| pdbrmsd {compas} | R Documentation |
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 |
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)