problem of network analysis

Hello:

I am following tutorial:

http://thegrantlab.org/bio3d/tutorials/protein-structure-networks

Here is my steps;

> library(bio3d)
> library(igraph)
> pdb <- read.pdb("md-ab-extraceullar.pdb")
  PDB has multiple END/ENDMDL records 
  multi=FALSE: taking first record only 
> modes <- nma(pdb)
 Building Hessian...        Done in 0.317 seconds.
 Diagonalizing Hessian...   Done in 3.849 seconds.
Warning message:
In nma.pdb(pdb) :
  Possible multi-chain structure or missing in-structure residue(s) present
  Fluctuations at neighboring positions may be affected.
> cij <- dccm(modes)
  |===============================================================| 100%
> net <- cna(cij, cutoff.cij=0.3)
> print(net)
> x <- summary(net)
> attributes(x)
$names
[1] "id"      "size"    "members" "tbl" 
> x$members[5]
> par(mfcol = c(1, 2), mar = c(0, 0, 0, 0))
> plot(net, pdb, full = TRUE, vertex.label.cex=0.7)
Obtaining layout from PDB structure
Error in cmdscale(dist(cent), k = k) : NA values not allowed in 'd'

In the last step, I don't why why it failed.....Does anybody has any idea?

thx a lot

Comments (3)