rmsf {bio3d}R Documentation

Atomic RMS Fluctuations

Description

Calculate atomic root mean squared fluctuations.

Usage

rmsf(xyz)

Arguments

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

Details

An often used measure of conformational variance.

Value

Returns a numeric vector of RMSF values.

Author(s)

Barry Grant

References

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

See Also

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

Examples

data(kinesin)
attach(kinesin)

r <- rmsf(xyz)
plot( r[aln$ali["d1bg2__",]!="-"], typ="h", ylab="RMSF (A)")

[Package bio3d version 1.0-6 Index]