Error: object 'plot.cna' not found

[B Albert]

Hello:

I am following the tutorial on page:

http://thegrantlab.org/bio3d/tutorials/protein-structure-networks

library(bio3d) library(igraph) pdbfile <- system.file("examples/hivp.pdb", package = "bio3d") pdb <- read.pdb( pdbfile ) modes <- nma(pdb) cij <- dccm(modes)

Loading required package: multicore |===============================================================| 100% Warning messages: 1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘multicore’ 2: In dccm.nma(modes) : multicore package missing

net <- cna(cij, cutoff.cij=0.3)

Error: could not find function "cna"

I am just wondering, how can we solve the problem?

thank you very much.

[Xinqiu Yao]

Hi,

Could you provide more information about your bio3d version, as well as R version and OS type? Note that we have greatly updated bio3d recently. See here https://bitbucket.org/Grantlab/bio3d/downloads for latest version. The vignette should work in version >=2.1 but we strongly recommend install the latest version.

[B Albert]

Hello:

It's OK now. However, it seems that it cannot find VMD pathway correctly:

view.cna(net, pdb, launch = TRUE) sh: vmd: command not found

May I ask how can we configure VMD correctly for bio3d so that it knows the location of VMD?

thx a lot

[Barry Grant]

Is VMD in your path? Can you call it successfully from any directory in your regular shell? This is basicaly what the the function is trying to do (unsuccessfully in this case).

The usual solution is to add the folder/directory where you installed VMD to your $PATH environment. You may then need to restart your R session.

I will also note that in your working directory there should be two files produced ("network.vmd" and "network.pdb"). You can open these in VMD from your regular terminal prompt with "vmd network.pdb -e network.vmd" and then set the Graphical display properties to however you like (e.g Tube colored by B-factor etc...). Hope this helps!