Plot NMA Results
Usage
"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.bio3dthat effect the atomic fluctuations plot only.
Description
Produces eigenvalue/frequency spectrum plots and an atomic fluctuations plot.
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.
Examples
## Fetch structure pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") ) ## Calculate modes modes <- nma(pdb)Building Hessian... Done in 0.049 seconds. Diagonalizing Hessian... Done in 0.133 seconds.plot(modes, sse=pdb)
