Juanxun Sorry for the slow response but you don't need to use the apply_cif_link because the links are automatically applied in phenix.refine. You can check this using the .geo file thus elbow.refine_geo_display PHE-SEP-ARG_minimized.geo SEP ! The output (see below) shows the restraints between SEP and anything else. The first RMS section is the entire model, the second is for the selection. In the latest nightly builds, there is also a graphical representation available via REEL. phenix.reel PHE-SEP-ARG_minimized.pdb PHE-SEP-ARG_minimized.geo Cheers Nigel RMS results for model RMS(D/Z) d-all d-none d-alt z-all z-none z-alt bond 0.001( 32) 0.001( 32) 0.000( 0) 0.024( 32) 0.024( 32) 0.000( 0) angle 0.216( 42) 0.216( 42) 0.000( 0) 0.080( 42) 0.080( 42) 0.000( 0) ----- bonds ----- bonds ----- bonds ----- bonds ----- bonds ----- bonds 1 " C PHE C 3 " - " N SEP C 4 " ['1.329', '1.329', '-0.000', '1.40e-02', '5.10e+03', '3.76e-04'] 2 " C SEP C 4 " - " N ARG C 5 " ['1.329', '1.329', '-0.000', '1.40e-02', '5.10e+03', '5.93e-05'] ---- angles ---- angles ---- angles ---- angles ---- angles ---- angles 1 " C PHE C 3 " - " N SEP C 4 " - " CA SEP C 4 " ['121.70', '121.80', '-0.10', '1.80e+00', '3.09e-01', '3.34e-03'] 2 " CA PHE C 3 " - " C PHE C 3 " - " N SEP C 4 " ['116.20', '116.25', '-0.05', '2.00e+00', '2.50e-01', '6.82e-04'] 3 " C SEP C 4 " - " N ARG C 5 " - " CA ARG C 5 " ['121.70', '121.73', '-0.03', '1.80e+00', '3.09e-01', '2.87e-04'] 4 " CA SEP C 4 " - " C SEP C 4 " - " N ARG C 5 " ['116.20', '116.23', '-0.03', '2.00e+00', '2.50e-01', '2.85e-04'] 5 " O PHE C 3 " - " C PHE C 3 " - " N SEP C 4 " ['123.00', '123.01', '-0.01', '1.60e+00', '3.91e-01', '1.81e-05'] 6 " O SEP C 4 " - " C SEP C 4 " - " N ARG C 5 " ['123.00', '123.00', '0.00', '1.60e+00', '3.91e-01', '5.79e-07'] ---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals 1 " CA PHE C 3 " - " C PHE C 3 " - " N SEP C 4 " - " CA SEP C 4 " ['180.00', '-179.13', '-0.87', '0', '5.00e+00', '4.00e-02', '3.05e-02'] 2 " CA SEP C 4 " - " C SEP C 4 " - " N ARG C 5 " - " CA ARG C 5 " ['180.00', '-179.41', '-0.59', '0', '5.00e+00', '4.00e-02', '1.38e-02'] ---- chirals ---- chirals ---- chirals ---- chirals ---- chirals ---- chirals RMS results for selection RMS(D/Z) d-all d-none d-alt z-all z-none z-alt bond 0.000( 2) 0.000( 2) 0.000( 0) 0.000( 2) 0.000( 2) 0.000( 0) angle 0.054( 6) 0.054( 6) 0.000( 0) 0.029( 6) 0.029( 6) 0.000( 0) Nigel On Tue, May 21, 2013 at 10:51 PM, Jianxun Qi wrote:

refinement.pdb_interpretation { apply_cif_link { data_link = "SEPC-N" residue_selection_1 = "chain C and resname PHE and resid 3" residue_selection_2 = "chain C and resname SEP and resid 4" } apply_cif_link { data_link = "SEPC-N" residue_selection_1 = "chain C and resname SEP and resid 4" residue_selection_2 = "chain C and resname ARG and resid 5" } }

-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty@LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov