A molecular model can contain the right information and still be difficult to interpret. A common reason is that its colors do not match the job they are meant to do: a palette intended to distinguish categories may be used to show a gradual value, or a smooth gradient may blur the boundaries between separate components. Choosing a palette by the kind of information you need to communicate can make a visualization easier to read before you change anything else.
SAMSON groups its default palettes into five types: discrete, sequential HCL, qualitative HCL, diverging HCL, and flexible diverging HCL. The labels are useful clues. Instead of starting with “Which colors look best?”, start with “What does each color represent?”
When colors identify separate things
Use a discrete or qualitative palette when colors stand for distinct groups rather than values on a scale—for example, when you want different parts of a scene to remain visually distinguishable. The colors act like labels, not measurements. SAMSON includes discrete options such as Accent, Okabe-Ito, Paired, Set1, and tab10, as well as qualitative options such as Default, Pastel, and Dynamic.
A practical check: if one category is not “more” or “less” than another, avoid implying an order with a light-to-dark gradient. A palette with clearly separated colors is usually a more natural starting point. If you have many categories, check that the colors still look distinct in the actual molecular scene; a palette preview alone cannot show how crowded or small features will appear.
When color represents a low-to-high scale
For a quantity that progresses from low to high, choose a sequential palette. Its colors move along a visual progression, making it easier to follow a continuous change than a set of unrelated hues. The SAMSON list includes options such as Viridis, Plasma, Inferno, Blue, Green, Gray, and Blue-Green-Yellow.
Use one sequential palette for one ordered quantity, and make the direction meaningful: viewers should be able to tell which end corresponds to lower values and which to higher values. If the relationship is not obvious from the image, include a legend or other explanation in the figure. A gradient without a defined interpretation is decoration, not a reliable key.
When the middle matters
Sometimes the important story is not simply low versus high, but how values fall on either side of a meaningful midpoint. A diverging palette is designed around two arms, which makes it a reasonable candidate when the data have a central reference and deviations in opposite directions need to be distinguished. SAMSON lists diverging HCL palettes including Berlin and Blue-Red, plus flexible diverging options such as RdBu, PiYG, and Spectral.
Before applying one, ask whether your data really have a meaningful center. If they do not, a diverging palette may suggest a divide that is not present in the analysis. When a palette has left and right arms, SAMSON lets you reverse them in the color palette or color scheme dialogs, which is useful when you need the visual direction to match your chosen interpretation.
A quick decision checklist
- Separate categories? Start with a discrete or qualitative palette.
- One ordered quantity? Start with a sequential palette.
- Values on opposite sides of a meaningful center? Consider a diverging palette.
- Unsure? Apply a candidate to the real scene, then check whether the colors clarify the intended message without hiding structural detail.
These categories are not a substitute for checking the finished figure. A palette that looks clear in a strip can behave differently when mapped onto a dense structure, a small region, or a background with similar colors. Compare a few options at the scale where the model will actually be viewed, and keep the mapping consistent with the story your data support.
SAMSON also allows users to create custom HCL palettes, and palettes can be used as part of broader colorizing and visual-preset workflows. For the complete list of defaults and palette previews, see the SAMSON color palettes reference.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.