orient.pdb: Orient a PDB Structure

In bio3d: Biological Structure Analysis

Orient a PDB Structure

Description

Center, to the coordinate origin, and orient, by principal axes, the coordinates of a given PDB structure or xyz vector.

Usage

orient.pdb(pdb, atom.subset = NULL, verbose = TRUE)

Arguments

pdb	a pdb data structure obtained from read.pdb or a vector of ‘xyz’ coordinates.
atom.subset	a subset of atom positions to base orientation on.
verbose	print dimension details.

Value

Returns a numeric vector of re-oriented coordinates.

Note

Centering and orientation can be restricted to a atom.subset of atoms.

Author(s)

Barry Grant

References

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

See Also

read.pdb, write.pdb, fit.xyz, rot.lsq , atom.select

Examples

# PDB server connection required - testing excluded
try({

pdb <- read.pdb( "1bg2" )
xyz <- orient.pdb(pdb)
#write.pdb(pdb, xyz = xyz, file = "mov1.pdb")


# Based on C-alphas
inds <- atom.select(pdb, "calpha")
xyz  <- orient.pdb(pdb, atom.subset=inds$atom)
#write.pdb(pdb, xyz = xyz, file = "mov2.pdb")


# Based on a central Beta-strand
inds <- atom.select(pdb, resno=c(224:232), elety='CA')
xyz  <- orient.pdb(pdb, atom.subset=inds$atom)
#write.pdb(pdb, xyz = xyz, file = "mov3.pdb")

}, silent=TRUE)
if(inherits(.Last.value, "try-error")) {
   message("Need internet to run the example")
}

bio3d documentation built on Oct. 30, 2024, 1:08 a.m.