bio3d (version 2.1-2)

mktrj.nma: NMA Atomic Displacement Trajectory

Description

Make a trajectory of atomic displacments along a given normal mode vector.

Usage

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

Arguments

x

a list object of class "nma" (obtained with nma).

mode

the mode 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 mode.

file

a character vector giving the output PDB file name.

...

extra arguments to be passed to the function write.pdb.

Value

• Returns a numeric matrix of interpolated coordinates with a row per structure.

Details

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

An optional magnification factor can be used to amplify displacements. This involves scaling the mode vector by mag-times.

References

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

See Also

nma, view.modes.

Examples

## 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")
m7 <- mktrj(modes, mode=7, file = outfile)
outfile