# NOT RUN {
## load transducin example data
attach(transducin)
## subset of pdbs to analyze
inds = c(1:5, 16:20)
pdbs <- trim(pdbs, row.inds=inds)
gaps.res = gap.inspect(pdbs$ali)
## reference RESNO and SSE for axis annotations
resno <- pdbs$resno[1, gaps.res$f.inds]
sse <- pdbs$sse[1, gaps.res$f.inds]
## eNMA calculation and obtain modes of motion including atomic fluctuations
modes <- nma(pdbs, ncore=NULL)
x = modes$fluctuation
## simple line plot with SSE annotation
plot.fluct(x, sse=sse, resno=resno)
## group data by specifying colors of each fluctuation line; same color indicates
## same group. Also do significance calculation and annotation
col = c(rep('red', 5), rep('blue', 5))
plot.fluct(x, col=col, signif=TRUE, sse=sse, resno=resno)
## spread lines
plot.fluct(x, col=col, signif=TRUE, sse=sse, resno=resno, typ='l', spread=TRUE)
## show only line of mean values for each group.
## Nicer plot with area shaded for the first group.
plot.fluct(x, col=col, signif=TRUE, sse=sse, resno=resno, mean=TRUE,
polygon=TRUE, label=c('GTP', 'GDI'))
detach(transducin)
# }
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