mktrj.pca {bio3d}R Documentation

PCA Atomic Displacement Trajectory

Description

Make a trajectory of atomic displacments along a given principal component.

Usage

mktrj.pca(pca = NULL, pc = 1, mag = 1, step = 0.125, file = NULL,
          resno = NULL, resid = NULL, ...)

Arguments

pca a list object of class "pca" (obtained with pca.xyz).
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.
file a character vector giving the output PDB file name.
resno a vector of residue numbers for the output PDB file.
resid a 3-letter residue sequence for the output PDB file.
... extra arguments to be passed to the function write.pdb.

Details

Trajectory frames are built from reconstructed Cartesian coordinates produced by interpolating from the mean structure along a given pc, 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).

Value

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

Note

The molecular graphics software VMD is useful for viewing trajectories see:
http://www.ks.uiuc.edu/Research/vmd/.

Author(s)

Barry Grant

References

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

See Also

pca.xyz

Examples

data(kinesin) # see pca.xyz for details
attach(kinesin)

# Ignore gap containing positions
cut.seqs <- which(pdbs$id %in% c("d1n6mb_","d1ry6a_"))
gaps <- gap.inspect(pdbs$ali[-cut.seqs,])

# Write PC trajectory
a <- mktrj.pca(pc.xray, pc=1, file="pc1.pdb",
               resno = pdbs$resno[1, gaps$f.inds],
               resid = aa123(pdbs$ali[1, gaps$f.inds]) )

b <- mktrj.pca(pc.xray, pc=2, file="pc2.pdb",
               resno = pdbs$resno[1, gaps$f.inds],
               resid = aa123(pdbs$ali[1, gaps$f.inds]) )

c <- mktrj.pca(pc.xray, pc=3, file="pc3.pdb",
               resno = pdbs$resno[1, gaps$f.inds],
               resid = aa123(pdbs$ali[1, gaps$f.inds]) )


[Package bio3d version 1.0-5 Index]