Nothing
"plot.nma" <-
function(x, pch = 16, col = par("col"), cex = 0.8,
mar = c(6, 4, 2, 2), ...) {
opar <- par(no.readonly = TRUE)
on.exit(par(opar))
par(cex = cex, mar = mar)
layout(matrix(c(1,2,3,3), 2, 2, byrow = TRUE))
if(!is.null(x$frequencies)) {
freqs <- x$frequencies
main <- "Frequencies"
}
else {
freqs <- x$force.constants
main <- "Force constants"
}
if(length(freqs)>=100)
n <- 100
else
n <- length(freqs)
plot(x$L[1:n], type = "h", pch = pch, xlab = "Mode index",
ylab = "", main = "Eigenvalues", col = col)
plot(freqs[1:n], type = "h", pch = pch, xlab = "Mode index",
ylab = "", main = main, col = col)
plot.bio3d(x$fluctuations, pch = pch, xlab = "Residue index",
ylab = "", main = "Fluctuations", col = col, ...)
}
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