bio3d (version 2.2-4)

rmsf: Atomic RMS Fluctuations

Description

Calculate atomic root mean squared fluctuations.

Usage

rmsf(xyz, average=FALSE)

Arguments

xyz

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

average

logical, if TRUE averaged over atoms.

Value

Returns a numeric vector of RMSF values.

Details

An often used measure of conformational variance.

References

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

See Also

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

Examples

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)