In the rgl package *rgl.postscript *can save 3d scatter plots you have
generated using the plot3d command .

For example
open3d()
  x <- sort(rnorm(1000))
  y <- rnorm(1000)
  z <- rnorm(1000) + atan2(x,y)
  plot3d(x, y, z, col=rainbow(1000))

rgl.postscript("persp3dd.pdf","pdf")

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