A molecular model can contain the information you need and still be difficult to read. A crowded structure, an unfamiliar chain layout, or a numerical property such as temperature factor may be hard to interpret when every atom has the same appearance. Color can make those patterns easier to see—but only if the scheme and palette match the question you are asking.
In SAMSON, color is part of a material, which can also include appearance settings such as roughness and metallic properties. A material applied to a node affects its descendants, so applying it to a structural model can color the contents beneath it. Keep that in mind when choosing what to select: the level of the node determines how broadly the change applies.
Start with the question, not the palette
If you want to distinguish chains, use Chain; to separate structural models, use Structural model. To inspect a property, choose a per-attribute scheme that represents it—for example, Temperature factor, Partial charge, or Secondary structure type. For atom identity, Per element (CPK) is the default for structural nodes. A constant color is useful when you want a uniform appearance rather than a property map.
This simple choice prevents a common interpretation problem: a striking color scheme is not automatically informative. A map of temperature factor answers a different question from a map of chain identity. Before applying color, decide what distinction you want a viewer to notice.
Apply a scheme to the right selection
Open a molecule, select the relevant node in the Document view, then apply a scheme through the context toolbar or Visualization > Color. For a property-based scheme, the menu is organized under Visualization > Color > Per attribute. The selected node’s descendants are affected, so check your selection if more of the structure changes than intended.
For example, selecting a structural model and applying a residue-related scheme can make differences across its residues visible. The illustration below shows a per-attribute colorization workflow.
Make the scale work for your data
A color palette determines how colors vary with the values represented by a scheme. SAMSON includes HSV palettes, discrete palettes, and palettes in the HCL color space, including qualitative, sequential, and diverging types. You can choose a scheme and palette together with Color > Custom….
When a per-attribute result looks too compressed or does not make the range you care about easy to distinguish, inspect the material. In the Inspector, you can change the palette and adjust the minimum and maximum values for per-attribute schemes. This is useful when you want to focus the color mapping on a particular value range, such as a temperature-factor interval. Changing the range changes how values are mapped to colors; it does not change the underlying molecular data.
The palette controls also offer a Reverse option, which swaps the left and right arms of the palette. If you are comparing palettes, enable Auto update or use Update to preview the current system. For a large system, updating may take time.
Check readability before sharing
A palette that looks clear on your screen may be difficult for someone else to distinguish. SAMSON’s Color Vision Deficiency Emulator previews how the current palette may be perceived by people with certain color vision deficiencies. Use it as a practical check before exporting or sharing a visualization. HCL palettes are also designed around perceptual dimensions—hue, chroma, and luminance—so palette choice can be made with more than hue alone in mind.
If you want to refine an existing result, select the material in the Inspector. Constant schemes let you change the color; per-attribute schemes let you change the palette and range. To return to the default colorization, use Color > Reset color or remove the material in the Inspector. And if a change was accidental, use Edit > Undo.
A useful habit is to save the visualization for the question it answers: use distinct colors to separate structural groups, and use a property-based scheme when the goal is to inspect a molecular attribute. That makes the color map easier to interpret—and easier to explain to the next person who sees it.
For more details, see the SAMSON colorizing documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.