bio3d (version 2.3-3)

rmsf: Atomic RMS Fluctuations

Description

Calculate atomic root mean squared fluctuations.

Usage

rmsf(xyz, grpby=NULL, average=FALSE)

Arguments

xyz

numeric matrix of coordinates with each row corresponding to an individual conformer.

grpby

a vector counting connective duplicated elements that indicate the elements of 'xyz' that should be considered as a group (e.g. atoms from a particular residue). If provided a 'pdb' object, grouping is automatically set by amino acid residues.

average

logical, if TRUE averaged over atoms.

Value

Returns a numeric vector of RMSF values. If average=TRUE a single numeric value representing the averaged RMSF value over all atoms will be returned.

Details

RMSF is an often used measure of conformational variance. It is calculated by $$f_i=\sqrt{\frac{1}{M-1}\sum_j \|r_i^j-r_i^0\|^2}$$, where \(f_i\) is the RMSF value for the ith atom, M the total number of frames (total number of rows of xyz), \(r_i^j\) the positional vector of the ith atom in the jth frame, and \(r_i^0\) the mean position of ith atom. ||r|| denotes the Euclidean norm of the vector r.

References

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

See Also

read.dcd, fit.xyz, read.fasta.pdb

Examples

# NOT RUN {
attach(transducin)

# Ignore Gaps
gaps <- gap.inspect(pdbs$ali)

r <- rmsf(pdbs$xyz)
plot(r[gaps$f.inds], typ="h", ylab="RMSF (A)")

detach(transducin)

# }
# NOT RUN {
pdb <- read.pdb("1d1d", multi=TRUE)
xyz <- pdb$xyz

# superimpose trajectory
xyz <- fit.xyz(xyz[1, ], xyz)

# select mainchain atoms
sele <- atom.select(pdb, elety=c("CA", "C", "N", "O"))

# residue numbers to group by
resno <- pdb$atom$resno[sele$atom]

# mean rmsf value of mainchain atoms of each residue
r <- rmsf(xyz[, sele$xyz], grpby=resno)
plot.bio3d(r, resno=pdb, sse=pdb, ylab="RMSF (A)")

# }
# NOT RUN {
# }