Orient a PDB Structure

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

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.

References

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

Author

Barry Grant

Note

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

See also

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

Examples

# \donttest{
# PDB server connection required - testing excluded

pdb <- read.pdb( "1bg2" )
#>   Note: Accessing on-line PDB file
#> Warning: /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/1bg2.pdb  exists. Skipping download
xyz <- orient.pdb(pdb)
#> Dimensions: 
#>  x  min= -33.358    max= 37.308    range= 70.666 
#>  y  min= -23.392    max= 27.583    range= 50.975 
#>  z  min= -19.521    max= 28.128    range= 47.65 
#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)
#> Dimensions: 
#>  x  min= -33.708    max= 37.75    range= 71.458 
#>  y  min= -23.485    max= 27.479    range= 50.965 
#>  z  min= -21.046    max= 27.17    range= 48.216 
#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)
#> Dimensions: 
#>  x  min= -42.58    max= 30.521    range= 73.101 
#>  y  min= -24.436    max= 21.585    range= 46.022 
#>  z  min= -27.759    max= 22.305    range= 50.064 
#write.pdb(pdb, xyz = xyz, file = "mov3.pdb")
# }