# \donttest{
##-- Read example trajectory file
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)
## Do PCA
pca <- pca.xyz(xyz)
## DCCM: only use first 10 PCs
cij <- dccm(pca, pc = c(1:10))
## Plot DCCM
plot(cij)
## DCCM: remove first 10 PCs
cij <- dccm(pca, pc = -c(1:10))
## Plot DCCM
plot(cij)
# }
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