A molecular model can contain a lot of information, but a color scheme that looks striking is not always easy to interpret. A chain of changing colors may represent temperature factors, residue properties, or something else entirely—and without a clear mapping, viewers can mistake decoration for data. The useful question is not simply “Which colors look good?” but “What should these colors help me see?”
In SAMSON, color schemes can colorize structural nodes, visual models, meshes, and labels. A scheme is applied through a material, which can also hold appearance settings such as roughness and metallic properties. Applying a material to a node affects its descendants, so a choice made at a structural-model level can influence the elements beneath it. Keeping that hierarchy in mind helps explain why a color change may affect more of a structure than expected.
Match the color scheme to the question
For a simple, consistent appearance, use a constant color. If you want atoms distinguished by their elements, the familiar CPK scheme is the default for structural nodes. Other schemes encode structural attributes: for example, chain ID, residue type, secondary structure, partial charge, or temperature factor. For proteins, the documentation also demonstrates a residue-hydrophobicity scheme.
A practical way to choose is to first decide whether your attribute is a category or a value. Chains and residue types are categories; temperature factor and charge are values. Categorical colors help distinguish groups, while a palette that changes across a range can make variation in a numerical attribute easier to inspect. This is a visualization choice, not a change to the molecular data itself.
SAMSON offers standard HSV palettes, discrete palettes, and HCL palettes, including qualitative, sequential, and diverging types. You can try a built-in scheme through Visualization > Color, or use Color > Custom… to choose a per-attribute scheme and palette together.
Make the mapping inspectable
Color is most useful when you can tell what it represents. Before sharing an image or using a colorized model to guide discussion, note the selected attribute and palette. If a color gradient looks compressed or fails to show the differences you care about, inspect the range as well as the palette. In the Inspector, per-attribute materials let you change the palette and adjust minimum and maximum values. This can help focus the visible mapping on a range relevant to your question.
Be deliberate when changing that range: a different min–max setting can make the same colors correspond to a different span of values. When comparing models or figures, use consistent settings where possible, and state the range if it matters to the interpretation. You can also preview palette changes in the palette window with Auto update or Update; the documentation notes that updating may be slow for large systems.
Check readability before you settle
A palette that separates values for one viewer may be harder for another viewer to distinguish. SAMSON’s color palette window includes a Color Vision Deficiency Emulator so you can preview how the current palette may appear to people with certain color vision deficiencies. If the distinctions you need become difficult to see in that preview, consider another palette rather than relying on the colors alone.
To apply a scheme, select the relevant node and use its context toolbar, Visualization > Color, or the Inspector. To remove a colorization, select the node and choose Color > Reset color, or clear the material in the Inspector. If an experiment goes in the wrong direction, the operation can also be undone.
These small checks—choosing a scheme that answers a specific question, verifying its range, and checking readability—make molecular colorizations easier to interpret and communicate. For the full walkthrough, see the SAMSON colorizing documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.