Root Mean Square Deviation

Usage

rmsd(a, b=NULL, a.inds=NULL, b.inds=NULL, fit=FALSE, ncore=1, nseg.scale=1)

Arguments

a

a numeric vector containing the reference coordinate set for comparison with the coordinates in b. Alternatively, if b=NULL then a can be a matrix or list object containing multiple coordinates for pairwise comparison.

b

a numeric vector, matrix or list object with an xyz component, containing one or more coordinate sets to be compared with a.

a.inds

a vector of indices that selects the elements of a upon which the calculation should be based.

b.inds

a vector of indices that selects the elements of b upon which the calculation should be based.

fit

logical, if TRUE coordinate superposition is performed prior to RMSD calculation.

ncore

number of CPU cores used to do the calculation. ncore>1 requires package ‘parallel’ installed.

nseg.scale

split input data into specified number of segments prior to running multiple core calculation. See fit.xyz.

Examples

# Redundant testing excluded

# -- Calculate RMSD between two or more structures
aln <- read.fasta(system.file("examples/kif1a.fa",package="bio3d"))
pdbs <- read.fasta.pdb(aln)

pdb/seq: 1   name: http://www.rcsb.org/pdb/files/1bg2.pdb 
pdb/seq: 2   name: http://www.rcsb.org/pdb/files/1i6i.pdb 
   PDB has ALT records, taking A only, rm.alt=TRUE
pdb/seq: 3   name: http://www.rcsb.org/pdb/files/1i5s.pdb 
   PDB has ALT records, taking A only, rm.alt=TRUE
pdb/seq: 4   name: http://www.rcsb.org/pdb/files/2ncd.pdb 


# Gap positions
inds <- gap.inspect(pdbs$xyz)

# Superposition before pairwise RMSD 
rmsd(pdbs$xyz, fit=TRUE)

Warning message:
No indices provided, using the 293 non NA positions

      [,1]  [,2]  [,3]  [,4]
[1,] 0.000 2.654 2.412 2.775
[2,] 2.654 0.000 2.202 3.063
[3,] 2.412 2.202 0.000 2.904
[4,] 2.775 3.063 2.904 0.000


# RMSD between structure 1 and structures 2 and 3
rmsd(a=pdbs$xyz[1,], b=pdbs$xyz[2:3,], a.inds=inds$f.inds, b.inds=inds$f.inds, fit=TRUE)

http://www.rcsb.org/pdb/files/1i6i.pdb http://www.rcsb.org/pdb/files/1i5s.pdb 
                                 2.654                                  2.412 


# RMSD between structure 1 and all structures in alignment
rmsd(a=pdbs$xyz[1,], b=pdbs, a.inds=inds$f.inds, b.inds=inds$f.inds, fit=TRUE)

http://www.rcsb.org/pdb/files/1bg2.pdb http://www.rcsb.org/pdb/files/1i6i.pdb 
                                 0.000                                  2.654 
http://www.rcsb.org/pdb/files/1i5s.pdb http://www.rcsb.org/pdb/files/2ncd.pdb 
                                 2.412                                  2.775 


# RMSD without superposition
rmsd(pdbs$xyz)

Warning message:
No indices provided, using the 293 non NA positions

       [,1]   [,2]   [,3]   [,4]
[1,]  0.000 48.901 48.533 63.343
[2,] 48.901  0.000 58.171 53.186
[3,] 48.533 58.171  0.000 88.198
[4,] 63.343 53.186 88.198  0.000

See also

Author