Plot RMSIP Results
Produces a heat plot of RMSIP (Root mean square inner product) for the visualization of modes similarity.
## S3 method for class 'rmsip'
plot(x, xlab = NULL, ylab = NULL, col = gray(50:0/50),
zlim=c(0,1), ...)x |
an object of class |
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 |
plot.rmsip produces a color image with the function
image.
Called for its effect.
Lars Skjaerven
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
## 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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.