Insert following code in .pymolrc (in your home directory) and follow the instruction... # start $HOME/.pymolrc modification one_letter = { ' VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q', \ 'ASP':'D', 'ASN':'N', 'HIS':'H', 'TRP':'W', 'PHE':'F', 'TYR':'Y', \ 'ARG':'R', 'LYS':'K', 'SER':'S', 'THR':'T', 'MET':'M', 'ALA':'A', \ 'GLY':'G', 'PRO':'P', 'CYS':'C' } # end modification #type following command in pymol terminal; > label n. ca, one_letter[resn]+resi #or > label bycalpha sele, (one_letter[resn]+resi) #to add chain ID after one letter code > label bycalpha sele, (one_letter[resn]+resi+ chain )