bio3d (version 2.1-2)

mktrj: PCA / NMA Atomic Displacement Trajectory

Description

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

Usage

mktrj(x, ...)

Arguments

x

a list object of class "pca" or "nma" as obtained with pca.xyz or nma, respectively.

...

additional arguments passed to the methods mktrj.pca or mktrj.nma.

Details

mktrj is a generic function calling the corresponding function determined by the class of the input argument x. Use methods("mktrj") to get all the methods for mktrj generic: mktrj.pca will be used when x is an object of "pca". mktrj.nma will be used when x is an object of "nma". See examples for each corresponding function for more details.

References

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

See Also

mktrj.pca, mktrj.nma, pca.xyz, nma, view.modes.

Examples

data(transducin)
attach(transducin, warn.conflicts=FALSE)

# Ignore gap containing positions
gaps.pos <- gap.inspect(pdbs$xyz)

# PCA
pc.xray <- pca.xyz(pdbs$xyz[, gaps.pos$f.inds])

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

detach(transducin)