red, as well as flexible diverging options including RdBu, PiYG, and Spectral.
Use this kind of palette only when a central value or boundary has meaning in your analysis. If the data do not have a meaningful midpoint, a diverging scheme may imply a distinction that is not actually present. The palette dialog also lets you reverse the left and right arms, which can be useful when you need the color direction to match your chosen interpretation.
A quick check before sharing a figure
- Name the meaning of color. Is it a category, an ordered value, or a comparison around a reference?
- Choose the matching palette type. Start with discrete for distinct categories, sequential for a low-to-high scale, and diverging for values on both sides of a meaningful center.
- Check the mapping, not just the colors. Confirm that the scale direction and any midpoint match the data and your explanation.
- Review the structure at the size people will see it. If neighboring regions or categories become difficult to distinguish, try another palette or simplify what you are displaying.
SAMSON also includes qualitative and flexible diverging HCL palettes, and lets you create custom HCL palettes. The default palette reference is a useful place to compare the available options; the related Colorizing guide explains colorization workflows.
For the full list of palette names and previews, visit the SAMSON default color palettes documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.