Colorizing

In this section, we will show how to colorize nodes. In SAMSON, you can colorize visual models, meshes, labels, and structural nodes using various color schemes. Several types of color schemes are available:

  • Constant: the same color is uniformly applied
  • Constant illustrative: applies a constant color (illustrative). It helps to depict molecules in a style similar to David S. Goodsell’s artwork.
  • CPK: the classic Corey-Pauling-Koltun color scheme
  • Per attribute: the color is determined based on an atom attribute (e.g. temperature factor, residue, etc.)

When a color scheme is applied to a node, all the node’s descendants are affected. You can apply different color schemes to different nodes.

You can colorize a node via its context menu or using the Visualization menu or Biology menu.

Let's open a molecule, e.g. 1YRF (use the "Fetch PDB" extension to download it from RCSB PDB). For the sake of the example, solvent, small molecules, and alternate locations were removed. Select 1YRF in the document view, and first apply a constant color scheme: right-click and the Set color > Constant.

Colorizing-Colorization.png
Applying color schemes

A dialog will appear in which you can choose the color.

SelectColorDialog.png
Choosing the color for a constant color scheme

As a result, all the chosen nodes will be colorized with the same color.

Colorizing-ColorScheme-Constant-White.png
Constant color scheme

Note: You can always undo operations by clicking Ctrl/ Cmd⌘ + Z (see History).

Let's now colorize according to the temperature factor. Select 1YRF in the document view, and in the context menu select Set color > Per attribute > Residue hydrophobicity.

Colorizing-ColorScheme-PerAttribute.png
Set color based on an attribute

As a result, all residues will be colorized according to their hydrophobicity.

Colorizing-ColorScheme-Hydrophobicity.png
Colorization according to the residue hydrophobicity

To reset the color scheme, select the node and in the context menu select Set color > Reset to go back to the default color scheme.