Plot RMSIP Results

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

# 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.

Details

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

Value

Called for its effect.

References

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

Author

Lars Skjaerven

See also

rmsip, overlap, nma, image.

Examples

## Read PDB structure
pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") )

## Perform NMA
modes.a <- nma(pdb, ff="calpha")
#>  Building Hessian...		Done in 0.012 seconds.
#>  Diagonalizing Hessian...	Done in 0.079 seconds.
modes.b <- nma(pdb, ff="anm")
#>  Building Hessian...		Done in 0.01 seconds.
#>  Diagonalizing Hessian...	Done in 0.076 seconds.

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