# NOT RUN {
attach(transducin)
gaps.res <- gap.inspect(pdbs$ali)
sse <- pdbs$sse[1, gaps.res$f.inds]
# calculate modes
modes <- nma(pdbs, ncore=NULL)
# calculate cross-correlation matrices from the modes
cijs <- dccm(modes, ncore=NULL)$all.dccm
# do PCA on cross-correlation matrices
pc <- pca.array(cijs)
# plot loadings
l <- plot.matrix.loadings(pc, sse=sse)
l[1:10, 1:10]
# plot loadings with elements 10-residue separated from diagonal masked
plot.matrix.loadings(pc, sse=sse, mask.n=10)
# }
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