Error in cmdscale(dist(cent), k = k) : NA values not allowed in 'd'

[B Albert]

Hello:

I am trying to follow tutorial http://thegrantlab.org/bio3d/tutorials/protein-structure-networks

here is my command line:

pdb <- read.pdb("apo-out.pdb")
modes <- nma(pdb)
cij <- dccm(modes)
net <- cna(cij, cutoff.cij=0.3)
print(net)



Call:
  cna.dccm(cij = cij, cutoff.cij = 0.3)

Structure: 
 - NETWORK NODES#:   323    EDGES#: 1453 
 - COMMUNITY NODES#: 10     EDGES#: 16 

 + attr: network, communities, community.network,
        community.cij, cij, call

attributes(x)
x$members[5]

par(mfcol = c(1, 2), mar = c(0, 0, 0, 0))
plot(net, pdb, full = TRUE, vertex.label.cex=0.7)

the above plot failed with erros:

Obtaining layout from PDB structure
Error in cmdscale(dist(cent), k = k) : NA values not allowed in 'd'

view.cna(net, pdb, launch = TRUE)

The view step also failed, with following information

Error in vec2resno(vec = x$communities$membership, resno = pdb$atom[,  : 
  Length miss-match of 'vec' and concetive 'resno'

[Xinqiu Yao]

Hi,

Can you show the content of the pdb object (Simply copy&paste the output of print(pdb))? Also, what version bio3d did you use? (The output of sessionInfo() would be helpful).

[B Albert]

Hello:

I updated to the latest version, and it is ok now.

Thanks a lot

[Barry Grant]

Tutorial step is for more recent version of BIo3D - perhaps we should begin online tutorials with a check for package version?