A molecular model can contain thousands of atoms, residues, and structural features. When everything is shown in the same color, it can be difficult to spot patterns. But adding color without a clear purpose can create a different problem: a striking image that is hard to interpret. A useful approach is to decide what you want color to explain, then choose a scheme and palette that fit that question.
Start with the question, not the palette
In SAMSON, color can represent a constant choice or information associated with structural nodes. For example, you can color atoms by element, distinguish chains, or show attributes such as temperature factor, formal charge, residue type, or secondary structure. These choices answer different questions. Element colors help identify atom types; chain colors help separate parts of a structure; an attribute-based scheme can make a property’s distribution easier to inspect.
Before applying a scheme, ask: am I trying to distinguish categories, compare values, or simply make a model easier to see? This small pause helps avoid using a visually appealing palette that does not support the task.
Choose a scheme that matches the information
For a quick view of a protein’s organization, a chain or structural-model scheme can distinguish components. For a property that varies across atoms or residues, use a per-attribute scheme. SAMSON includes options such as temperature factor, occupancy, partial charge, residue index, residue type, and secondary-structure type. The available choice depends on the selected nodes and the information in the model.
For example, the image below shows colorization by residue hydrophobicity. Instead of treating the protein as one uniform object, the colors make the selected property visible across its residues.
Color is a visual cue, not a replacement for checking the underlying data. If a pattern matters to your analysis, inspect the relevant nodes and values rather than relying on the appearance alone.
Use palettes with care
A palette determines how colors change with the values or categories being displayed. SAMSON offers palettes in HSV and HCL color spaces, including qualitative, sequential, and diverging HCL palettes. As a practical rule of thumb, qualitative palettes suit distinctions between categories, while sequential palettes are useful for values arranged from lower to higher. Diverging palettes can help when values are meaningful on both sides of a central point. Choose based on what the data represents, not just on which colors look most vivid.
For a per-attribute scheme, open Visualization > Color > Custom… to select the scheme and palette. You can also change a palette through the Inspector by clicking its color bar. For schemes where a value range is available, the Inspector lets you adjust the minimum and maximum. That can be useful when you want to focus the display on a particular range, but remember that changing the range changes how colors map to values.
When comparing views, keep the scheme and range consistent where possible. Otherwise, two structures that look different may simply be using different color mappings. If the colors are difficult to distinguish, SAMSON’s Color Vision Deficiency Emulator can preview how the current palette may appear to people with certain color vision deficiencies.
A simple workflow
- Open a molecule and select the structural model or other nodes you want to color.
- Choose a scheme that matches your question, such as chain, residue type, or temperature factor.
- Use the default palette first, then adjust it if the distinctions are unclear or the display does not suit the data.
- Check the value range in the Inspector when applicable, and preview the palette with the emulator.
- Reset the colorization if you want to return to the default appearance: use Visualization > Color > Reset color, or clear the material in the Inspector.
Materials affect a selected node and its descendants, so check the selection level before applying a scheme. You can apply different schemes to different nodes, which is useful when one part of a scene needs to show a property while another needs to remain visually distinct.
For a step-by-step reference to schemes, palettes, and material editing, see the SAMSON colorizing documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at www.samson-connect.net.