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

[Former user]

Hello, I get the error Error in cmdscale(dist(cent), k = k) : NA values not allowed in 'd' here is my command line

> inds <-atom.select(pdb, elety = "CA")
> trj <-fit.xyz(fixed = pdb$xyz, mobile = dcd, fixed.inds = inds$xyz, mobile.inds = inds$xyz)

> 
> cij <- dccm(trj,ncore=6)
> net <- cna(cij, cutoff.cij=0.3)
Warning messages:
1: In (function (graph, weights = E(graph)$weight, directed = TRUE,  :
  At community.c:460 :Membership vector will be selected based on the lowest modularity score.
2: In (function (graph, weights = E(graph)$weight, directed = TRUE,  :
  At community.c:467 :Modularity calculation with weighted edge betweenness community detection might not make sense -- modularity treats edge weights as similarities while edge betwenness treats them as distances
 > plot(net, pdb)
Obtaining layout from PDB structure
Error in cmdscale(dist(cent), k = k) : NA values not allowed in 'd'

I get this only when i try to use the Backbone or Main chain of a protein (Ca seem to work fine)

Thank you in advance

[Xinqiu Yao]

Hi,

Currently cna() only supports C-alpha based network analysis. One way to temporarily make it work is changing all backbone or main chain atom names in the pdb to 'CA'. For example,

inds2 <- atom.select(pdb, 'backbone')
pdb2 <- pdb
pdb2$atom$elety[inds2$atom] <- 'CA'
plot(net, pdb2)

Let me know if it works.

[Xinqiu Yao]

Not a bug.

[nastaziales]

Thank you very much, so the problem is the name of the atom and not the residue number that is repeating or should i change them both ?

[Xinqiu Yao]

It should be okay without changing residue numbers. Let me know if it doesn't work.