Plot RMSIP Results

Usage

"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.

Description

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

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.

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 0.05 seconds.
 Diagonalizing Hessian...	Done in 0.135 seconds.



modes.b <- nma(pdb, ff="anm")



 Building Hessian...		Done in 0.045 seconds.
 Diagonalizing Hessian...	Done in 0.136 seconds.




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

See also

rmsip, overlap, nma, image.

Author

Lars Skjaerven