Plot NMA Results

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

# 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.

Details

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

Value

Called for its effect.

References

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

Author

Lars Skjaerven

Examples

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

## Calculate modes
modes <- nma(pdb)
#>  Building Hessian...		Done in 0.011 seconds.
#>  Diagonalizing Hessian...	Done in 0.08 seconds.

plot(modes, sse=pdb)