Root Mean Square Deviation

Calculate the RMSD between coordinate sets.

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.

Details

RMSD is a standard measure of structural distance between coordinate sets.

Structure a[a.inds] and b[b.inds] should have the same length.

A least-squares fit is performed prior to RMSD calculation by setting fit=TRUE. See the function fit.xyz for more details of the fitting process.

Value

Returns a numeric vector of RMSD value(s).

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

Author

Barry Grant

See also

fit.xyz, rot.lsq, read.pdb, read.fasta.pdb

Examples

# \donttest{
# 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: No indices provided, using the 293 non NA positions
#>       1bg2  1i6i  1i5s  2ncd
#> 1bg2 0.000 2.654 2.412 2.775
#> 1i6i 2.654 0.000 2.202 3.063
#> 1i5s 2.412 2.202 0.000 2.904
#> 2ncd 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)
#>  1i6i  1i5s 
#> 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)
#>  1bg2  1i6i  1i5s  2ncd 
#> 0.000 2.654 2.412 2.775 

# RMSD without superposition
rmsd(pdbs$xyz)
#> Warning: No indices provided, using the 293 non NA positions
#>        1bg2   1i6i   1i5s   2ncd
#> 1bg2  0.000 48.901 48.533 63.343
#> 1i6i 48.901  0.000 58.171 53.186
#> 1i5s 48.533 58.171  0.000 88.198
#> 2ncd 63.343 53.186 88.198  0.000

# }