Error in cij.network[cij.network > 0]

[Former user]

I'm trying to compute a network for as shown below, but I get an error.

pdb = GetStructure("4beh")
pdb = trim.pdb(pdb, inds = atom.select(pdb, chain = "A"))
pdb = clean.pdb(pdb, force.renumber = TRUE, rm.lig = TRUE, fix.aa = TRUE, rm.wat = TRUE)
modes = nma(pdb)
cij = dccm(modes, ncore=1)
network = cna(cij, cutoff.cij = 0.3, cm = cm)

The error message:

Error in cij.network[cij.network > 0] <- exp(-cij.network[cij.network >  : 
  NAs are not allowed in subscripted assignments

Any guidance on what the problem is? Thanks.

[Xinqiu Yao]

Hi,

It seems you have an unusual structure with a very long loop. This might cause a problem in the NMA calculations. If you really want to do correlation network analysis for a super-flexible system (which is not recommended), you could run MD and calculate correlations directly from the trajectory.

Just a quick test, modes=nma(pdb, ff="anm", cutoff=60) will work. But it uses a very large distance cutoff (60 angstrom), which physically doesn't make sense. However, it tells us that the problem is because of the flexible loop (which most likely causes a disconnected network using regular cutoffs).

Hope it helps.

[Xinqiu Yao]

Not a bug.