How to Measure Distances and Angles in PyMOL: Complete Guide

Two ways to measure: wizard vs command

The distance wizard — click to measure

The fastest way to measure a distance when you’re working interactively and don’t know the exact atom names. Access it from the menu: Wizard → Measurement. The wizard appears in the right panel with four measurement types — distance, angle, dihedral, and H-bond. Select Distance, then click two atoms in the viewer. PyMOL draws a dashed line between them and displays the distance in ångströms.

• Click the first atom — it highlights in pink
• Click the second atom — the distance appears as a dashed line with a label
• Click New Measurement in the wizard panel to start another measurement without clearing the previous one
• Click Done when finished — this exits the wizard but keeps all measurements visible

The distance command — precise and scriptable

The distance command creates a named measurement object between any two selections — individual atoms, residues, or entire selections (in which case it finds the closest atoms between them).

# Basic syntax
distance name, selection1, selection2 [, cutoff] [, mode]

# Simple examples
distance d1, resi 185 and name OG, resn LIG and name O3

# Distance between two residues (finds closest atoms between them)
distance gap, resi 50, resi 200

# Named measurement — appears in object list, reusable
distance catalytic_dist, resi 35 and name NE2, resi 57 and name SG

# Distance with cutoff (only show pairs within 3.5 Å)
distance close_contacts, LIG, pocket, 3.5

Understanding atom identifiers

Precise distance measurements require knowing how to specify exactly which atom you mean. PyMOL uses a hierarchical identifier:

In practice, you rarely need the full identifier. A selection expression like resi 185 and name OG and chain A is cleaner, equally precise, and more readable in scripts. The full slash-separated format is most useful when you have multiple loaded structures with the same residue numbers and need to distinguish them unambiguously.

Measuring H-bond distances automatically

Rather than measuring individual atom pairs manually, distance with mode=2 detects all H-bond donor-acceptor pairs between two selections and draws distance lines for all of them simultaneously:

# All H-bonds between ligand and protein pocket
distance hbonds, LIG, pocket, mode=2

# H-bonds between two chains
distance interface_hbonds, chain A, chain B, mode=2

# H-bonds within a specific region
distance local_hbonds, resi 100-150, resi 100-150, mode=2

# Color H-bond lines yellow (standard publication convention)
color yellow, hbonds

Angle and dihedral measurements

# Measure bond angle between three atoms (A-B-C)
angle a1, atom_A, atom_B, atom_C

# Example: N-CA-C backbone angle of residue 100
angle phi_100, (resi 100 and name N), (resi 100 and name CA), (resi 100 and name C)

# Dihedral angle between four atoms (A-B-C-D)
dihedral d1, atom_A, atom_B, atom_C, atom_D

# Example: chi1 dihedral of a serine residue
dihedral chi1, (resi 185 and name N), (resi 185 and name CA), \
               (resi 185 and name CB), (resi 185 and name OG)

# Hide measurement labels after recording the value
hide labels, a1
hide labels, d1

Measuring across chains

Distances between chains — interface gaps, chain separation, domain movements — use the same commands with chain-specific selections:

# Distance between closest atoms of two chains
distance chain_gap, chain A, chain B

# Distance between specific interface residues across chains
distance iface_contact, resi 73 and chain A, resi 156 and chain B

# All contacts between chain A and chain B within 4 Å
distance contacts, chain A, chain B, 4.0, mode=1

# Distance between Cα atoms of equivalent residues in two structures
distance ca_dist, /structure1//A/GLU`100/CA, /structure2//A/GLU`100/CA

# Center-of-mass distance (via Python)
com_A = cmd.centerofmass("chain A")
com_B = cmd.centerofmass("chain B")
import math
dist = math.sqrt(sum((a-b)**2 for a,b in zip(com_A, com_B)))
print(f"Chain center-of-mass distance: {dist:.2f} Å")

Displaying measurements in publication figures

Measurement objects (distance lines and labels) are rendered during ray tracing and appear in exported figures. Fine-tune their appearance before exporting:

# ── Line style ────────────────────────────────────
set dash_gap,    0.4     # space between dashes (default 0.4)
set dash_length, 0.2     # length of each dash segment
set dash_width,  2.5     # line thickness (default 2.0)
set dash_radius, 0.05    # cylinder radius for 3D dash lines

# ── Label style ───────────────────────────────────
set label_size,     14   # font size in points
set label_color, black   # label text color
set label_font_id,   7   # font style (7=sans-serif bold)
set label_position, [0, 0, 1.5]  # offset from midpoint

# ── Selective display ─────────────────────────────
show labels,  hbonds     # show labels for H-bond distances
hide labels,  contacts   # hide labels — keep lines only
hide dashes,  contacts   # hide lines but keep labels

# ── Color ─────────────────────────────────────────
color yellow, hbonds     # H-bonds: yellow (standard)
color cyan,   key_dist   # key distances: cyan
color gray60, contacts   # background contacts: gray