orient.pdb(pdb, atom.subset = NULL, verbose = TRUE)
read.pdb
or a vector of ‘xyz’ coordinates. Center, to the coordinate origin, and orient, by principal axes, the coordinates of a given PDB structure or xyz vector.
Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
Centering and orientation can be restricted to a atom.subset of atoms.
# PDB server connection required - testing excluded pdb <- read.pdb( "1bg2" )Note: Accessing on-line PDB filexyz <- 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")