1. Bio3D Project Avatar Bio3D Project
  2. Bio3D
  3. bio3d
  4. Issues

Missing view.cna module

Issue #429 resolved
Mamta Mohan created an issue

Hello,

I am taking tutorial for Network generation. http://thegrantlab.org/bio3d/tutorials/protein-structure-networks

module view.cna seems to be missing.

view.cna(net, pdb, launch = TRUE) Error: could not find function "view.cna"

I would appreciate your response.

Listed below is the list of bio3d ver 2.3.1 library.

lbio3d() [1] "aa123" "aa2index"
[3] "aa2mass" "aa321"
[5] "aa.index" "aanma"
[7] "aanma.pdb" "aanma.pdbs"
[9] "aa.table" "aln2html"
[11] "amsm.xyz" "angle.xyz"
[13] "as.fasta" "as.pdb"
[15] "as.pdb.default" "as.pdb.mol2"
[17] "as.pdb.prmtop" "as.select"
[19] "as.xyz" "atom2ele"
[21] "atom2ele.default" "atom2ele.pdb"
[23] "atom2mass" "atom2mass.default"
[25] "atom2mass.pdb" "atom2xyz"
[27] "atom.index" "atom.select"
[29] "atom.select.mol2" "atom.select.pdb"
[31] "atom.select.prmtop" "basename.pdb"
[33] "bhattacharyya" "bhattacharyya.array" [35] "bhattacharyya.enma" "bhattacharyya.matrix" [37] "bhattacharyya.nma" "bhattacharyya.pca"
[39] "binding.site" "biounit"
[41] "blast.pdb" "bounds"
[43] "bounds.sse" "build.hessian"
[45] "bwr.colors" "cat.pdb"
[47] "chain.pdb" "check.utility"
[49] "clean.pdb" "cmap"
[51] "cmap.default" "cmap.pdb"
[53] "cmap.xyz" "cna"
[55] "cna.dccm" "cna.ensmb"
[57] "cnapath" "com"
[59] "combine.select" "community.aln"
[61] "community.tree" "com.pdb"
[63] "com.xyz" "consensus"
[65] "conserv" "convert.pdb"
[67] "core.find" "core.find.default"
[69] "core.find.pdb" "core.find.pdbs"
[71] "cov2dccm" "cov.enma"
[73] "cov.nma" "covsoverlap"
[75] "covsoverlap.enma" "covsoverlap.nma"
[77] "dccm" "dccm.egnm"
[79] "dccm.enma" "dccm.gnm"
[81] "dccm.nma" "dccm.pca"
[83] "dccm.xyz" "deformation.nma"
[85] "diag.ind" "difference.vector"
[87] "dist.xyz" "dm"
[89] "dm.pdb" "dm.pdbs"
[91] "dm.xyz" "dssp"
[93] "dssp.pdb" "dssp.pdbs"
[95] "dssp.xyz" "elements"
[97] "entropy" "ff.aaenm"
[99] "ff.aaenm2" "ff.anm"
[101] "ff.calpha" "ff.pfanm"
[103] "ff.reach" "ff.sdenm"
[105] "filter.cmap" "filter.dccm"
[107] "filter.identity" "filter.rmsd"
[109] "fit.xyz" "fluct.nma"
[111] "formula2mass" "gap.inspect"
[113] "geostas" "geostas.default"
[115] "geostas.enma" "geostas.nma"
[117] "geostas.pdb" "geostas.pdbs"
[119] "geostas.xyz" "get.blast"
[121] "get.pdb" "get.seq"
[123] "gnm" "gnm.pdb"
[125] "gnm.pdbs" "hclustplot"
[127] "hivp" "hmmer"
[129] "identify.cna" "inner.prod"
[131] "inspect.connectivity" "is.gap"
[133] "is.mol2" "is.pdb"
[135] "is.pdbs" "is.select"
[137] "is.xyz" "kinesin"
[139] "layout.cna" "lbio3d"
[141] "lmi" "load.enmff"
[143] "mask" "mask.dccm"
[145] "mktrj" "mktrj.enma"
[147] "mktrj.nma" "mktrj.pca"
[149] "mono.colors" "motif.find"
[151] "mustang" "network.amendment"
[153] "nma" "nma.pdb"
[155] "nma.pdbs" "normalize.vector"
[157] "orient.pdb" "overlap"
[159] "pairwise" "pca"
[161] "pca.array" "pca.pdbs"
[163] "pca.tor" "pca.xyz"
[165] "pdb2aln" "pdb2aln.ind"
[167] "pdb2sse" "pdbaln"
[169] "pdb.annotate" "pdbfit"
[171] "pdbfit.pdb" "pdbfit.pdbs"
[173] "pdb.pfam" "pdbs2pdb"
[175] "pdbs2sse" "pdbseq"
[177] "pdbsplit" "pfam"
[179] "plotb3" "plot.bio3d"
[181] "plot.blast" "plot.cmap"
[183] "plot.cna" "plot.core"
[185] "plot.dccm" "plot.dmat"
[187] "plot.enma" "plot.fasta"
[189] "plot.fluct" "plot.geostas"
[191] "plot.hmmer" "plot.matrix.loadings" [193] "plot.nma" "plot.pca"
[195] "plot.pca.loadings" "plot.pca.score"
[197] "plot.pca.scree" "plot.rmsip"
[199] "print.cna" "print.cnapath"
[201] "print.core" "print.enma"
[203] "print.fasta" "print.geostas"
[205] "print.mol2" "print.nma"
[207] "print.pca" "print.pdb"
[209] "print.prmtop" "print.rle2"
[211] "print.select" "print.sse"
[213] "print.xyz" "project.pca"
[215] "prune.cna" "pymol"
[217] "pymol.dccm" "pymol.modes"
[219] "pymol.nma" "pymol.pca"
[221] "pymol.pdbs" "read.all"
[223] "read.cif" "read.crd"
[225] "read.crd.amber" "read.crd.charmm"
[227] "read.dcd" "read.fasta"
[229] "read.fasta.pdb" "read.mol2"
[231] "read.ncdf" "read.pdb"
[233] "read.pdb2" "read.pdcBD"
[235] "read.pqr" "read.prmtop"
[237] "rgyr" "rle2"
[239] "rmsd" "rmsf"
[241] "rmsip" "rmsip.default"
[243] "rmsip.enma" "rot.lsq"
[245] "rtb" "sdENM"
[247] "seq2aln" "seqaln"
[249] "seqaln.pair" "seqbind"
[251] "seqidentity" "setup.ncore"
[253] "sip" "sip.default"
[255] "sip.enma" "sip.nma"
[257] "sse.bridges" "store.atom"
[259] "stride" "struct.aln"
[261] "summary.cna" "summary.cnapath"
[263] "summary.pdb" "torsion.pdb"
[265] "torsion.xyz" "transducin"
[267] "trim" "trim.mol2"
[269] "trim.pdb" "trim.pdbs"
[271] "trim.xyz" "unbound"
[273] "uniprot" "var.pdbs"
[275] "var.xyz" "vec2resno"
[277] "vmd" "vmd.cna"
[279] "vmd.cnapath" "vmd_colors"
[281] "wrap.tor" "write.crd"
[283] "write.fasta" "write.mol2"
[285] "write.ncdf" "write.pdb"
[287] "write.pir" "write.pqr"
[289] "xyz2atom" "xyz2z.pca"
[291] "z2xyz.pca"

Comments (10)

  1. Xinqiu Yao

    Hi,

    The name of the function has been changed to vmd.cna(). We will update the online document soon. Thanks for pointing it out.

  2. Mamta Mohan reporter

    Hi,

    I tried vmd.cna() before posting issue.

    It does not seem to work.

    vmd.cna(net, pdb, launch = TRUE) Error in vec2resno(vec = x$communities$membership, resno = pdb$atom[, : Length miss-match of 'vec' and concetive 'resno'

  3. Xinqiu Yao

    It is possibly that your input pdb does not match the network net. A quick check is length(net$x$communities$membership)==sum(pdb$calpha). Is it TRUE?

  5. Mamta Mohan reporter

    I was wondering if you might be able to guide me this this open issue.

    I did check the length and they are unequal. Net printed ok and it seems to have memberships but apparently this call fails.

    length(net$x$communities$membership) == sum(pdb$calpha) [1] FALSE length(net$x$communities$membership) [1] 0 sum(pdb$calpha) [1] 162

  8. Xinqiu Yao

    Can you type length(net$communities$membership) and see what number it is? If it is not 162 (unequal to the number of C-alpha atoms in the pdb), you need to check how your network was constructed. The reasons causing the mismatch can be very complicated and you need to provide examples and details of your calculations if you want us to help figure out the problem.

  9. Mamta Mohan reporter

    Dear Xin-Qiu,

    The number as expected is off.

    length(net$communities$membership) [1] 164

    In another issue Lars explained to me selection of "CA".

    I will try that.

    If issue persists I will write again.

    Thank you.

  11. Log in to comment
Assignee
–
Type
bug
Priority
major
Status
resolved
Component
–
Version
–
Votes
0
Watchers
1
Jira: the preferred issue tracker for Bitbucket. Join the team!