A molecular structure can contain the information you need and still be difficult to read. When every chain looks alike, or a color gradient has no clear meaning, it becomes harder to inspect a model and harder to explain what you see to someone else. In SAMSON, colorization can help make structural differences visible—but the useful choice is not simply the brightest palette. It is the scheme that makes the feature you care about easy to interpret.
Here is a practical workflow for turning color into a readable visual cue, while keeping in mind how SAMSON applies color and materials.
Start with the question, not the palette
Before choosing colors, decide what you want the view to communicate. Are you distinguishing chains? Showing residue types? Looking for variation in an atom attribute such as temperature factor, occupancy, or charge? SAMSON offers schemes for these purposes, including Chain, Residue type, Temperature factor, and Partial charge.
For example, a per-attribute scheme can make differences in temperature factor visible across a structure. A chain-based scheme, by contrast, helps separate structural parts that might otherwise be difficult to follow. These are different questions, so they call for different color schemes. Applying a palette before deciding what the colors represent can produce a striking view that is not especially informative.
Apply color at the right level
Select the node you want to color, then apply a scheme from the context toolbar, Visualization > Color, or the Inspector. You can apply different schemes to different nodes. This is useful when, for instance, you want to distinguish chains in one part of a model while showing an attribute on another.
One detail matters when planning the result: a material applied to a node also affects its descendants. A color applied to a structural model can therefore affect the nodes contained within it. If a selection appears to color more of the structure than expected, check which node received the material. The material icon in the Document view can help identify nodes that have materials.
Choose a palette that supports the data
Per-attribute schemes use a color palette to map values to colors. SAMSON provides standard HSV palettes, discrete palettes, and palettes in the HCL color space, including qualitative, sequential, and diverging types. A sequential palette is one option to consider when the goal is to show a progression of values; a diverging palette may be useful when the distinction around a central value matters. The appropriate choice depends on the attribute and the story the view needs to tell.
Use Color > Custom… to choose both a per-attribute scheme and a palette. The palette dialog also offers a Reverse option, which swaps the palette’s left and right arms. If you are comparing palette options, enable Auto update or click Update to preview them on the model. The documentation notes that updating can be slow for large systems.
Color perception also affects whether a view is easy to read. SAMSON’s Color Vision Deficiency Emulator previews how the current palette may appear to people with certain color vision deficiencies. Checking this can help reveal when distinctions that seem clear to you are difficult to distinguish for others.
Refine the range, then review the result
After applying a per-attribute scheme, open the material in the Inspector. You can change its palette and adjust its minimum and maximum values. This is useful when you want to focus the color mapping on a particular range of an attribute, such as temperature factor. Review the resulting view in context: a color gradient is most useful when its differences remain legible and its meaning is clear.
If you want to return to the default appearance, select the relevant node and choose Color > Reset color from the context toolbar or the Visualization menu. You can also clear the material in the Inspector. As with other SAMSON operations, you can undo a change with Edit > Undo.
The goal is not to use more color; it is to make a specific structural distinction easier to see. For details on schemes, palettes, and materials, read the SAMSON colorizing documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.