open vmd
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$atom[, : Length miss-match of 'vec' and concetive 'resin'
I've noticed that the n-terminus of my PDB file is #161 and the output from other utilities within Bio3d always renumbers the output to start at residue #1. Is this related to above problem?
Comments (10)
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Thank you for the suggestion. I tried adding clean.pdb(pdb) and I still get the following error
vmd.cna(net, clean.pdb(pdb), launch=FALSE) Error in vec2resno(1:length(unique(res)), res) : Length miss-match of 'vec' and concetive 'resno'
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Can you copy&paste the output of
clean.pdb(pdb)$log
?Also, make sure pdb and net match each other. You can check it by simply typing
pdb
ornet
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.
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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?
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provide your files and we can perhaps investigate further. Most likely to be an input PDB format problem leading to mismatch.
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- marked as minor
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Could you provide an example pdb file here (by editing your original post and attache the file) that I can reproduce the error?
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by removing waters from the PDB file I was able to correct the error
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- changed status to resolved
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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
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COMMUNITY NODES#: 9 EDGES#: 11
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attr: network, communities, community.network,
community.cij, cij, call
Can you please help me where I am going wrong ?
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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.