pdbrmsd: Root Mean Squared Deviation (RMSD) of Two Protein...

In compas: Conformational Manipulations of Protein Atomic Structures

Description

RMSD calculation between the atoms of two PDB objects.

Usage

pdbrmsd(pdb1, pdb2, start, end, type='all', optimal=FALSE)

Arguments

pdb1	PDB object containing reference coordinates of atoms in protein conformation.
pdb2	PDB object containing coordinates of atoms in protein conformation to compare with pdb1.
start	The starting residue position for the RMSD calculation. If not supplied, defaults to first residue of chain.
end	The ending residue position for the RMSD calculation. If not supplied, defaults to final residue of chain.
type	Specifies atoms to be included in the calculation. Can be 'all', 'CA' (CA atoms only), or 'backbone' (CA, N, C, O).
optimal	Apply optimal rotation and superposition? As described in https://cnx.org/contents/HV-RsdwL@23/Molecular-Distance-Measures

Details

Similar to rmsd, but with implementation in C++.

Value

Returns a list with calculated RMSD value and the optimal rotation matrix.

Examples

pdbrmsd(nat879, pred879, start=10, end=20, 'all', optimal=TRUE)

compas documentation built on Jan. 9, 2022, 1:06 a.m.