A molecular structure can contain thousands of atoms, several chains, and multiple kinds of information. When everything is shown in similar colors, it becomes difficult to tell one part from another—or to spot the property you meant to investigate. The solution is not simply to add more color. It is to choose a color scheme that answers a specific visual question, then check that its palette makes the answer easy to read.
In SAMSON, colorization can help distinguish structural features such as elements, chains, residues, or selected atom properties. A useful first step is to decide what you want to see. To identify atom types, use Per element (the CPK scheme). To distinguish chains, choose Chain. To visualize a property such as temperature factor, partial charge, or residue type, choose the corresponding per-attribute scheme. For protein residues, the documentation also demonstrates coloring by hydrophobicity.
This distinction matters: a color is meaningful only in relation to the scheme that produced it. A bright region might represent a particular chain in one view and a high attribute value in another. When preparing a figure or sharing a model, make the chosen scheme clear so viewers do not have to guess what the colors encode.
Start with the selection
Select the node you want to color, such as a structural model or a visual model. Then apply a scheme from the context toolbar, from Visualization > Color, or through the Inspector. For a single, uniform appearance, choose a constant color. For information-rich coloring, choose a per-attribute scheme. Applying a material to a node affects its descendants, so check the selected node carefully: coloring a higher-level node can affect more of the structure than coloring a smaller part.
After applying a scheme, inspect the result rather than assuming the default appearance is ideal. If the mapping is hard to interpret, use Color > Custom… to choose a different palette, or adjust the material in the Inspector. Per-attribute materials let you modify the palette and its minimum and maximum values. Changing that range can help focus the display on values of interest—for example, when coloring by temperature factor. Keep in mind that changing the range changes how values map to colors, so record or communicate the range when comparisons need to be reproducible.
Choose a palette for the kind of data
SAMSON provides several palette types, including sequential, diverging, and qualitative palettes in the HCL color space, as well as discrete palettes and a standard HSV palette. These choices give you ways to represent different kinds of distinctions: for example, a palette can vary across an attribute’s values, or use distinct colors to separate categories. You can reverse a palette’s left and right arms in the dialog when the direction of the mapping needs to be changed.
Color perception also varies. The palette window includes a Color Vision Deficiency Emulator, which lets you preview how the current palette may appear to people with certain color vision deficiencies. Use it as a practical check before settling on a palette, especially when the distinction between colors carries important information.
For a quick review, enable Auto update in the palette window or use Update to see changes on the model. The documentation notes that updating can be slow for large systems. If a change makes the model less legible, return to the palette settings or reset the colorization through Visualization > Color > Reset color. You can also manage materials in the Inspector.
A dependable workflow is simple: decide what distinction matters, select the appropriate scheme, choose a palette that is easy to read, inspect the mapping and range, and reset or revise it if the result obscures the structure. For more details, see the SAMSON colorizing documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.