bio3d (version 2.3-3)

plot.nma: Plot NMA Results

Description

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

Usage

# S3 method for 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

Skjaerven, L. et al. (2014) BMC Bioinformatics 15, 399. Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

See Also

nma, plot.bio3d

Examples

# NOT RUN {
## Fetch structure
pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") )

## Calculate modes
modes <- nma(pdb)

plot(modes, sse=pdb)

# }