Using Bio3D to convert 3 letter amino acid to 1 letter

Bio3D is a package written for the R platform. Details are in thegrantlab.org/bio3d/index.php


library(bio3d, lib.loc = "~/R")

pdb < - read.pdb("File.pdb")

atom.select(pdb,"calpha")$atom   ---- Gives the atom index of all alpha carbons

pdb$atom$resid    -- Gives the residue ID of all atoms

pdb$atom$resid(atom.select(pdb,"calpha")$atom)  --- Combines the two