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)
pdb |
a pdb data structure obtained from |
atom.subset |
a subset of atom positions to base orientation on. |
verbose |
print dimension details. |
Returns a numeric vector of re-oriented coordinates.
Centering and orientation can be restricted to a atom.subset of atoms.
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
# PDB server connection required - testing excluded 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")
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