A color map can make a molecular model easier to interpret—or quietly make it harder. A common frustration is choosing colors that look appealing but do not help readers distinguish structural groups, follow a numerical range, or spot values that differ from a meaningful reference point. The useful first step is not picking a favorite color. It is deciding what the colors need to communicate.
SAMSON’s default palettes are grouped into discrete, sequential HCL, qualitative HCL, diverging HCL, and flexible diverging HCL palettes. That organization offers a practical starting point: match the palette family to the kind of information you are showing, then compare a few options in the molecular view.
When the goal is to distinguish categories
If colors identify separate items—such as chains, regions, or groups—use a palette intended for distinct categories rather than a gradient. The discrete collection includes options such as Okabe-Ito, Set1, Set2, tab10, and Carto Safe. These palettes provide separate colors, helping viewers tell categories apart without implying that one category is numerically greater than another.
Before applying a discrete palette, consider how many categories need to remain recognizable at once. If your model contains more groups than are easy to tell apart, color alone may not be enough: labels, selection, or another visual distinction can help. This is especially useful when the structure will be viewed at a smaller size or shared as a static image.
When the values have an order
For a quantity that runs from lower to higher values, a sequential palette gives the viewer a visual progression. SAMSON’s sequential HCL options include Viridis, Plasma, Inferno, Blue, Green, and Gray, among others. Choose a progression that remains legible against the background and on the molecular representation. A restrained gradient can make a continuous pattern easier to follow than a collection of unrelated hues.
Keep the interpretation anchored to the data: a color transition only communicates a trend if the underlying values are mapped consistently. Include a legend or clear explanation in figures so viewers can tell what the palette represents.
When a reference point matters
Sometimes the key message is not simply low-to-high. You may want to show values on either side of a meaningful center, such as deviations around a reference. A diverging palette is a natural candidate for that situation. SAMSON lists diverging HCL palettes including Berlin and Blue-Red, as well as flexible diverging options such as RdBu, PiYG, PRGn, and pLDDT. The center should correspond to an interpretable reference in the data; otherwise, the visual split can suggest a distinction that is not meaningful.
A quick check before sharing
- Ask whether the colors represent categories, an ordered scale, or values around a reference.
- Check that neighboring regions remain distinguishable in the molecular view, not just in the palette preview.
- Use a consistent palette and mapping when comparing structures or figures.
- Remember that palette arms can be reversed in the color palette or color scheme dialogs if the direction better matches your interpretation.
SAMSON also allows users to create custom HCL palettes. For the full list of defaults and information on using palettes in colorization workflows, see the Default color palettes reference and the Colorizing guide.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.