bio3d (version 2.3-4)

plot.rmsip: Plot RMSIP Results

Description

Produces a heat plot of RMSIP (Root mean square inner product) for the visualization of modes similarity.

Usage

# S3 method for rmsip
plot(x, xlab = NULL, ylab = NULL, col = gray(50:0/50),
      zlim=c(0,1), …)

Arguments

x

an object of class rmsip.

xlab

a label for the x axis, defaults to ‘a’.

ylab

a label for the y axis, defaults to ‘b’.

col

a vector of colors for the RMSIP map (or overlap values).

zlim

the minimum and maximum ‘z’ values for which colors should be plotted.

…

additional arguments to function image.

Value

Called for its effect.

Details

plot.rmsip produces a color image with the function image.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

See Also

rmsip, overlap, nma, image.

Examples

# NOT RUN {
## Read PDB structure
pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") )

## Perform NMA
modes.a <- nma(pdb, ff="calpha")
modes.b <- nma(pdb, ff="anm")

## Calculate and plot RMSIP
r <- rmsip(modes.a, modes.b)
plot(r)
# }