bio3d (version 2.1-2)

plot.nma: Plot NMA Results

Description

Produces eigenvalue/frequency spectrum plots and an atomic fluctuations plot.

Usage

## S3 method for class 'nma':
plot(x, pch = 16, col = par("col"), cex=0.8, mar=c(6, 4, 2, 2),...)

Arguments

x

the results of normal modes analysis obtained with nma.

pch

a vector of plotting characters or symbols: see points.

col

a character vector of plotting colors.

cex

a numerical single element vector giving the amount by which plotting text and symbols should be magnified relative to the default.

mar

A numerical vector of the form c(bottom, left, top, right) which gives the number of lines of margin to be specified on the four sides of the plot.

...

extra plotting arguments passed to plot.bio3d that effect the atomic fluctuations plot only.

Value

• Called for its effect.

Details

plot.nma produces an eigenvalue (or frequency) spectrum plot together with a plot of the atomic fluctuations.

References

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

See Also

nma, plot.bio3d

Examples

## Fetch structure
pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") )

## Calculate modes
modes <- nma(pdb)

plot(modes, sse=pdb)