How to Color Proteins in PyMOL: Every Method Explained

Color by chain assigns a distinct color to each polypeptide chain. It’s the standard first coloring for any multi-chain structure — complexes, dimers, antibody-antigen pairs — because it immediately makes chain boundaries visible without requiring any structural knowledge.

# Color all chains automatically (most common)
util.cbc

# Color specific chains manually
color slate, chain A
color salmon, chain B
color palegreen, chain C

# Color by chain but only for a specific object
util.cbc protein_name

util.cbc stands for “color by chain” and cycles through a built-in set of distinct, publication-friendly colors. It’s a single-command solution that works for any number of chains. For figures where you need specific colors per chain — to match other figure panels, or to use your journal’s preferred palette — override individual chains with color color_name, chain X after running util.cbc.

Coloring by secondary structure makes alpha helices, beta sheets, and loops immediately distinguishable. It’s particularly useful when explaining a protein’s fold to an audience that may not be familiar with the structure — the coloring communicates topology without requiring any annotation.

# Standard secondary structure coloring
util.cbs

# Manually set colors for each element type
color red, ss h        # helices
color yellow, ss s     # sheets (strands)
color green, ss l      # loops
color green, ss ""     # unassigned (same as loops)

PyMOL’s spectrum command colors each atom by the value in its B-factor column — which in crystal structures reflects thermal motion (higher B-factor = more flexible) and in AlphaFold structures holds the pLDDT confidence score (higher = more confident). This is the standard visualization for showing which regions of a predicted structure are reliable.

# AlphaFold pLDDT coloring (standard scale)
# Blue = very high confidence, red = very low
spectrum b, blue_cyan_yellow_orange_red, minimum=50, maximum=100

# Crystal structure B-factor coloring
spectrum b, blue_white_red

# Simple two-color gradient
spectrum b, blue_red

# Green to white to red (neutral midpoint)
spectrum b, green_white_red

The minimum and maximum arguments clamp the color scale. For AlphaFold structures, using minimum=50, maximum=100 means anything with pLDDT below 50 gets the same “lowest” color and the full gradient covers the meaningful 50–100 range. Without these arguments PyMOL scales to the actual min/max values in the file, which can compress the useful range.

CPK coloring (named after Corey, Pauling, and Koltun) assigns colors based on element — the universal chemistry convention that anyone familiar with molecular models will immediately recognize. It’s the standard coloring for ligands, active site residues shown as sticks, and any context where individual atoms need to be identified.

# CPK with white carbons (standard for protein context)
util.cbaw selection

# CPK with green carbons (standard for ligands)
util.cbag selection

# CPK with cyan carbons (common for second molecule in figure)
util.cbac selection

# CPK with yellow carbons
util.cbay selection

# Typical binding site figure: protein gray, ligand green CPK
color gray80, binding_site_residues
util.cbag LIG

The suffix letter in util.cba_ sets the carbon color: w=white, g=green, c=cyan, y=yellow, m=magenta, n=marine. When showing multiple ligands or molecules in the same figure, using different carbon colors (green for ligand, cyan for second molecule, white for protein) is the standard way to keep them visually distinct while keeping all non-carbon atoms on the universal CPK scheme.

The spectrum command maps any per-atom numeric property to a color gradient. Beyond B-factor and pLDDT, it can color by residue number (N→C direction), chain count, or any custom property you assign. It’s the most flexible coloring tool in PyMOL.

# N-terminus → C-terminus rainbow (communicates chain direction)
spectrum count, rainbow

# N→C with a specific two-color gradient
spectrum count, blue_red

# Color by residue number within a specific range
spectrum resi, blue_red, minimum=100, maximum=200

# Color by hydrophobicity (built-in property)
spectrum hydrophobicity, white_orange, selection=protein

# Color surface by custom property (after running calculations)
spectrum my_property, blue_white_red

PyMOL’s built-in color palettes for spectrum include: rainbow, blue_red, blue_white_red, green_white_red, blue_cyan_yellow_orange_red, white_orange, white_blue. For any two named colors, PyMOL will generate a smooth gradient between them automatically.

When the built-in PyMOL colors don’t match your journal’s color scheme, your figure panel requirements, or your personal preference, you can define any color by its RGB values and use it exactly like any named color.

# Define a custom color with RGB values (0.0 to 1.0 scale)
set_color structblue, [0.17, 0.35, 0.63]
set_color lightgray, [0.85, 0.85, 0.85]
set_color warmred,   [0.75, 0.15, 0.10]

# Use exactly like any named color
color structblue, chain A
color lightgray,  chain B
color warmred,    active_site

# Convert hex color to RGB for PyMOL
# #2B5AA0 → R=43/255=0.169, G=90/255=0.353, B=160/255=0.627
set_color pymolblue, [0.169, 0.353, 0.627]