bio3d: plot.nma – R documentation

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plot.nma

Plot NMA Results

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

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

`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.

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

Called for its effect.

Lars Skjaerven

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

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

## Calculate modes
modes <- nma(pdb)

plot(modes, sse=pdb)

Biological Structure Analysis

v2.4-2

GPL (>= 2)

Authors

Barry Grant [aut, cre], Xin-Qiu Yao [aut], Lars Skjaerven [aut], Julien Ide [aut]

Initial release