Plot eNMA Results
Produces a plot of atomic fluctuations of aligned normal modes.
## S3 method for class 'enma'
plot(x,
pdbs = NULL,
xlab = NULL,
ylab="Fluctuations", ...)x |
the results of ensemble NMA obtained with
|
pdbs |
an object of class ‘pdbs’ in which the
‘enma’ object |
xlab |
a label for the x axis. |
ylab |
labels for the y axes. |
... |
extra plotting arguments passed to |
plot.enma produces a fluctuation plot of aligned nma
objects. If corresponding pdbs object is provided the plot
contains SSE annotation and appropriate resiude index numbering.
Called for its effect.
Lars Skjaerven, Barry Grant
Skjaerven, L. et al. (2014) BMC Bioinformatics 15, 399. Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
## Not run:
ids <- c("1a70_A", "1czp_A", "1frd_A", "1fxi_A", "1iue_A", "1pfd_A")
raw.files <- get.pdb(ids, path = "raw_pdbs")
files <- pdbsplit(raw.files, ids, path = "raw_pdbs/split_chain")
## Sequence/structure alignement
pdbs <- pdbaln(files)
## Normal mode analysis on aligned data
modes <- nma(pdbs)
## Plot fluctuations
plot(modes, pdbs=pdbs)
## Group and spread fluctuation profiles
hc <- hclust(as.dist(1-modes$rmsip))
col <- cutree(hc, k=2)
plot(modes, pdbs=pdbs, col=col, spread=TRUE)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.