R: PCA / NMA Atomic Displacement Trajectory

mktrj {bio3d} | R Documentation

## PCA / NMA Atomic Displacement Trajectory

### Description

Make a trajectory of atomic displacments along a given principal component / normal mode.

### Usage

    mktrj(...)

    ## S3 method for class 'pca'
    mktrj(pca = NULL, pc = 1, mag = 1, step = 0.125, file =
    NULL, pdb = NULL, rock=TRUE, ...)

    ## S3 method for class 'nma'
    mktrj(nma = NULL, mode = 7, mag = 10, step = 1.25, file = NULL,
          pdb = NULL, rock=TRUE,  ...)

    ## S3 method for class 'enma'
    mktrj(enma = NULL, pdbs = NULL, s.inds = NULL, m.inds = NULL,
          mag = 10, step = 1.25, file = NULL, rock = TRUE, ncore = NULL, ...)

### Arguments

`pca` | an object of class `"pca"` as obtained with function `pca.xyz` or `pca`.
`nma` | an object of class `"nma"` as obtained with function `nma.pdb`.
`enma` | an object of class `"enma"` as obtained with function `nma.pdbs`.
`pc` | the PC number along which displacements should be made.
`mag` | a magnification factor for scaling the displacements.
`step` | the step size by which to increment along the pc/mode.
`file` | a character vector giving the output PDB file name.
`pdb` | an object of class `"pdb"` as obtained from `read.pdb` or class `"pdbs"` as obtained from `read.fasta.pdb`. If not NULL, used as reference to write the PDB file.
`rock` | logical, if TRUE the trajectory rocks.
`mode` | the mode number along which displacements should be made.
`pdbs` | a list object of class `"pdbs"` (obtained with `pdbaln` or `read.fasta.pdb`) which corresponds to the `"enma"` object.
`s.inds` | index or indices pointing to the structure(s) in the `enma` object for which the trajectory shall be generated.
`m.inds` | the mode number(s) along which displacements should be made.
`ncore` | number of CPU cores used to do the calculation. `ncore>1` requires package ‘parallel’ installed.
`...` | additional arguments passed to and from functions (e.g. to function `write.pdb`).

### Details

Trajectory frames are built from reconstructed Cartesian coordinates produced by interpolating from the mean structure along a given `pc` or `mode`, in increments of `step`.

An optional magnification factor can be used to amplify displacements. This involves scaling by `mag`-times the standard deviation of the conformer distribution along the given `pc` (i.e. the square root of the associated eigenvalue).

### Note

Molecular graphics software such as VMD or PyMOL is useful for viewing trajectories see e.g:
http://www.ks.uiuc.edu/Research/vmd/.

### Author(s)

Barry Grant, Lars Skjaerven

### References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

### See Also

`pca`, `nma`, `nma.pdbs`, `pymol.modes`.

### Examples

    ## Not run:

    ##- PCA example
    attach(transducin)

    # Calculate principal components
    pc.xray <- pca(pdbs, fit=TRUE)

    # Write PC trajectory of pc=1
    outfile = tempfile()
    a <- mktrj(pc.xray, file = outfile)
    outfile

    detach(transducin)

    ##- NMA example
    ## Fetch stucture
    pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") )

    ## Calculate (vibrational) normal modes
    modes <- nma(pdb)

    ## Visualize modes
    outfile = file.path(tempdir(), "mode_7.pdb")
    mktrj(modes, mode=7, pdb=pdb, file = outfile)
    outfile

    ## End(Not run)

[Package bio3d version 2.4-0 Index]