R: Plot eNMA Results

plot.enma {bio3d} | R Documentation

## Plot eNMA Results

### Description

Produces a plot of atomic fluctuations of aligned normal modes.

### Usage

    ## S3 method for class 'enma'
    plot(x,
            pdbs = NULL,
            xlab = NULL,
            ylab="Fluctuations", ...)

### Arguments

`x` | the results of ensemble NMA obtained with `nma.pdbs`. Alternatively, a matrix in the similar format as `enma$fluctuations` can be provided.
`pdbs` | an object of class ‘pdbs’ in which the ‘enma’ object `x` was obtained from. If provided SSE data of the first structure of `pdbs` will drawn.
`xlab` | a label for the x axis.
`ylab` | labels for the y axes.
`...` | extra plotting arguments passed to `plot.fluct` that effect the atomic fluctuations plot only.

### Details

`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.

### Value

Called for its effect.

### Author(s)

Lars Skjaerven, Barry Grant

### References

Skjaerven, L. et al. (2014) BMC Bioinformatics 15, 399. Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

### See Also

`nma`, `plotb3`, `plot.fluct`

### Examples

    ## 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)

[Package bio3d version 2.4-0 Index]