open vmd

[Former user]

I am trying to visualize my results with VMD. When I type the following command

vmd.cna(net, pdb, lauch=FALSE)

I get the following error.

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

I've noticed that the n-terminus of my PDB file is #161 and the output from other utilities within Bio3d always renumbers the output to start at residue #1. Is this related to above problem?

[Xinqiu Yao]

Renumbering shouldn't be a problem, as long as the number of residues in the pdb matches the number of nodes in the network. Is the pdb has "insert" residues (which sometimes is the source of problems)? Could you try vmd.cna(net, clean.pdb(pdb), launch=FALSE) and see if it solves the problem? clean.pdb() checks and automatically removes "insert" by renumbering residues.

[jhold]

Thank you for the suggestion. I tried adding clean.pdb(pdb) and I still get the following error

vmd.cna(net, clean.pdb(pdb), launch=FALSE) Error in vec2resno(1:length(unique(res)), res) : Length miss-match of 'vec' and concetive 'resno'

[Xinqiu Yao]

Can you copy&paste the output of clean.pdb(pdb)$log?

Also, make sure pdb and net match each other. You can check it by simply typing pdb or net and return. It will tell how many residues/nodes in each object, which should be the same.

You can also attach example 'pdb' and 'net' objects here and so we can better look into the problems.

[jhold]

Hi Xin-Qiu, Sorry for the delay in response.

There appears to be a mismatch between # of network nodes (233) and # of C-alpha (232)

Below is output of log file:

clean.pdb(pdb)$log Error in vec2resno(1:length(unique(res)), res) : Length miss-match of 'vec' and concetive 'resin'

Any suggestions?

[Barry Grant]

provide your files and we can perhaps investigate further. Most likely to be an input PDB format problem leading to mismatch.

[Xinqiu Yao]

Could you provide an example pdb file here (by editing your original post and attache the file) that I can reproduce the error?

[jhold]

by removing waters from the PDB file I was able to correct the error

[Gauri Thapa]

I am also getting the same error even when the vec and resno have same numbers

pdb

Call: read.pdb(file = "../b_no_water.pdb")

Total Models#: 1
Total Atoms#: 632, XYZs#: 1896 Chains#: 2 (values: C K)

 Protein Atoms#: 630  (residues/Calpha atoms#: 157)
 Nucleic acid Atoms#: 0  (residues/phosphate atoms#: 0)

 Non-protein/nucleic Atoms#: 2  (residues: 2)
 Non-protein/nucleic resid values: [ CAL (2) ]

Protein sequence:
DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNG
TIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEV
DEMIREADIDGDGQVNYEEFVQMMTAAWASLKRLVTR

• attr: atom, xyz, calpha, call

with selection made of only C-alpha atoms using

inds<-atom.select(pdb, elety="CA")

net_cutoff0.6

Call:
cna.dccm(cij = cij, cutoff.cij = 0.6)

Structure:

• NETWORK NODES#: 157 EDGES#: 962

• COMMUNITY NODES#: 9 EDGES#: 11

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

Can you please help me where I am going wrong ?

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