A molecular structure can contain several chains, residues, interaction groups, or values that change across a model. Color can help distinguish them—but the wrong palette can make unrelated categories look ordered, or hide the pattern you are trying to inspect. A useful first step is to decide what your colors mean, then choose a palette type that matches that meaning.
SAMSON’s default palettes are grouped into five types: discrete, sequential HCL, qualitative HCL, diverging HCL, and flexible diverging HCL. HCL means Hue-Chroma-Luminance. The groups are a practical starting point for choosing colors; the palette alone does not determine which molecular property or selection is being colored.
Start with the meaning of the data
- Separate categories: Use a palette intended to distinguish categories when colors represent distinct groups, such as different chains or selected components. Discrete palettes include Okabe-Ito, Set1, Paired, and tab10. Qualitative HCL options include Default, Pastel, and Harmonic.
- A value that increases or decreases: A sequential palette is a natural choice when color represents an ordered quantity that progresses from lower to higher values. The available sequential palettes include Viridis, Plasma, Blue, Green, and Gray.
- Values on either side of a meaningful midpoint: A diverging palette can help show two sides of a reference value. The diverging HCL palettes include Berlin and Blue-Red; flexible diverging palettes include RdBu, PiYG, and PRGn.
These are general visual-design guidelines, not rules about which colors have a scientific meaning. Make sure the mapping and its reference point are clear to anyone reading the figure.
Think about the comparison, not just the colors
When a figure feels hard to interpret, check whether the palette matches the question. If you are comparing named groups, a smooth gradient may suggest an order that is not present. If you are showing a continuous quantity, a collection of unrelated categorical colors can make gradual changes difficult to follow. If the important distinction is above versus below a reference point, a diverging palette may make that contrast easier to see than a one-direction gradient.
It is also worth checking the colors at the scale where the figure will actually be used. A palette that looks distinct in a large view may be harder to read in a small screenshot or printed figure. For category colors, ask whether neighboring groups remain distinguishable. For value maps, ask whether the progression is easy to follow and whether the midpoint, if there is one, is apparent.
Examples from the default palettes
The palette previews below let you compare some of the options available in SAMSON. They are previews of the palettes themselves; choose and apply a palette as part of your colorization workflow.
One useful detail: the left and right arms of palettes can be reversed in the color palette or color scheme dialogs. That can be helpful when you want the ends of a gradient to correspond to the opposite ends of your chosen value range. SAMSON also supports creating custom HCL palettes, so the defaults are not the only option.
For the colorization workflow, see Colorizing. The full reference lists the default palette names and previews: Default color palettes.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.