vmd.cna

[Former user]

Hello, I am doing cna anlysis for my protein. To view the results I have used

vmd.cna(net_cutoff0.5) the ouput of which when loaded into vmd gives the following message floating point value is Not a Number. The plot in vmd shows two edges connecting a pair of communities, instead of only one.

When i look into network.vmd file , it has following written, draw sphere {NaN NaN NaN} radius 14.2 resolution 25.

Can you please help me find my mistake. Thank you

[Xinqiu Yao]

Can you provide example data for us to reproduce the error? That will be helpful.

[Gauri Thapa]

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[Gauri Thapa]

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[Gauri Thapa]

‌

pdb<-read.pdb("no_water.pdb")
inds<-atom.select(pdb, elety="CA")
cij<-read.table("lmi.txt")
cij<-data.matrix(cij)

net_cutoff0.7<-cna(cij, cutoff.cij=0.7)
vmd.cna(net_cutoff0.7, pdb)

Above are the commands that I had used. (Sorry I previously told cutoff=0.5 instead of 0.7)

Thanks so much for your help.

‌

[Xinqiu Yao]

Hi,

‌

Using your example, I couldn’t reproduce the error you reported but ran into another problem. After checking the PDB, I noticed that there are multiple residues that have the same chain ID and residue number simultaneously, which is not allowed by the standard PDB format. Note that bio3d may not appreciate non-standard PDB format.

‌

I recommend fixing the labeling issue first (e.g., changing some chain IDs to a different one from those sharing the same residue numbers). Then, using clean.pdb() to renumber residues and remove ligands (both are required to successfully run vmd.cna()):

pdb ← clean.pdb(pdb, force.renumber=TRUE, rm.lig=TRUE)

‌

Hope it helps.

[Gauri Thapa]

Hi,

The above command did help.

Can you please explain what does it mean to have two edges connecting a pair of nodes.

Thanks a lot.