A crowded molecular scene can be hard to read: chains overlap, residues blend together, and a structural property may be difficult to spot. Color can make these patterns easier to inspect—but only when the scheme and palette match the question you are asking. In SAMSON, color is not just a paint bucket: a material can combine a color scheme with appearance settings, and applying it to a node affects that node’s descendants.
A useful starting point is to decide what you need to distinguish. Are you separating chains, viewing residue types, or looking for variation in an atomic attribute? That choice matters more than choosing a vivid palette.
Choose color for the information you need
For a quick overview of a protein, a per-attribute scheme can reveal structure that is otherwise difficult to see. For example, coloring by chain ID helps distinguish chains; coloring by residue type or secondary structure emphasizes different kinds of organization. If you are interested in a numeric property, schemes such as temperature factor, occupancy, formal charge, or partial charge map that attribute to color. SAMSON also includes a residue hydrophobicity scheme, which can help make hydrophobicity patterns visible.
By contrast, a constant color is useful when you want a uniform visual treatment, while the default per-element CPK scheme identifies atoms by element. These answer different questions: a single color is not intended to show variation in an attribute, and an attribute scheme is not necessarily the clearest way to identify individual elements.
Apply color at the right level
Open a molecule—for example, with Home > Fetch—and select the node you want to color. You can apply a scheme from the context toolbar, through Visualization > Color, or in the Inspector. The selected node’s descendants are affected too, so applying a material to a structural model can color the structures beneath it. If the result looks broader than expected, check which node is selected before changing the palette.
To try an attribute scheme, select a suitable node and choose it from Visualization > Color > Per attribute. The example below shows how different schemes can be applied to a visual model.
Make the palette work for the data
A color scheme determines what is being encoded; its palette determines how values appear. SAMSON offers palettes in HSV and HCL color spaces, including qualitative, sequential, and diverging palettes. As a practical guide, use a qualitative palette when separating categories, a sequential palette when showing a progression, and a diverging palette when values are meaningfully compared around a midpoint. This helps keep the visual encoding aligned with the kind of information on screen.
Choose Color > Custom… to select both a per-attribute scheme and a palette. You can preview changes with Auto update or click Update; for large systems, previewing may take longer. The color vision deficiency emulator at the bottom of the palette window can help you check how the current palette may appear to people with certain color vision deficiencies.
Check the range before interpreting a gradient
When a per-attribute scheme is applied, the Inspector lets you modify its palette and its minimum and maximum values. This is useful when you want to focus the color mapping on a specific range—for example, when examining temperature factors. Before comparing two views, check that their ranges and palettes are set as intended; a changed range changes how values map to colors.
If you want to adjust an existing material, select its node and use the Inspector to change the scheme, palette, or range. To return to the default colorization, use Color > Reset color from the context toolbar or Visualization > Color > Reset color. You can also undo an operation with Edit > Undo.
The key habit is simple: decide what distinction matters, apply color at the appropriate node level, and inspect the palette and range before drawing conclusions from the view. For more details, see the SAMSON colorizing documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.