A molecular structure can contain far more information than a single view can show. Color helps bring some of that information forward—but choosing a palette can be surprisingly difficult. A gradient may make categories look ordered, while a set of distinct colors may hide a smooth change in a measured value. The result is a molecular view that looks polished but is harder to interpret.
A practical way to choose is to start with the meaning of the data, not with the palette name. Are you showing separate groups, a value that increases, or values that depart in two directions from a meaningful reference point? SAMSON’s default palettes are organized into types that help answer that question.
For separate groups, use distinct colors
If colors identify categories—such as different chains, selected groups, or classes of atoms—you generally want viewers to distinguish one group from another, not read the colors as a low-to-high scale. Start with a discrete palette or a qualitative HCL palette. The SAMSON defaults include discrete options such as Okabe-Ito, Set1, and tab10, and qualitative options such as Default, Pastel, and Harmonic.
When comparing several groups, check that the colors remain distinguishable in the actual molecular view. Crowded structures, small features, and overlapping labels can make a palette that looks clear in a strip harder to use in context. If there are many categories, consider whether all of them need separate colors or whether the view would be clearer when split into smaller comparisons.
For a value that moves in one direction, use a sequential palette
Use a sequential palette when the data has a natural order, such as a value progressing from lower to higher. A single progression makes it easier to read the color as a scale rather than as unrelated categories. SAMSON’s sequential HCL defaults include Viridis, Plasma, Blue, Gray, and Heat.
Before applying one, ask what “low” and “high” mean for the quantity being shown. The palette does not explain the measurement on its own: include a clear legend or scale, and use consistent limits when comparing structures or views. Otherwise, two similar colors might represent different values in different views.
For values around a reference, use a diverging palette
Some results are easiest to understand in relation to a meaningful center: for example, values below and above a reference, or two opposing directions of change. A diverging palette gives the two sides different color treatments, making the center part of the visual story. SAMSON lists diverging HCL palettes such as Blue-Red and Berlin, as well as flexible diverging palettes including RdBu, PiYG, and pLDDT.
The important choice is the reference value. If the data has no meaningful midpoint, a diverging palette may imply a distinction that is not present. Conversely, if the midpoint matters, a one-directional gradient can make the two sides harder to compare. Set and communicate the center deliberately.
A quick check before you share a view
- Groups: choose distinct colors rather than a low-to-high progression.
- Ordered values: choose a sequential palette and show what its endpoints represent.
- Values around a reference: choose a diverging palette only when the center has meaning.
- Comparisons: keep the scale consistent across views and make the legend visible.
These are starting points, not rules about which specific palette is best for every molecule or dataset. Preview the colorization in the structure itself, where occlusion and visual density can change how well colors work. SAMSON also lets you reverse the left and right arms of palettes in the color palette or color scheme dialogs, and create custom HCL palettes when the defaults do not fit your visual goal.
For the full lists of default palettes and related guidance, see the SAMSON color palettes reference, along with the pages on colorizing and visual presets.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.