Least RMSD align#

Aligning structures with different topologies via sequence alignment and least-RMSD fitting.

The function molsysmt.structure.least_rmsd_align() superposes two macromolecular systems that may have different sequence lengths, point mutations, or topologies. It first conducts a sequence alignment to identify matching equivalent residues, and then executes a Kabsch least-RMSD spatial fit over the mapped atom pairs.

Added in version 1.0.0.

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects of this function: molsysmt.structure.least_rmsd_align().

Basic usage#

Let’s show how to align two mutant variants of T4 lysozyme with different sequence lengths (PDB IDs: 181L with 162 residues and 1L17 with 164 residues):

import molsysmt as msm

molsys_1 = msm.convert('181l', selection='molecule_type=="protein"')
molsys_2 = msm.convert('1l17', selection='molecule_type=="protein"')

We inspect the sequences of both protein systems to observe the length discrepancy:

seq_1 = msm.convert(molsys_1, to_form='string:amino_acids_1')
seq_2 = msm.convert(molsys_2, to_form='string:amino_acids_1')
print(f'System 1 (181L) length: {len(seq_1)} residues')
print(f'System 2 (1L17) length: {len(seq_2)} residues')

System 1 (181L) length: 162 residues
System 2 (1L17) length: 164 residues

Sequence-guided structural superposition#

We superpose molsys_2 onto molsys_1 using molsysmt.structure.least_rmsd_align():

molsys_2_aligned = msm.structure.least_rmsd_align(molsys_2, reference_molecular_system=molsys_1)

print('Original center of system 2:', msm.structure.get_center(molsys_2))
print('Aligned center of system 2: ', msm.structure.get_center(molsys_2_aligned))
print('Reference center (system 1):', msm.structure.get_center(molsys_1))

Original center of system 2: [[[3.5281599388379186 1.1290532874617745 0.946882262996938]]] nanometer

Aligned center of system 2:  [[[3.5028394190107877 1.127098545600861 0.9431480632093274]]] nanometer

Reference center (system 1): [[[3.4858737781225804 1.1384903801396447 0.9543625290923174]]] nanometer