A crowded molecular view can be hard to read even when every atom and chain is visible. Color can help separate parts of a structure or reveal a changing value—but the wrong palette can make categories look related, hide differences, or add visual noise. A useful first step is to decide what the colors need to communicate.
SAMSON’s default palettes are grouped by type. That grouping is more than a way to browse colors: it helps match a palette to the kind of information you want to show. Here’s a practical guide to choosing among them.
For distinct groups, use distinct colors
If you are coloring separate chains, domains, ligands, or other categories, the key is to make each group easy to tell apart. Start with a discrete palette, such as Okabe-Ito, Carto Safe, or Set2. Discrete palettes provide a set of separate colors rather than a gradual ramp.
Think about how many groups you need to distinguish. A palette with many colors may seem convenient, but neighboring or similar-looking colors can be difficult to tell apart in a dense view. If the image will be viewed small or printed, check that the groups remain recognizable at that size. Avoid relying on color alone when the distinction is important: labels or other visual cues can help readers verify what they are seeing.
For a value that increases, use a sequential palette
When color represents an ordered quantity—such as a low-to-high value—a sequential HCL palette is a natural place to look. Examples include Viridis, Blue, Heat, and Gray. A sequential palette gives the viewer a sense of progression, rather than suggesting that every color represents an unrelated category.
Before applying one, ask whether the underlying values really have an order. If they do, make sure the visual progression is easy to follow and that the palette does not distract from the molecular shape. A restrained single-hue option such as Blue or Gray may suit a focused view, while a more varied ramp such as Viridis can make changes more noticeable.
For values on either side of a reference, use a diverging palette
Sometimes the important message is not simply “less to more.” You may want to show values below and above a meaningful center, or contrast two directions of change. In that case, consider a diverging palette, such as Blue-Red, or a flexible diverging palette, such as RdBu, BrBG, or pLDDT.
The reference point matters: a diverging palette is most informative when the center corresponds to something meaningful in the data. If there is no meaningful midpoint, a sequential palette may communicate the pattern more clearly. SAMSON also lets you reverse the left and right arms of palettes in the color palette or color scheme dialogs—useful when you want the two directions to match a particular visual convention.
A quick selection checklist
- Separate identities? Try a discrete palette.
- One ordered value? Try a sequential HCL palette.
- Contrast around a meaningful center? Try a diverging palette.
- Still unsure? Preview the result on the structure and check whether the colors clarify the view rather than compete with it.
These are starting points, not fixed rules. The same palette can work differently depending on the structure, background, and number of features being shown. SAMSON also supports creating custom HCL palettes when the defaults do not fit your intended visualization.
See the default color palettes reference for the complete palette lists, and explore Colorizing for more on applying palettes in colorization workflows.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.