bio3d (version 2.1-1)

view.cna: View CNA Protein Structure Network Community Output in VMD

Description

This function generates a VMD scene file and a PDB file that can be read and rendered by the VMD molecular viewer. Chose color by chain to see corresponding regions of structure colored by community along with the community protein structure network.

Usage

view.cna(x, pdb, layout = layout.cna(x, pdb, k=3), 
		col.sphere=NULL, col.lines = "silver", weights = NULL, 
		radius = table(x$communities$membership)/5, alpha = 1, 
		vmdfile = "network.vmd", pdbfile = "network.pdb", 
		launch = FALSE)

Arguments

x

A 'cna' class object such as obtained from cna function/

pdb

A 'pdb' class object such as obtained from read.pdb function.

layout

A numeric matrix of Nx3 XYZ coordinate matrix, where N is the number of community spheres to be drawn.

col.sphere

A numeric vector containing the sphere colors.

col.lines

A character object specifying the color of the edges (default 'silver'). Must use VMD colors names.

weights

A numeric vector specifying the edge width. Default is taken from E(x$community.network)$weight.

radius

A numeric vector containing the sphere radii. Default is taken from the number of community members divided by 5.

alpha

A single element numeric vector specifying the VMD alpha transparency parameter. Default is set to 1.

vmdfile

A character element specifying the output VMD scene file name that will be loaded in VMD.

pdbfile

A character element specifying the output pdb file name to be loaded in VMD.

launch

Logical. If TRUE, a VMD session will be started with the output of view.cna.

Value

• Two files are generated as output. A pdb file with the residue chains assigned according to the community and a text file containing The drawing commands for the community representation.

Details

This function generates a scaled sphere (communities) and stick (edges) representation of the community network along with the corresponding protein structure divided into chains, one chain for each community. The sphere radii are proportional to the number of community members and the edge widths correspond to network edge weights.

References

Humphrey, W., Dalke, A. and Schulten, K., ``VMD - Visual Molecular Dynamics'' J. Molec. Graphics 1996, 14.1, 33-38.

Examples

##-- From MD
trtfile <- system.file("examples/hivp.dcd", package="bio3d")
trj <- read.dcd(trtfile)

# Read the starting PDB file to determine atom correspondence
pdbfile <- system.file("examples/hivp.pdb", package="bio3d")
pdb <- read.pdb(pdbfile)

# select residues 24 to 27 and 85 to 90 in both chains
inds <- atom.select(pdb, resno=c(24:27, 85:90), elety="CA")

# lsq fit of trj on pdb
xyz <- fit.xyz(pdb$xyz, trj, fixed.inds=inds$xyz, mobile.inds=inds$xyz)

# calculate dynamical cross-correlation matrix
cij <- dccm(xyz)
#plot(cij)

# Build, and betweenness cluster, a network graph
net <- cna(cij)

# View cna 
view.cna(net, pdb, launch=FALSE)
## within VMD set 'coloring method' to 'Chain' and 'Drawing method' to Tube


##-- From NMA
pdb.gdi = read.pdb("1KJY")
pdb.gdi = trim.pdb(pdb.gdi, inds=atom.select(pdb.gdi, chain="A", elety="CA")) 
modes.gdi = nma(pdb.gdi)
cij.gdi = dccm(modes.gdi)
net.gdi = cna(cij.gdi, cutoff.cij=0.35)
#view.cna(net.gdi, pdb.gdi, alpha = 0.7, launch=TRUE)