bio3d (version 2.4-4)

plot.enma: Plot eNMA Results

Description

Produces a plot of atomic fluctuations of aligned normal modes.

Usage

# S3 method for enma
plot(x,
        pdbs = NULL,
        xlab = NULL,
        ylab="Fluctuations", ...)

Value

Called for its effect.

Arguments

x

the results of ensemble NMA obtained with nma.pdbs. Alternatively, a matrix in the similar format as enma$fluctuations can be provided.

pdbs

an object of class ‘pdbs’ in which the ‘enma’ object x was obtained from. If provided SSE data of the first structure of pdbs will drawn.

xlab

a label for the x axis.

ylab

labels for the y axes.

...

extra plotting arguments passed to plot.fluct that effect the atomic fluctuations plot only.

Author

Lars Skjaerven, Barry Grant

Details

plot.enma produces a fluctuation plot of aligned nma objects. If corresponding pdbs object is provided the plot contains SSE annotation and appropriate resiude index numbering.

References

Skjaerven, L. et al. (2014) BMC Bioinformatics 15, 399. Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

See Also

nma, plotb3, plot.fluct

Examples

if (FALSE) {
ids <- c("1a70_A", "1czp_A", "1frd_A", "1fxi_A", "1iue_A", "1pfd_A")
raw.files <- get.pdb(ids, path = "raw_pdbs")
files <- pdbsplit(raw.files, ids, path = "raw_pdbs/split_chain")

## Sequence/structure alignement
pdbs <- pdbaln(files)

## Normal mode analysis on aligned data
modes <- nma(pdbs)

## Plot fluctuations
plot(modes, pdbs=pdbs)

## Group and spread fluctuation profiles
hc <- hclust(as.dist(1-modes$rmsip))
col <- cutree(hc, k=2)
plot(modes, pdbs=pdbs, col=col, spread=TRUE)
}