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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),...)
the results of normal modes analysis obtained with nma.
nma
a vector of plotting characters or symbols: see points.
points
a character vector of plotting colors.
a numerical single element vector giving the amount by which plotting text and symbols should be magnified relative to the default.
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.bio3d
Called for its effect.
plot.nma produces an eigenvalue (or frequency) spectrum plot together with a plot of the atomic fluctuations.
plot.nma
Skjaerven, L. et al. (2014) BMC Bioinformatics 15, 399. Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
nma, plot.bio3d
# NOT RUN { ## Fetch structure pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") ) ## Calculate modes modes <- nma(pdb) plot(modes, sse=pdb) # }
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