A molecular model can contain the answer you are looking for and still be difficult to read. When every chain, residue, or atom looks alike, patterns are hard to spot. But color can also mislead: a palette that is difficult to distinguish, or a range that compresses meaningful variation, may obscure what the model is showing.
In SAMSON, colorization is more than choosing a paint color. A material applied to a node controls its color scheme and other appearance settings, and affects that node’s descendants. This makes it useful to think first about the question you want the view to answer, then choose a color scheme that makes that information legible.
Choose colors for the question
If you want to tell chains apart, use a chain-based scheme. To inspect residue identity or secondary structure, choose the corresponding per-attribute scheme. For atom elements, the default CPK scheme uses familiar element-based colors. And if you want to highlight a particular part of a structure without encoding a data value, a constant color may be more appropriate.
This distinction matters: a constant color highlights an object, while a per-attribute scheme communicates differences in a property. For example, the documentation demonstrates coloring residues by hydrophobicity. That kind of view can make a property easier to scan, but it is still a visual encoding—not a substitute for checking the underlying values.
Apply the scheme to the right part of the model
Select the node you want to change, then apply a scheme through the context toolbar or Visualization > Color. You can also edit materials in the Inspector. Because an applied material affects descendants, take a moment to check which node is selected: applying a scheme high in the structure can colorize more than the specific atoms or residues you had in mind.
For a quick, uniform highlight, choose a constant color and select the color in the dialog. To restore the default appearance later, select the relevant node and use Color > Reset color from the context toolbar or Visualization menu. You can also clear the material in the Inspector. If an experiment with color does not help, SAMSON supports undo through Edit > Undo.
Tune the palette, not just the scheme
A per-attribute scheme uses a color palette to represent values. SAMSON provides palettes in HSV and HCL color spaces, including qualitative, sequential, and diverging options. As a practical starting point, qualitative palettes can help distinguish categories, while sequential or diverging palettes are useful options to explore when the view represents changing values. The best choice depends on the data and the comparison you want to make.
Use Color > Custom… to choose both a per-attribute scheme and a palette. You can reverse a palette’s left and right arms with the Reverse option. For an existing material, click its color bar in the Inspector to change the palette. For per-attribute schemes, the Inspector also lets you adjust the minimum and maximum values. This is helpful when you want to focus the color mapping on a specific range, such as a temperature-factor interval.
When comparing palettes, enable Auto update or click Update to preview the change on the model. Large systems may update slowly, so testing a few options at a time can keep the process manageable. The Color Vision Deficiency Emulator can help you check how the current palette may appear to people with certain color vision deficiencies.
A useful final check is to ask whether the important differences remain easy to see, whether the colors correspond to the property you intended to show, and whether the view still makes sense when you switch back to the default scheme. Clear colorization should help you interpret the structure—not compete with it.
For the full walkthrough of color schemes, palettes, and material editing, see the SAMSON colorizing documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.