# NOT RUN {
# }
# NOT RUN {
##-- Read example trajectory file
trtfile <- system.file("examples/hivp.dcd", package="bio3d")
trj <- read.dcd(trtfile)
## Read reference PDB and trim it to match the trajectory
pdb <- trim(read.pdb("1W5Y"), 'calpha')
## select residues 24 to 27 and 85 to 90 in both chains
inds <- atom.select(pdb, resno=c(24:27,85:90))
## lsq fit of trj on pdb
xyz <- fit.xyz(pdb$xyz, trj, fixed.inds=inds$xyz, mobile.inds=inds$xyz)
## Dynamic cross-correlations of atomic displacements
cij <- dccm(xyz)
## Default plot
plot.dccm(cij)
## Change the color scheme and the range of colored data levels
plot.dccm(cij, contour=FALSE, col.regions=bwr.colors(200), at=seq(-1,1,by=0.01) )
## Add secondary structure annotation to plot margins
plot.dccm(cij, sse=pdb)
## Add additional margin annotation for chains
## Also label x- and y-axis with PDB residue numbers
ch <- ifelse(pdb$atom$chain=="A", 1,2)
plot.dccm(cij, resno=pdb, sse=pdb, margin.segments=ch)
## Plot with cluster annotation from dynamic network analysis
#net <- cna(cij)
#plot.dccm(cij, margin.segments=net$raw.communities$membership)
## Focus on major communities (i.e. exclude those below a certain total length)
#plot.dccm(cij, margin.segments=net$raw.communities$membership, segment.min=25)
# }
# NOT RUN {
# }
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