plot.nma {bio3d} | R Documentation |
Plot NMA Results
Description
Produces eigenvalue/frequency spectrum plots and an atomic fluctuations plot.
Usage
## S3 method for class '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
|
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 |
Details
plot.nma
produces an eigenvalue (or frequency) spectrum plot
together with a plot of the atomic fluctuations.
Value
Called for its effect.
Author(s)
Lars Skjaerven
References
Skjaerven, L. et al. (2014) BMC Bioinformatics 15, 399. Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
See Also
Examples
## Fetch structure
pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") )
## Calculate modes
modes <- nma(pdb)
plot(modes, sse=pdb)