plot.nma.Rd
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),...)
x  the results of normal modes analysis obtained with


pch  a vector of plotting characters or symbols: see 
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.nma
produces an eigenvalue (or frequency) spectrum plot
together with a plot of the atomic fluctuations.
Called for its effect.
Skjaerven, L. et al. (2014) BMC Bioinformatics 15, 399. Grant, B.J. et al. (2006) Bioinformatics 22, 26952696.
Lars Skjaerven
## 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.