How to compute RMSD and RMSF#

Goal#

Measure structural deviation across frames (RMSD) or per-atom positional fluctuation over a trajectory (RMSF).

Minimal example#

from moleculekit.molecule import Molecule
from moleculekit.util import molRMSD

mol = Molecule("3PTB")
ref = mol.copy()

# Select Cα indices for both molecule and reference
ca_idx = mol.atomselect("protein and name CA", indexes=True)

# RMSD of all frames against the reference (returns one value per frame)
rmsd = molRMSD(mol, ref, ca_idx, ca_idx)
print(rmsd)

Parameters that matter#

Parameter

Type

What it does

mol

Molecule

Trajectory to analyse

refmol

Molecule

Reference structure

rmsdsel1

integer np.ndarray

Atom indices in mol

rmsdsel2

integer np.ndarray

Matching atom indices in refmol

Common variations#

# RMSF per Cα atom over a trajectory
from moleculekit.projections.metricfluctuation import MetricFluctuation

rmsf = MetricFluctuation("protein and name CA").project(mol)
# rmsf shape: (n_frames, n_CA); for a single per-atom value over the trajectory use rmsf.mean(axis=0)

# Align before computing RMSD to separate rotation from internal motion
mol.align("protein and name CA", refmol=ref)
rmsd_aligned = molRMSD(mol, ref, ca_idx, ca_idx)

Gotchas#

  • molRMSD() computes raw (non-mass-weighted) RMSD; align the structures first if you want to remove rigid-body motion.

  • RMSF is per-atom and depends on the choice of reference (mean structure); the result is sensitive to conformational heterogeneity.

  • Both mol and refmol must have the same number of selected atoms.

  • MetricFluctuation returns an (n_frames, n_atoms) array — use rmsf.mean(axis=0) to get a per-atom fluctuation averaged over all frames.

See also#