compas (version 0.1.1)

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

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

Value

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

Details

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

Examples

# NOT RUN {
pdbrmsd(nat879, pred879, start=10, end=20, 'all', optimal=TRUE)

# }