mktrj.enma: Ensemble NMA Atomic Displacement Trajectory

Description

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

Usage

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

Arguments

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

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.

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.

rock

logical, if TRUE the trajectory rocks.

ncore

number of CPU cores used to do the calculation. ncore>1 requires package parallel installed.

...

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.