bio3d (version 2.1-2)

view.modes: Vector Field Visualization of Modes

Description

Structural visualization of mode vectors obtained from PCA or NMA.

Usage

view.modes(modes, mode=NULL, outprefix="mode_vecs",
          scale=5, dual=FALSE, launch=FALSE, exefile="pymol")

Arguments

modes

an object of class nma or pca as obtained from functions nma or pca.xyz.

mode

the mode number for which the vector field should be made.

outprefix

character string specifying the file prefix. If NULL the temp directory will be used.

scale

global scaling factor.

dual

logical, if TRUE mode vectors are also drawn in both direction.

launch

logical, if TRUE PyMol will be launched.

exefile

file path to the PYMOL program on your system (i.e. how is PYMOL invoked).

Value

• Called for its action.

Details

This function generates a PyMOL (python) script for drawing mode vectors on a PDB structure. The PyMOL script file is stored in the working directory with filename mode_vecs.py, with coordinates in PDB format mode_vecs.inpcrd.pdb. PyMOL will only be launched when using argument launch=TRUE.

References

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

See Also

nma, pca.xyz

Examples

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

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

view.modes(modes, mode=7)