vmd.cna error
I am trying to visualize my results with VMD. When I type the following command
vmd.cna(net_cutoff0.6, pdb, )
I get the following error.
Error in vec2resno(vec = x$communities$membership, resno = pdb$atom[, : Length miss-match of 'vec' and concetive 'resin'
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
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
Comments (14)
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reporter Hi,
Thank you so much.
I tried both the command and still getting the error. I even renumbered the repeating residue number so that the residue number is not repeated and tried using vmd.cna but still getting the same error.
Thanking you
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Can you provide a short example that can reproduce the problem? Then, I can take a look.
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reporter - attached lmi.txt
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reporter - attached b_no_water.pdb
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reporter The commands that I used are
pdb<-read.pdb(“b_no_water.pdb”)
inds<-atom.select(pdb, elety=”CA”)
cij<-read.table(“lmi.txt”)
cij<-data.matrix(cij)
net_cutoff0.5<-cna(cij, cutoff.cij=0.5)
vmd.cna(net_cutoff0.5, pdb)
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reporter And after your suggestions ,
vmd.cna(net_cutoff0.5, clean.pdb(pdb, force.renumber=TRUE))
I also changed the residue numbers in the pdb file as given in b_resno_new.pdb and redid the calculation ,again getting the same error.
Thank you so much for your help.
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reporter - attached b_resno_new.pdb
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reporter The residues were repeated in the segname KC in the pdb file which I have changed in b_resno_new.pdb.
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The pdb has non-protein atoms that should be cleaned out before calling
vmd.cna()
. Tryvmd.cna(net_cutoff0.5, clean.pdb(pdb, force.renumber=TRUE, rm.lig=TRUE))
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reporter Hi,
Thank you so much for all your help. Now it is working.
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Hi Xinqiu Yao,
vmd.can() does not recognize non-standard amino acid. e.g. vmd.can() does not recognize phosphorylated aspartic (PHD) acid residue. After I replaced PHD with ASP in PDB file (just change residue name), vmd.can() can works well. I hope that my feedback can help me to improve your software.
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Thanks for the feedback! Will put it on the to-do list for the next release shortly.
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- changed component to ToDo
Add features in
vmd.cna()
to recognize non-standard amino acid residues. - Log in to comment
Hi,
It might be because the residue number is repeated in the two chains. Renumber residues using
clean.pdb(pdb, force.renumber=TRUE)
orconvert.pdb(pdb, renumber=TRUE)
and try again.