network plot

Hi,

I have a protein with two domains, so i successfully performed the cna(). But the network plot i got looks skewed.

Basically i cant use interactive=TRUE in the plot command and am not able to highlight the domains which are important

for my study. Are there any ways to represent the network in a better way, the same as your papers show.

I have attached the network plot.

i have used following commands.

ca.inds <- atom.select(pdb, "calpha")
trj <- read.ncdf("tmp.nc", at.sel=ca.inds,first=300, last=500, stride=2)
cm <-cmap.xyz(trj,dcut=10,pcut=0.75, grpby = pdb$atom[ca.inds$atom,'resno'])
xyz <- fit.xyz(fixed=pdb$xyz,mobile=dcd, fixed.inds=ca.inds$xyz,mobile.inds=ca.inds$xyz)
cij<-dccm(xyz[,ca.inds$xyz],cutoff.cij=0.35)
net <- cna(cij,cm=cm)
plot(net,pdb)

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